The Exomiser - A Tool to Annotate and Prioritise Whole-Exome Sequencing Data

Exomiser Analysis Results for Anonymous

Analysis Settings

Settings used for this analysis:

---
vcf: "C:\\Users\\Elizabeth Owen\\Desktop\\Nebula\\Raw_Data\\NG1RDRPK1V_vcf\\NG1RDRPK1V.vcf"
genomeAssembly: "HG38"
pedigree:
  individuals: []
proband: ""
hpoIds:
- "HP:0007302"
inheritanceModes:
  maxFreq: 2.0
  definedModes:
  - "AUTOSOMAL_DOMINANT"
  - "AUTOSOMAL_RECESSIVE"
  - "X_RECESSIVE"
  - "X_DOMINANT"
  - "MITOCHONDRIAL"
  definedSubModes:
  - "AUTOSOMAL_DOMINANT"
  - "AUTOSOMAL_RECESSIVE_COMP_HET"
  - "AUTOSOMAL_RECESSIVE_HOM_ALT"
  - "X_RECESSIVE_COMP_HET"
  - "X_RECESSIVE_HOM_ALT"
  - "X_DOMINANT"
  - "MITOCHONDRIAL"
  empty: false
analysisMode: "PASS_ONLY"
frequencySources:
- "THOUSAND_GENOMES"
- "TOPMED"
- "UK10K"
- "ESP_AFRICAN_AMERICAN"
- "ESP_EUROPEAN_AMERICAN"
- "ESP_ALL"
- "EXAC_AFRICAN_INC_AFRICAN_AMERICAN"
- "EXAC_AMERICAN"
- "EXAC_EAST_ASIAN"
- "EXAC_FINNISH"
- "EXAC_NON_FINNISH_EUROPEAN"
- "EXAC_OTHER"
- "EXAC_SOUTH_ASIAN"
- "GNOMAD_E_AFR"
- "GNOMAD_E_AMR"
- "GNOMAD_E_ASJ"
- "GNOMAD_E_EAS"
- "GNOMAD_E_FIN"
- "GNOMAD_E_NFE"
- "GNOMAD_E_OTH"
- "GNOMAD_E_SAS"
- "GNOMAD_G_AFR"
- "GNOMAD_G_AMR"
- "GNOMAD_G_ASJ"
- "GNOMAD_G_EAS"
- "GNOMAD_G_FIN"
- "GNOMAD_G_NFE"
- "GNOMAD_G_OTH"
- "GNOMAD_G_SAS"
pathogenicitySources:
- "POLYPHEN"
- "MUTATION_TASTER"
- "SIFT"
- "CADD"
analysisSteps:
- priorityType: "HIPHIVE_PRIORITY"
- minPriorityScore: 0.501
  priorityType: "HIPHIVE_PRIORITY"
- offTargetVariantTypes:
  - "SYNONYMOUS_VARIANT"
- {}
- decoratedFilter:
    maxFreq: 2.0
- decoratedFilter:
    keepNonPathogenic: true
- compatibleModes:
  - "AUTOSOMAL_DOMINANT"
  - "AUTOSOMAL_RECESSIVE"
  - "X_RECESSIVE"
  - "X_DOMINANT"
  - "MITOCHONDRIAL"
- priorityType: "OMIM_PRIORITY"
---
outputContributingVariantsOnly: true
outputPrefix: "results/Cooper_results"
outputFormats:
- "HTML"
- "VCF"
- "TSV_GENE"
- "TSV_VARIANT"
- "JSON"
numGenes: 0

Filtering Summary

Filter	Report	Passed filter
Gene priority score	Genes filtered for minimum HIPHIVE_PRIORITY score of 0.501	538
Variant effect	Removed variants with effects of type: [SYNONYMOUS_VARIANT]	4151
Regulatory feature		4151
Frequency	Variants filtered for maximum allele frequency of 2.00%	4151
Pathogenicity	Retained all non-pathogenic variants of all types. Scoring was applied, but the filter passed all variants.	4151
Inheritance	Genes filtered for compatibility with AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL inheritance.	538

Variant Type Distribution

Variant Type	NG1RDRPK1V
FRAMESHIFT_ELONGATION	0
FRAMESHIFT_TRUNCATION	1
FRAMESHIFT_VARIANT	0
INTERNAL_FEATURE_ELONGATION	0
FEATURE_TRUNCATION	0
MNV	0
STOP_GAINED	0
STOP_LOST	0
START_LOST	0
SPLICE_ACCEPTOR_VARIANT	0
SPLICE_DONOR_VARIANT	1
MISSENSE_VARIANT	15
INFRAME_INSERTION	2
DISRUPTIVE_INFRAME_INSERTION	0
INFRAME_DELETION	0
DISRUPTIVE_INFRAME_DELETION	0
FIVE_PRIME_UTR_TRUNCATION	0
THREE_PRIME_UTR_TRUNCATION	0
SPLICE_REGION_VARIANT	2
STOP_RETAINED_VARIANT	1
INITIATOR_CODON_VARIANT	0
SYNONYMOUS_VARIANT	0
CODING_TRANSCRIPT_INTRON_VARIANT	2767
THREE_PRIME_UTR_EXON_VARIANT	74
FIVE_PRIME_UTR_INTRON_VARIANT	336
THREE_PRIME_UTR_INTRON_VARIANT	6
NON_CODING_TRANSCRIPT_EXON_VARIANT	0
NON_CODING_TRANSCRIPT_INTRON_VARIANT	0
UPSTREAM_GENE_VARIANT	128
DOWNSTREAM_GENE_VARIANT	394
INTERGENIC_VARIANT	330
REGULATORY_REGION_VARIANT	79

Prioritised Genes

Exomiser Score: 0.998

Phenotype Score: 1.000

Variant Score: 0.990

Phenotype matches:

Phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617443 Bleeding disorder, platelet-type, 21 - autosomal dominant/recessive; ORPHA:2308 Jacobsen syndrome; ORPHA:851 Paris-Trousseau thrombocytopenia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.998

Phenotype Score: 1.000

Variant Score: 0.990

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128718998G>A [0/1] rs1020937059 (variation viewer)

Variant score: 0.990 CONTRIBUTING VARIANT

Transcripts:: FLI1:ENST00000527786.7:c.18+24722G>A:p.(=); FLI1:ENST00000281428.12:c.-352+24722G>A:p.(=); FLI1:ENST00000344954.10:c.-203+32297G>A:p.(=); FLI1:ENST00000534087.3:c.-136+24722G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9908799; CADD: 0.991 (20.400)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.995

Phenotype Score: 1.000

Variant Score: 0.882

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128718998G>A [0/1] rs1020937059 (variation viewer)

Variant score: 0.990 CONTRIBUTING VARIANT

Transcripts:: FLI1:ENST00000527786.7:c.18+24722G>A:p.(=); FLI1:ENST00000281428.12:c.-352+24722G>A:p.(=); FLI1:ENST00000344954.10:c.-203+32297G>A:p.(=); FLI1:ENST00000534087.3:c.-136+24722G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9908799; CADD: 0.991 (20.400)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.128692400A>G [0/1] rs144217150 (variation viewer)

Variant score: 0.773 CONTRIBUTING VARIANT

Transcripts:: FLI1:ENST00000344954.10:c.-203+5699A>G:p.(=)

Pathogenicity Data:: Best Score: 0.98574394; CADD: 0.986 (18.460)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.7303%; gnomAD_G_AFR: 0.2311%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4891%; gnomAD_G_NFE: 0.9528%; gnomAD_G_OTH: 0.6160%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.128690866C>T [0/1]

Variant score: 0.719

Transcripts:: FLI1:ENST00000344954.10:c.-203+4165C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7194566; CADD: 0.719 (5.520)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128754308C>T [0/1] rs916130052 (variation viewer)

Variant score: 0.665

Transcripts:: FLI1:ENST00000527786.7:c.19-3807C>T:p.(=); FLI1:ENST00000281428.12:c.-351-3807C>T:p.(=); FLI1:ENST00000344954.10:c.-202-3807C>T:p.(=); FLI1:ENST00000534087.3:c.-81-3807C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6708454; CADD: 0.671 (4.826)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_AFR: 0.0115%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128809459T>C [0/1] rs143980672 (variation viewer)

Variant score: 0.420

Transcripts:: FLI1:ENST00000281428.12:c.631+255T>C:p.(=); FLI1:ENST00000344954.10:c.250+255T>C:p.(=); FLI1:ENST00000527786.7:c.829+255T>C:p.(=); FLI1:ENST00000534087.3:c.730+255T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7552628; CADD: 0.755 (6.113)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 1.0620%; UK10K: 1.4546%; gnomAD_G_AFR: 0.1947%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.6583%; gnomAD_G_NFE: 1.0060%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128760520CTTTTTTT>C [0/1] rs1179242159 (variation viewer)

Variant score: 0.354

Transcripts:: FLI1:ENST00000344954.10:c.10+2195_10+2201del:p.(=); FLI1:ENST00000527786.7:c.230+2195_230+2201del:p.(=); FLI1:ENST00000534087.3:c.131+2195_131+2201del:p.(=); FLI1:ENST00000281428.12:c.-140+2195_-140+2201del:p.(=)

Pathogenicity Data:: Best Score: 0.3538996; CADD: 0.354 (1.897)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128797164A>G [0/1] rs550680407 (variation viewer)

Variant score: 0.189

Transcripts:: FLI1:ENST00000281428.12:c.458-8202A>G:p.(=); FLI1:ENST00000344954.10:c.77-8202A>G:p.(=); FLI1:ENST00000527786.7:c.656-8202A>G:p.(=); FLI1:ENST00000534087.3:c.557-8202A>G:p.(=)

Pathogenicity Data:: Best Score: 0.18922567; CADD: 0.189 (0.911)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.128760523T>* [-/1]

Variant score: 0.000

Transcripts:: FLI1:ENST00000344954.10:c.10+2197T>*:p.(=); FLI1:ENST00000527786.7:c.230+2197T>*:p.(=); FLI1:ENST00000534087.3:c.131+2197T>*:p.(=); FLI1:ENST00000281428.12:c.-140+2197T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr11:g.128812821A>ACTCAATTTTGAAATCTGCAAAGTATTCATTAGGGAAAATGGAGGCATATATTTCTGAGT [0/1] rs1565514831 (variation viewer)

Variant score: 0.000

Transcripts:: FLI1:ENST00000281428.12:c.*1833_*1834insCTCAATTTTGAAATCTGCAAAGTATTCATTAGGGAAAATGGAGGCATATATTTCTGAGT:p.(=); FLI1:ENST00000344954.10:c.*1833_*1834insCTCAATTTTGAAATCTGCAAAGTATTCATTAGGGAAAATGGAGGCATATATTTCTGAGT:p.(=); FLI1:ENST00000527786.7:c.*1833_*1834insCTCAATTTTGAAATCTGCAAAGTATTCATTAGGGAAAATGGAGGCATATATTTCTGAGT:p.(=); FLI1:ENST00000534087.3:c.*1833_*1834insCTCAATTTTGAAATCTGCAAAGTATTCATTAGGGAAAATGGAGGCATATATTTCTGAGT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: gnomAD_G_AFR: 0.1060%; gnomAD_G_AMR: 0.2451%; gnomAD_G_ASJ: 0.3571%; gnomAD_G_EAS: 0.2635%; gnomAD_G_FIN: 0.4627%; gnomAD_G_NFE: 0.3283%; gnomAD_G_OTH: 0.9132%

Exomiser Score: 0.990

Phenotype Score: 0.864

Variant Score: 0.968

Phenotype matches:

Phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.511 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:219090 Pituitary adenoma 4, ACTH-secreting, somatic - autosomal dominant/recessive; ORPHA:96253 Cushing disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.990

Phenotype Score: 0.864

Variant Score: 0.968

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr15:g.50421000A>G [0/1] rs895956798 (variation viewer)

Variant score: 0.968 CONTRIBUTING VARIANT

Transcripts:: USP8:ENST00000396444.7::; USP8:ENST00000560847.2::

Pathogenicity Data:: Best Score: 0.968158; CADD: 0.968 (14.970)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.983

Phenotype Score: 0.864

Variant Score: 0.913

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50453860C>CTTT [1/1] rs71124355 (variation viewer)

Variant score: 0.913 CONTRIBUTING VARIANT

Transcripts:: USP8:ENST00000307179.9:c.335+4375_335+4376insTTT:p.(=); USP8:ENST00000396444.7:c.335+4375_335+4376insTTT:p.(=); USP8:ENST00000425032.7:c.105-5140_105-5139insTTT:p.(=); USP8:ENST00000625664.2:c.*1+4375_*1+4376insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.91270286; CADD: 0.913 (10.590)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_EXON_VARIANT chr15:g.50424402G>A [0/1] rs115420394 (variation viewer)

Variant score: 0.764

Transcripts:: USP8:ENST00000396444.7:c.-318G>A:p.(=); USP8:ENST00000425032.7:c.-178G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9925869; CADD: 0.993 (21.300)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4237%; UK10K: 0.6348%; gnomAD_G_AFR: 0.0801%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.7450%; gnomAD_G_NFE: 0.6870%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50479270C>T [0/1] rs1194744400 (variation viewer)

Variant score: 0.708

Transcripts:: USP8:ENST00000307179.9:c.1218+1771C>T:p.(=); USP8:ENST00000396444.7:c.1218+1771C>T:p.(=); USP8:ENST00000425032.7:c.987+1771C>T:p.(=); USP8:ENST00000625664.2:c.*884+1771C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7087271; CADD: 0.709 (5.357)

Frequency Data:: gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50485550A>AT [0/1] rs71424071 (variation viewer)

Variant score: 0.670

Transcripts:: USP8:ENST00000307179.9:c.1890+1189_1890+1190insT:p.(=); USP8:ENST00000396444.7:c.1890+1189_1890+1190insT:p.(=); USP8:ENST00000425032.7:c.1572+3485_1572+3486insT:p.(=)

Pathogenicity Data:: Best Score: 0.66955435; CADD: 0.670 (4.809)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50453750C>T [0|1]

Variant score: 0.542

Transcripts:: USP8:ENST00000307179.9:c.335+4265C>T:p.(=); USP8:ENST00000396444.7:c.335+4265C>T:p.(=); USP8:ENST00000425032.7:c.105-5250C>T:p.(=); USP8:ENST00000625664.2:c.*1+4265C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5415415; CADD: 0.542 (3.387)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50484046A>T [0/1] rs543630612 (variation viewer)

Variant score: 0.477

Transcripts:: USP8:ENST00000307179.9:c.1804-229A>T:p.(=); USP8:ENST00000396444.7:c.1804-229A>T:p.(=); USP8:ENST00000425032.7:c.1572+1981A>T:p.(=)

Pathogenicity Data:: Best Score: 0.51224697; CADD: 0.512 (3.118)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1840%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0688%; gnomAD_G_FIN: 0.3501%; gnomAD_G_NFE: 0.4147%; gnomAD_G_OTH: 0.3086%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50453748C>T [0|1]

Variant score: 0.305

Transcripts:: USP8:ENST00000307179.9:c.335+4263C>T:p.(=); USP8:ENST00000396444.7:c.335+4263C>T:p.(=); USP8:ENST00000425032.7:c.105-5252C>T:p.(=); USP8:ENST00000625664.2:c.*1+4263C>T:p.(=)

Pathogenicity Data:: Best Score: 0.30545563; CADD: 0.305 (1.583)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50464539C>T [0/1] rs1482906822 (variation viewer)

Variant score: 0.274

Transcripts:: USP8:ENST00000307179.9:c.542-508C>T:p.(=); USP8:ENST00000396444.7:c.542-508C>T:p.(=); USP8:ENST00000425032.7:c.311-508C>T:p.(=); USP8:ENST00000625664.2:c.*208-508C>T:p.(=)

Pathogenicity Data:: Best Score: 0.27456254; CADD: 0.275 (1.394)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50471271A>G [0/1] rs72738973 (variation viewer)

Variant score: 0.144

Transcripts:: USP8:ENST00000307179.9:c.687-362A>G:p.(=); USP8:ENST00000396444.7:c.687-362A>G:p.(=); USP8:ENST00000425032.7:c.456-362A>G:p.(=); USP8:ENST00000625664.2:c.*353-362A>G:p.(=)

Pathogenicity Data:: Best Score: 0.29773664; CADD: 0.298 (1.535)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.7733%; UK10K: 1.2034%; gnomAD_G_AFR: 0.2062%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.5741%; gnomAD_G_NFE: 1.0994%; gnomAD_G_OTH: 1.3238%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50472824C>T [0|1] rs778350329 (variation viewer)

Variant score: 0.142

Transcripts:: USP8:ENST00000307179.9:c.849+1029C>T:p.(=); USP8:ENST00000396444.7:c.849+1029C>T:p.(=); USP8:ENST00000425032.7:c.618+1029C>T:p.(=); USP8:ENST00000625664.2:c.*515+1029C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14236993; CADD: 0.142 (0.667)

Frequency Data:: UK10K: 0.0132%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50441969CT>C [0/1] rs1011150634 (variation viewer)

Variant score: 0.079

Transcripts:: USP8:ENST00000307179.9:c.249+477del:p.(=); USP8:ENST00000396444.7:c.249+477del:p.(=); USP8:ENST00000425032.7:c.104+2793del:p.(=); USP8:ENST00000625664.2:c.104+2793del:p.(=)

Pathogenicity Data:: Best Score: 0.07933849; CADD: 0.079 (0.359)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.50495239TATATACGTGTATATATACATACATATATACACATATATATACACATACATATATAC>* [-/1]

Variant score: 0.000

Transcripts:: USP8:ENST00000307179.9:c.2659-609_2659-553delTATATACGTGTATATATACATACATATATACACATATATATACACATACATATATACins*:p.(=); USP8:ENST00000396444.7:c.2659-609_2659-553delTATATACGTGTATATATACATACATATATACACATATATATACACATACATATATACins*:p.(=); USP8:ENST00000425032.7:c.2341-609_2341-553delTATATACGTGTATATATACATACATATATACACATATATATACACATACATATATACins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Exomiser Score: 0.986

Phenotype Score: 0.864

Variant Score: 0.931

Phenotype matches:

Phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Phenotypic similarity 0.514 to mouse mutant involving CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Proximity score 0.500 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:601067 Usher syndrome, type 1D/F digenic - autosomal recessive; OMIM:601386 Deafness, autosomal recessive 12 - autosomal recessive; OMIM:617540 Pituitary adenoma 5, multiple types (susceptibility); ORPHA:231169 Usher syndrome type 1; ORPHA:96253 Cushing disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.986

Phenotype Score: 0.864

Variant Score: 0.931

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71662376C>T [0/1] rs559075053 (variation viewer)

Variant score: 0.931 CONTRIBUTING VARIANT

Transcripts:: CDH23:ENST00000224721.12:c.1450-12736C>T:p.(=); CDH23:ENST00000299366.11:c.1450-12736C>T:p.(=); CDH23:ENST00000398809.8:c.1450-12736C>T:p.(=); CDH23:ENST00000442677.4:c.1450-12736C>T:p.(=); CDH23:ENST00000616684.4:c.1450-12736C>T:p.(=); CDH23:ENST00000622827.4:c.1450-12736C>T:p.(=)

Pathogenicity Data:: Best Score: 0.93176615; CADD: 0.932 (11.660)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.976

Phenotype Score: 0.864

Variant Score: 0.871

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71662376C>T [0/1] rs559075053 (variation viewer)

Variant score: 0.931 CONTRIBUTING VARIANT

Transcripts:: CDH23:ENST00000224721.12:c.1450-12736C>T:p.(=); CDH23:ENST00000299366.11:c.1450-12736C>T:p.(=); CDH23:ENST00000398809.8:c.1450-12736C>T:p.(=); CDH23:ENST00000442677.4:c.1450-12736C>T:p.(=); CDH23:ENST00000616684.4:c.1450-12736C>T:p.(=); CDH23:ENST00000622827.4:c.1450-12736C>T:p.(=)

Pathogenicity Data:: Best Score: 0.93176615; CADD: 0.932 (11.660)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71795061G>T [0/1] rs921741111 (variation viewer)

Variant score: 0.812 CONTRIBUTING VARIANT

Transcripts:: CDH23:ENST00000224721.12:c.6712+1421G>T:p.(=); CDH23:ENST00000622827.4:c.6712+1421G>T:p.(=)

Pathogenicity Data:: Best Score: 0.81176513; CADD: 0.812 (7.253)

Frequency Data:: TOPMed: 0.0016%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71802839G>A [0/1] rs1040161004 (variation viewer)

Variant score: 0.638

Transcripts:: CDH23:ENST00000224721.12:c.7483-59G>A:p.(=); CDH23:ENST00000398788.4:c.763-59G>A:p.(=); CDH23:ENST00000619887.4:c.763-59G>A:p.(=); CDH23:ENST00000622827.4:c.7483-59G>A:p.(=)

Pathogenicity Data:: Best Score: 0.63825715; CADD: 0.638 (4.416)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71719747C>A [0/1] rs187097695 (variation viewer)

Variant score: 0.605

Transcripts:: CDH23:ENST00000224721.12:c.3370-4298C>A:p.(=); CDH23:ENST00000398809.8:c.3374-4305C>A:p.(=); CDH23:ENST00000616684.4:c.3370-4298C>A:p.(=); CDH23:ENST00000622827.4:c.3370-4298C>A:p.(=); CDH23:ENST00000441508.4:c.-126G>T:p.(=); CDH23:ENST00000398786.2:c.-5-3405G>T:p.(=)

Pathogenicity Data:: Best Score: 0.6839906; CADD: 0.684 (5.003)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2150%; gnomAD_G_AFR: 0.6187%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71661870T>C [0|1] rs563804534 (variation viewer)

Variant score: 0.573

Transcripts:: CDH23:ENST00000224721.12:c.1450-13242T>C:p.(=); CDH23:ENST00000299366.11:c.1450-13242T>C:p.(=); CDH23:ENST00000398809.8:c.1450-13242T>C:p.(=); CDH23:ENST00000442677.4:c.1450-13242T>C:p.(=); CDH23:ENST00000616684.4:c.1450-13242T>C:p.(=); CDH23:ENST00000622827.4:c.1450-13242T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6198982; CADD: 0.620 (4.201)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.1597%; gnomAD_G_AFR: 0.0465%; gnomAD_G_FIN: 0.4425%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71633381T>C [0/1] rs1003393133 (variation viewer)

Variant score: 0.556

Transcripts:: CDH23:ENST00000224721.12:c.1135-10480T>C:p.(=); CDH23:ENST00000299366.11:c.1135-10480T>C:p.(=); CDH23:ENST00000398809.8:c.1135-10480T>C:p.(=); CDH23:ENST00000398842.7:c.886-12450T>C:p.(=); CDH23:ENST00000442677.4:c.1135-10480T>C:p.(=); CDH23:ENST00000461841.7:c.1135-10480T>C:p.(=); CDH23:ENST00000616684.4:c.1135-10480T>C:p.(=); CDH23:ENST00000622827.4:c.1135-12444T>C:p.(=)

Pathogenicity Data:: Best Score: 0.55730975; CADD: 0.557 (3.539)

Frequency Data:: TOPMed: 0.0191%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71661867A>G [0|1] rs1351073375 (variation viewer)

Variant score: 0.543

Transcripts:: CDH23:ENST00000224721.12:c.1450-13245A>G:p.(=); CDH23:ENST00000299366.11:c.1450-13245A>G:p.(=); CDH23:ENST00000398809.8:c.1450-13245A>G:p.(=); CDH23:ENST00000442677.4:c.1450-13245A>G:p.(=); CDH23:ENST00000616684.4:c.1450-13245A>G:p.(=); CDH23:ENST00000622827.4:c.1450-13245A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5719446; CADD: 0.572 (3.685)

Frequency Data:: gnomAD_G_FIN: 0.3198%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71661864T>A [0|1] rs1297531529 (variation viewer)

Variant score: 0.412

Transcripts:: CDH23:ENST00000224721.12:c.1450-13248T>A:p.(=); CDH23:ENST00000299366.11:c.1450-13248T>A:p.(=); CDH23:ENST00000398809.8:c.1450-13248T>A:p.(=); CDH23:ENST00000442677.4:c.1450-13248T>A:p.(=); CDH23:ENST00000616684.4:c.1450-13248T>A:p.(=); CDH23:ENST00000622827.4:c.1450-13248T>A:p.(=)

Pathogenicity Data:: Best Score: 0.42733586; CADD: 0.427 (2.421)

Frequency Data:: gnomAD_G_FIN: 0.2326%; gnomAD_G_NFE: 0.0257%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71689126G>A [1/1] rs111987249 (variation viewer)

Variant score: 0.383

Transcripts:: CDH23:ENST00000224721.12:c.2060-1342G>A:p.(=); CDH23:ENST00000299366.11:c.2060-1342G>A:p.(=); CDH23:ENST00000398809.8:c.2060-1342G>A:p.(=); CDH23:ENST00000442677.4:c.2060-1342G>A:p.(=); CDH23:ENST00000616684.4:c.2060-1342G>A:p.(=); CDH23:ENST00000622827.4:c.2060-1342G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5891342; CADD: 0.589 (3.863)

Frequency Data:: gnomAD_G_AFR: 1.2759%; gnomAD_G_AMR: 0.9358%; gnomAD_G_ASJ: 0.8475%; gnomAD_G_EAS: 0.4060%; gnomAD_G_FIN: 1.0168%; gnomAD_G_NFE: 0.5474%; gnomAD_G_OTH: 0.6313%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71661890CCCCTCCCACCCAGCG>C [0|1] rs1204353088 (variation viewer)

Variant score: 0.284

Transcripts:: CDH23:ENST00000224721.12:c.1450-13221_1450-13207del:p.(=); CDH23:ENST00000299366.11:c.1450-13221_1450-13207del:p.(=); CDH23:ENST00000398809.8:c.1450-13221_1450-13207del:p.(=); CDH23:ENST00000442677.4:c.1450-13221_1450-13207del:p.(=); CDH23:ENST00000616684.4:c.1450-13221_1450-13207del:p.(=); CDH23:ENST00000622827.4:c.1450-13221_1450-13207del:p.(=)

Pathogenicity Data:: Best Score: 0.29238015; CADD: 0.292 (1.502)

Frequency Data:: gnomAD_G_FIN: 0.1826%; gnomAD_G_NFE: 0.0188%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71710130C>T [0/1] rs147121327 (variation viewer)

Variant score: 0.245

Transcripts:: CDH23:ENST00000224721.12:c.3220+919C>T:p.(=); CDH23:ENST00000398809.8:c.3220+919C>T:p.(=); CDH23:ENST00000442677.4:c.3220+919C>T:p.(=); CDH23:ENST00000616684.4:c.3220+919C>T:p.(=); CDH23:ENST00000622827.4:c.3220+919C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2626053; CADD: 0.263 (1.323)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.1999%; UK10K: 0.4099%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.2134%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71792852A>AT [1/1] rs1227417285 (variation viewer)

Variant score: 0.180

Transcripts:: CDH23:ENST00000224721.12:c.6254-330_6254-329insT:p.(=); CDH23:ENST00000622827.4:c.6254-330_6254-329insT:p.(=)

Pathogenicity Data:: Best Score: 0.18021494; CADD: 0.180 (0.863)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71797744A>G [0/1] rs1017786018 (variation viewer)

Variant score: 0.169

Transcripts:: CDH23:ENST00000224721.12:c.6829+524A>G:p.(=); CDH23:ENST00000398788.4:c.109+524A>G:p.(=); CDH23:ENST00000619887.4:c.109+524A>G:p.(=); CDH23:ENST00000622827.4:c.6829+524A>G:p.(=)

Pathogenicity Data:: Best Score: 0.16919327; CADD: 0.169 (0.805)

Frequency Data:: TOPMed: 0.0008%

INTERGENIC_VARIANT chr10:g.71383633C>CA [1/1] rs1158598454 (variation viewer)

Variant score: 0.154

Transcripts:: CDH23:ENST00000224721.12::; CDH23:ENST00000373189.6::

Pathogenicity Data:: Best Score: 0.1543318; CADD: 0.154 (0.728)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71667367T>A [1|1] rs371043904 (variation viewer)

Variant score: 0.154

Transcripts:: CDH23:ENST00000224721.12:c.1450-7745T>A:p.(=); CDH23:ENST00000299366.11:c.1450-7745T>A:p.(=); CDH23:ENST00000398809.8:c.1450-7745T>A:p.(=); CDH23:ENST00000442677.4:c.1450-7745T>A:p.(=); CDH23:ENST00000616684.4:c.1450-7745T>A:p.(=); CDH23:ENST00000622827.4:c.1450-7745T>A:p.(=)

Pathogenicity Data:: Best Score: 0.19425058; CADD: 0.194 (0.938)

Frequency Data:: gnomAD_G_AFR: 0.1877%; gnomAD_G_ASJ: 0.8929%; gnomAD_G_EAS: 0.9288%; gnomAD_G_FIN: 0.1542%; gnomAD_G_NFE: 0.5785%; gnomAD_G_OTH: 0.8734%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.71438347CAA>C [1/1] rs10596696 (variation viewer)

Variant score: 0.145

Transcripts:: CDH23:ENST00000224721.12:c.-5-1479_-5-1478del:p.(=); CDH23:ENST00000299366.11:c.-5-1479_-5-1478del:p.(=); CDH23:ENST00000398809.8:c.-5-1479_-5-1478del:p.(=); CDH23:ENST00000398842.7:c.-33+41030_-33+41031del:p.(=); CDH23:ENST00000461841.7:c.-5-1479_-5-1478del:p.(=); CDH23:ENST00000616684.4:c.-5-1479_-5-1478del:p.(=); CDH23:ENST00000622827.4:c.-5-1479_-5-1478del:p.(=)

Pathogenicity Data:: Best Score: 0.14473641; CADD: 0.145 (0.679)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71759846C>CACACACAT [1|1] rs776230069 (variation viewer)

Variant score: 0.107

Transcripts:: CDH23:ENST00000224721.12:c.4846-17834_4846-17833insACACACAT:p.(=); CDH23:ENST00000622827.4:c.4846-17834_4846-17833insACACACAT:p.(=); CDH23:ENST00000394957.8:c.568+1021_568+1022insATGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.10731137; CADD: 0.107 (0.493)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.71427195GA>G [1|1] rs1254669401 (variation viewer)

Variant score: 0.106

Transcripts:: CDH23:ENST00000224721.12:c.-5-12631del:p.(=); CDH23:ENST00000299366.11:c.-5-12631del:p.(=); CDH23:ENST00000398809.8:c.-5-12631del:p.(=); CDH23:ENST00000398842.7:c.-33+29878del:p.(=); CDH23:ENST00000461841.7:c.-5-12631del:p.(=); CDH23:ENST00000616684.4:c.-5-12631del:p.(=); CDH23:ENST00000622827.4:c.-5-12631del:p.(=)

Pathogenicity Data:: Best Score: 0.10587138; CADD: 0.106 (0.486)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71642544G>A [0/1] rs534110366 (variation viewer)

Variant score: 0.085

Transcripts:: CDH23:ENST00000224721.12:c.1135-1317G>A:p.(=); CDH23:ENST00000299366.11:c.1135-1317G>A:p.(=); CDH23:ENST00000398809.8:c.1135-1317G>A:p.(=); CDH23:ENST00000398842.7:c.886-3287G>A:p.(=); CDH23:ENST00000442677.4:c.1135-1317G>A:p.(=); CDH23:ENST00000461841.7:c.1135-1317G>A:p.(=); CDH23:ENST00000616684.4:c.1135-1317G>A:p.(=); CDH23:ENST00000622827.4:c.1135-3281G>A:p.(=)

Pathogenicity Data:: Best Score: 0.08483374; CADD: 0.085 (0.385)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0279%; gnomAD_G_AFR: 0.0230%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71632814TCACCTGCCTTCC>T [0/1] rs146674300 (variation viewer)

Variant score: 0.047

Transcripts:: CDH23:ENST00000224721.12:c.1135-11046_1135-11035del:p.(=); CDH23:ENST00000299366.11:c.1135-11046_1135-11035del:p.(=); CDH23:ENST00000398809.8:c.1135-11046_1135-11035del:p.(=); CDH23:ENST00000398842.7:c.886-13016_886-13005del:p.(=); CDH23:ENST00000442677.4:c.1135-11046_1135-11035del:p.(=); CDH23:ENST00000461841.7:c.1135-11046_1135-11035del:p.(=); CDH23:ENST00000616684.4:c.1135-11046_1135-11035del:p.(=); CDH23:ENST00000622827.4:c.1135-13010_1135-12999del:p.(=)

Pathogenicity Data:: Best Score: 0.28451586; CADD: 0.285 (1.454)

Frequency Data:: TOPMed: 0.5933%; gnomAD_G_AFR: 1.9698%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71556120G>A [0/1] rs149539390 (variation viewer)

Variant score: 0.007

Transcripts:: CDH23:ENST00000224721.12:c.430-10622G>A:p.(=); CDH23:ENST00000299366.11:c.430-10622G>A:p.(=); CDH23:ENST00000398809.8:c.430-10622G>A:p.(=); CDH23:ENST00000398842.7:c.253-10622G>A:p.(=); CDH23:ENST00000442677.4:c.430-10622G>A:p.(=); CDH23:ENST00000461841.7:c.430-10622G>A:p.(=); CDH23:ENST00000616684.4:c.430-10622G>A:p.(=); CDH23:ENST00000622827.4:c.430-10622G>A:p.(=)

Pathogenicity Data:: Best Score: 0.010536015; CADD: 0.011 (0.046)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2851%; UK10K: 0.4496%; gnomAD_G_AFR: 0.0572%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 1.2021%; gnomAD_G_NFE: 0.6996%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71496824GGTGTACAGATGGACAGTTGGGATGTCAAAAGGGCTACAGGTGATTCTAAGCTGCAGCCAGGGCTGAAATGACCCTTTGTTGCACTGGGACAGAGGCCCAAGACGGAAGGGATGCCCCGGA>G [0/1] rs68040631 (variation viewer)

Variant score: 0.000

Transcripts:: CDH23:ENST00000224721.12:c.146-13257_146-13138del:p.(=); CDH23:ENST00000299366.11:c.146-13257_146-13138del:p.(=); CDH23:ENST00000398809.8:c.146-13257_146-13138del:p.(=); CDH23:ENST00000442677.4:c.146-13257_146-13138del:p.(=); CDH23:ENST00000461841.7:c.146-13257_146-13138del:p.(=); CDH23:ENST00000616684.4:c.146-13257_146-13138del:p.(=); CDH23:ENST00000622827.4:c.146-13257_146-13138del:p.(=); CDH23:ENST00000398842.7:c.-32-13257_-32-13138del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71671645TGC>* [-/1]

Variant score: 0.000

Transcripts:: CDH23:ENST00000224721.12:c.1450-3467_1450-3465delTGCins*:p.(=); CDH23:ENST00000299366.11:c.1450-3467_1450-3465delTGCins*:p.(=); CDH23:ENST00000398809.8:c.1450-3467_1450-3465delTGCins*:p.(=); CDH23:ENST00000442677.4:c.1450-3467_1450-3465delTGCins*:p.(=); CDH23:ENST00000616684.4:c.1450-3467_1450-3465delTGCins*:p.(=); CDH23:ENST00000622827.4:c.1450-3467_1450-3465delTGCins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.71680764G>* [-/1]

Variant score: 0.000

Transcripts:: CDH23:ENST00000224721.12:c.1858+1272G>*:p.(=); CDH23:ENST00000299366.11:c.1858+1272G>*:p.(=); CDH23:ENST00000398809.8:c.1858+1272G>*:p.(=); CDH23:ENST00000442677.4:c.1858+1272G>*:p.(=); CDH23:ENST00000616684.4:c.1858+1272G>*:p.(=); CDH23:ENST00000622827.4:c.1858+1272G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MECP2

Exomiser Score: 0.964

Phenotype Score: 0.909

Variant Score: 0.776

Phenotype matches:

Phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Phenotypic similarity 0.458 to mouse mutant involving MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300055 Mental retardation, X-linked, syndromic 13 - X-linked recessive; OMIM:300260 Mental retardation, X-linked syndromic, Lubs type - X-linked recessive; OMIM:300496 Autism susceptibility, X-linked 3 (susceptibility); OMIM:300673 Encephalopathy, neonatal severe - X-linked recessive; OMIM:312750 Rett syndrome, atypical - X-linked dominant; ORPHA:1762 Trisomy Xq28; ORPHA:3077 X-linked intellectual disability-psychosis-macroorchidism syndrome; ORPHA:3095 Atypical Rett syndrome; ORPHA:777 X-linked non-syndromic intellectual disability; ORPHA:778 Rett syndrome

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.964

Phenotype Score: 0.909

Variant Score: 0.776

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154097423G>C [1/1] rs1299656947 (variation viewer)

Variant score: 0.776 CONTRIBUTING VARIANT

Transcripts:: MECP2:ENST00000407218.5:c.62+181C>G:p.(=); MECP2:ENST00000453960.7:c.62+181C>G:p.(=); MECP2:ENST00000303391.11:c.-99+181C>G:p.(=); MECP2:ENST00000628176.2:c.-99+181C>G:p.(=)

Pathogenicity Data:: Best Score: 0.7760763; CADD: 0.776 (6.499)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.964

Phenotype Score: 0.909

Variant Score: 0.776

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154097423G>C [1/1] rs1299656947 (variation viewer)

Variant score: 0.776 CONTRIBUTING VARIANT

Transcripts:: MECP2:ENST00000407218.5:c.62+181C>G:p.(=); MECP2:ENST00000453960.7:c.62+181C>G:p.(=); MECP2:ENST00000303391.11:c.-99+181C>G:p.(=); MECP2:ENST00000628176.2:c.-99+181C>G:p.(=)

Pathogenicity Data:: Best Score: 0.7760763; CADD: 0.776 (6.499)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154033236G>C [1/1] rs868921038 (variation viewer)

Variant score: 0.702

Transcripts:: MECP2:ENST00000303391.11:c.27-679C>G:p.(=); MECP2:ENST00000407218.5:c.63-679C>G:p.(=); MECP2:ENST00000453960.7:c.63-679C>G:p.(=); MECP2:ENST00000611468.1:c.15-679C>G:p.(=); MECP2:ENST00000622433.4:c.15-679C>G:p.(=); MECP2:ENST00000628176.2:c.27-679C>G:p.(=); MECP2:ENST00000640414.1:c.27-679C>G:p.(=)

Pathogenicity Data:: Best Score: 0.70440304; CADD: 0.704 (5.293)

Frequency Data:: TOPMed: 0.0120%; gnomAD_G_NFE: 0.0285%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154069602T>C [0|1]

Variant score: 0.659

Transcripts:: MECP2:ENST00000303391.11:c.26+22582A>G:p.(=); MECP2:ENST00000407218.5:c.62+28002A>G:p.(=); MECP2:ENST00000453960.7:c.62+28002A>G:p.(=); MECP2:ENST00000611468.1:c.14+22582A>G:p.(=); MECP2:ENST00000622433.4:c.14+22582A>G:p.(=); MECP2:ENST00000628176.2:c.26+22582A>G:p.(=); MECP2:ENST00000640414.1:c.26+22582A>G:p.(=)

Pathogenicity Data:: Best Score: 0.65872854; CADD: 0.659 (4.669)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154085266A>G [1/1] rs868986485 (variation viewer)

Variant score: 0.548

Transcripts:: MECP2:ENST00000303391.11:c.26+6918T>C:p.(=); MECP2:ENST00000407218.5:c.62+12338T>C:p.(=); MECP2:ENST00000453960.7:c.62+12338T>C:p.(=); MECP2:ENST00000611468.1:c.14+6918T>C:p.(=); MECP2:ENST00000622433.4:c.14+6918T>C:p.(=); MECP2:ENST00000628176.2:c.26+6918T>C:p.(=); MECP2:ENST00000640414.1:c.26+6918T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5513579; CADD: 0.551 (3.481)

Frequency Data:: TOPMed: 0.0120%; gnomAD_G_NFE: 0.0385%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154090197T>G [1/1] rs56108594 (variation viewer)

Variant score: 0.384

Transcripts:: MECP2:ENST00000303391.11:c.26+1987A>C:p.(=); MECP2:ENST00000407218.5:c.62+7407A>C:p.(=); MECP2:ENST00000453960.7:c.62+7407A>C:p.(=); MECP2:ENST00000611468.1:c.14+1987A>C:p.(=); MECP2:ENST00000622433.4:c.14+1987A>C:p.(=); MECP2:ENST00000628176.2:c.26+1987A>C:p.(=); MECP2:ENST00000640414.1:c.26+1987A>C:p.(=)

Pathogenicity Data:: Best Score: 0.38439804; CADD: 0.384 (2.107)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154088984C>CT [1|1] rs1465018260 (variation viewer)

Variant score: 0.285

Transcripts:: MECP2:ENST00000303391.11:c.26+3199_26+3200insA:p.(=); MECP2:ENST00000407218.5:c.62+8619_62+8620insA:p.(=); MECP2:ENST00000453960.7:c.62+8619_62+8620insA:p.(=); MECP2:ENST00000611468.1:c.14+3199_14+3200insA:p.(=); MECP2:ENST00000622433.4:c.14+3199_14+3200insA:p.(=); MECP2:ENST00000628176.2:c.26+3199_26+3200insA:p.(=); MECP2:ENST00000640414.1:c.26+3199_26+3200insA:p.(=)

Pathogenicity Data:: Best Score: 0.28451586; CADD: 0.285 (1.454)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154088986C>CTAA [1|1] rs1172480951 (variation viewer)

Variant score: 0.266

Transcripts:: MECP2:ENST00000303391.11:c.26+3197_26+3198insTTA:p.(=); MECP2:ENST00000407218.5:c.62+8617_62+8618insTTA:p.(=); MECP2:ENST00000453960.7:c.62+8617_62+8618insTTA:p.(=); MECP2:ENST00000611468.1:c.14+3197_14+3198insTTA:p.(=); MECP2:ENST00000622433.4:c.14+3197_14+3198insTTA:p.(=); MECP2:ENST00000628176.2:c.26+3197_26+3198insTTA:p.(=); MECP2:ENST00000640414.1:c.26+3197_26+3198insTTA:p.(=)

Pathogenicity Data:: Best Score: 0.26599336; CADD: 0.266 (1.343)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154055808C>A [1/1] rs868909541 (variation viewer)

Variant score: 0.193

Transcripts:: MECP2:ENST00000303391.11:c.27-23251G>T:p.(=); MECP2:ENST00000407218.5:c.63-23251G>T:p.(=); MECP2:ENST00000453960.7:c.63-23251G>T:p.(=); MECP2:ENST00000611468.1:c.15-23251G>T:p.(=); MECP2:ENST00000622433.4:c.15-23251G>T:p.(=); MECP2:ENST00000628176.2:c.27-23251G>T:p.(=); MECP2:ENST00000640414.1:c.27-23251G>T:p.(=)

Pathogenicity Data:: Best Score: 0.19702876; CADD: 0.197 (0.953)

Frequency Data:: gnomAD_G_AFR: 0.0399%; gnomAD_G_FIN: 0.1258%; gnomAD_G_NFE: 0.0572%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154069607C>T [0|1]

Variant score: 0.120

Transcripts:: MECP2:ENST00000303391.11:c.26+22577G>A:p.(=); MECP2:ENST00000407218.5:c.62+27997G>A:p.(=); MECP2:ENST00000453960.7:c.62+27997G>A:p.(=); MECP2:ENST00000611468.1:c.14+22577G>A:p.(=); MECP2:ENST00000622433.4:c.14+22577G>A:p.(=); MECP2:ENST00000628176.2:c.26+22577G>A:p.(=); MECP2:ENST00000640414.1:c.26+22577G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11976224; CADD: 0.120 (0.554)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154094965CT>C [1/1] rs11410993 (variation viewer)

Variant score: 0.110

Transcripts:: MECP2:ENST00000407218.5:c.62+2638del:p.(=); MECP2:ENST00000453960.7:c.62+2638del:p.(=); MECP2:ENST00000303391.11:c.-99+2638del:p.(=); MECP2:ENST00000628176.2:c.-99+2638del:p.(=)

Pathogenicity Data:: Best Score: 0.10956955; CADD: 0.110 (0.504)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154069606C>G [0|1]

Variant score: 0.099

Transcripts:: MECP2:ENST00000303391.11:c.26+22578G>C:p.(=); MECP2:ENST00000407218.5:c.62+27998G>C:p.(=); MECP2:ENST00000453960.7:c.62+27998G>C:p.(=); MECP2:ENST00000611468.1:c.14+22578G>C:p.(=); MECP2:ENST00000622433.4:c.14+22578G>C:p.(=); MECP2:ENST00000628176.2:c.26+22578G>C:p.(=); MECP2:ENST00000640414.1:c.26+22578G>C:p.(=)

Pathogenicity Data:: Best Score: 0.09925884; CADD: 0.099 (0.454)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154084900TG>T [1/1] rs1374860864 (variation viewer)

Variant score: 0.063

Transcripts:: MECP2:ENST00000303391.11:c.26+7283del:p.(=); MECP2:ENST00000407218.5:c.62+12703del:p.(=); MECP2:ENST00000453960.7:c.62+12703del:p.(=); MECP2:ENST00000611468.1:c.14+7283del:p.(=); MECP2:ENST00000622433.4:c.14+7283del:p.(=); MECP2:ENST00000628176.2:c.26+7283del:p.(=); MECP2:ENST00000640414.1:c.26+7283del:p.(=)

Pathogenicity Data:: Best Score: 0.06286967; CADD: 0.063 (0.282)

Frequency Data:: No frequency data

RREB1

Exomiser Score: 0.934

Phenotype Score: 0.864

Variant Score: 0.757

Phenotype matches:

Phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with RREB1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:567 22q11.2 deletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.934

Phenotype Score: 0.864

Variant Score: 0.757

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr6:g.7253453C>CA [0/1] rs1169956662 (variation viewer)

Variant score: 0.757 CONTRIBUTING VARIANT

Transcripts:: RREB1:ENST00000379938.7::; RREB1:ENST00000474597.5::

Pathogenicity Data:: Best Score: 0.7569476; CADD: 0.757 (6.143)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.083

Phenotype Score: 0.432

Variant Score: 0.696

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.7117388GTTTTTTTTTTTTTT>G [1/1] rs70978941 (variation viewer)

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: RREB1:ENST00000334984.10:c.-285+9329_-285+9342del:p.(=); RREB1:ENST00000349384.10:c.-285+9329_-285+9342del:p.(=); RREB1:ENST00000379933.7:c.-285+9621_-285+9634del:p.(=); RREB1:ENST00000379938.7:c.-285+9329_-285+9342del:p.(=)

Pathogenicity Data:: Best Score: 0.69584143; CADD: 0.696 (5.169)

Frequency Data:: No frequency data

Other passed variants:

REGULATORY_REGION_VARIANT chr6:g.7074168C>CT [1/1] rs11423832 (variation viewer)

Variant score: 0.615

Transcripts:: RREB1:ENST00000379933.7::; RREB1:ENST00000407097.2::

Pathogenicity Data:: Best Score: 0.61531967; CADD: 0.615 (4.149)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.7198445G>A [0/1] rs116539774 (variation viewer)

Variant score: 0.221

Transcripts:: RREB1:ENST00000334984.10:c.425+9123G>A:p.(=); RREB1:ENST00000349384.10:c.425+9123G>A:p.(=); RREB1:ENST00000379933.7:c.425+9123G>A:p.(=); RREB1:ENST00000379938.7:c.425+9123G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3527084; CADD: 0.353 (1.889)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.8370%; UK10K: 1.3224%; gnomAD_G_AFR: 0.2520%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.0876%; gnomAD_G_NFE: 1.3265%; gnomAD_G_OTH: 1.1247%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.7188254C>* [-/1]

Variant score: 0.000

Transcripts:: RREB1:ENST00000334984.10:c.261+731C>*:p.(=); RREB1:ENST00000349384.10:c.261+731C>*:p.(=); RREB1:ENST00000379933.7:c.261+731C>*:p.(=); RREB1:ENST00000379938.7:c.261+731C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CEP85L

Exomiser Score: 0.905

Phenotype Score: 0.913

Variant Score: 0.658

Phenotype matches:

Phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618873 Lissencephaly 10 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.905

Phenotype Score: 0.913

Variant Score: 0.658

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118560777A>G [0/1] rs866813543 (variation viewer)

Variant score: 0.658 CONTRIBUTING VARIANT

Transcripts:: CEP85L:ENST00000360290.7:c.714+4752T>C:p.(=); CEP85L:ENST00000368488.9:c.1029+4752T>C:p.(=); CEP85L:ENST00000368491.8:c.1020+4752T>C:p.(=); CEP85L:ENST00000392500.7:c.1029+4752T>C:p.(=); CEP85L:ENST00000419517.2:c.1020+4752T>C:p.(=); CEP85L:ENST00000357525.6:c.*1697A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6595134; CADD: 0.660 (4.679)

Frequency Data:: TOPMed: 0.0088%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.104

Phenotype Score: 0.457

Variant Score: 0.696

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118549978A>G [0/1] rs572489248 (variation viewer)

Variant score: 0.733 CONTRIBUTING VARIANT

Transcripts:: CEP85L:ENST00000360290.7:c.714+15551T>C:p.(=); CEP85L:ENST00000368488.9:c.1029+15551T>C:p.(=); CEP85L:ENST00000368491.8:c.1020+15551T>C:p.(=); CEP85L:ENST00000392500.7:c.1029+15551T>C:p.(=); CEP85L:ENST00000419517.2:c.1020+15551T>C:p.(=); CEP85L:ENST00000357525.6:c.-98+1586A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7744203; CADD: 0.774 (6.467)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0295%; UK10K: 0.0132%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.0268%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118560777A>G [0/1] rs866813543 (variation viewer)

Variant score: 0.658 CONTRIBUTING VARIANT

Transcripts:: CEP85L:ENST00000360290.7:c.714+4752T>C:p.(=); CEP85L:ENST00000368488.9:c.1029+4752T>C:p.(=); CEP85L:ENST00000368491.8:c.1020+4752T>C:p.(=); CEP85L:ENST00000392500.7:c.1029+4752T>C:p.(=); CEP85L:ENST00000419517.2:c.1020+4752T>C:p.(=); CEP85L:ENST00000357525.6:c.*1697A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6595134; CADD: 0.660 (4.679)

Frequency Data:: TOPMed: 0.0088%; gnomAD_G_NFE: 0.0133%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118553288C>T [0/1] rs934882835 (variation viewer)

Variant score: 0.646

Transcripts:: CEP85L:ENST00000360290.7:c.714+12241G>A:p.(=); CEP85L:ENST00000368488.9:c.1029+12241G>A:p.(=); CEP85L:ENST00000368491.8:c.1020+12241G>A:p.(=); CEP85L:ENST00000392500.7:c.1029+12241G>A:p.(=); CEP85L:ENST00000419517.2:c.1020+12241G>A:p.(=); CEP85L:ENST00000357525.6:c.-98+4896C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6561255; CADD: 0.656 (4.636)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1066%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118558660C>G [0/1] rs441037 (variation viewer)

Variant score: 0.454

Transcripts:: CEP85L:ENST00000360290.7:c.714+6869G>C:p.(=); CEP85L:ENST00000368488.9:c.1029+6869G>C:p.(=); CEP85L:ENST00000368491.8:c.1020+6869G>C:p.(=); CEP85L:ENST00000392500.7:c.1029+6869G>C:p.(=); CEP85L:ENST00000419517.2:c.1020+6869G>C:p.(=); CEP85L:ENST00000357525.6:c.-97-165C>G:p.(=)

Pathogenicity Data:: Best Score: 0.45424217; CADD: 0.454 (2.630)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118589705G>T [0/1] rs9489452 (variation viewer)

Variant score: 0.440

Transcripts:: CEP85L:ENST00000368488.9:c.242-23389C>A:p.(=); CEP85L:ENST00000368491.8:c.233-23389C>A:p.(=); CEP85L:ENST00000392500.7:c.242-23389C>A:p.(=); CEP85L:ENST00000419517.2:c.233-23389C>A:p.(=); CEP85L:ENST00000360290.7:c.-74-23389C>A:p.(=)

Pathogenicity Data:: Best Score: 0.44011354; CADD: 0.440 (2.519)

Frequency Data:: TOPMed: 0.0008%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.118691128A>AT [0|1] rs1480028681 (variation viewer)

Variant score: 0.367

Transcripts:: CEP85L:ENST00000368488.9:c.-28+18907_-28+18908insA:p.(=); CEP85L:ENST00000392500.7:c.-139+18907_-139+18908insA:p.(=)

Pathogenicity Data:: Best Score: 0.3691879; CADD: 0.369 (2.001)

Frequency Data:: gnomAD_G_NFE: 0.0359%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118488140C>T [0/1] rs975784272 (variation viewer)

Variant score: 0.352

Transcripts:: CEP85L:ENST00000368488.9:c.1446+3546G>A:p.(=); CEP85L:ENST00000368491.8:c.1437+3546G>A:p.(=)

Pathogenicity Data:: Best Score: 0.35716426; CADD: 0.357 (1.919)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1025%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.118691125A>ATACATTGT [0|1] rs1249202087 (variation viewer)

Variant score: 0.346

Transcripts:: CEP85L:ENST00000368488.9:c.-28+18910_-28+18911insACAATGTA:p.(=); CEP85L:ENST00000392500.7:c.-139+18910_-139+18911insACAATGTA:p.(=)

Pathogenicity Data:: Best Score: 0.34837162; CADD: 0.348 (1.860)

Frequency Data:: gnomAD_G_AFR: 0.0230%; gnomAD_G_NFE: 0.0400%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.118691130G>GATACATTGATAGAAGTATAGATACAAT [0|1] rs1254207286 (variation viewer)

Variant score: 0.238

Transcripts:: CEP85L:ENST00000368488.9:c.-28+18905_-28+18906insATTGTATCTATACTTCTATCAATGTAT:p.(=); CEP85L:ENST00000392500.7:c.-139+18905_-139+18906insATTGTATCTATACTTCTATCAATGTAT:p.(=)

Pathogenicity Data:: Best Score: 0.23879784; CADD: 0.239 (1.185)

Frequency Data:: gnomAD_G_NFE: 0.0180%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118500451A>AGCACCTATTGTTCGAAGGATGCAGTCTCACAAGCCT [1/1] rs138456612 (variation viewer)

Variant score: 0.219

Transcripts:: CEP85L:ENST00000360290.7:c.952-8587_952-8586insAGGCTTGTGAGACTGCATCCTTCGAACAATAGGTGC:p.(=); CEP85L:ENST00000368488.9:c.1267-8587_1267-8586insAGGCTTGTGAGACTGCATCCTTCGAACAATAGGTGC:p.(=); CEP85L:ENST00000368491.8:c.1258-8587_1258-8586insAGGCTTGTGAGACTGCATCCTTCGAACAATAGGTGC:p.(=); CEP85L:ENST00000392500.7:c.1267-8587_1267-8586insAGGCTTGTGAGACTGCATCCTTCGAACAATAGGTGC:p.(=); CEP85L:ENST00000419517.2:c.1258-8587_1258-8586insAGGCTTGTGAGACTGCATCCTTCGAACAATAGGTGC:p.(=)

Pathogenicity Data:: Best Score: 0.21873206; CADD: 0.219 (1.072)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118627198CA>C [1/1] rs56203910 (variation viewer)

Variant score: 0.216

Transcripts:: CEP85L:ENST00000368488.9:c.241+5254del:p.(=); CEP85L:ENST00000368491.8:c.232+5254del:p.(=); CEP85L:ENST00000392500.7:c.241+5254del:p.(=); CEP85L:ENST00000419517.2:c.232+5254del:p.(=); CEP85L:ENST00000360290.7:c.-75+5254del:p.(=)

Pathogenicity Data:: Best Score: 0.21602899; CADD: 0.216 (1.057)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118569341CAAAAA>C [1/1] rs56123225 (variation viewer)

Variant score: 0.170

Transcripts:: CEP85L:ENST00000368488.9:c.242-3030_242-3026del:p.(=); CEP85L:ENST00000368491.8:c.233-3030_233-3026del:p.(=); CEP85L:ENST00000392500.7:c.242-3030_242-3026del:p.(=); CEP85L:ENST00000419517.2:c.233-3030_233-3026del:p.(=); CEP85L:ENST00000360290.7:c.-74-3030_-74-3026del:p.(=)

Pathogenicity Data:: Best Score: 0.1703403; CADD: 0.170 (0.811)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118483157C>A [0/1] rs1358399582 (variation viewer)

Variant score: 0.029

Transcripts:: CEP85L:ENST00000368488.9:c.1599+549G>T:p.(=); CEP85L:ENST00000368491.8:c.1590+549G>T:p.(=)

Pathogenicity Data:: Best Score: 0.029043019; CADD: 0.029 (0.128)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118491194T>TAC [0/1] rs375795893 (variation viewer)

Variant score: 0.026

Transcripts:: CEP85L:ENST00000368488.9:c.1446+491_1446+492insGT:p.(=); CEP85L:ENST00000368491.8:c.1437+491_1437+492insGT:p.(=)

Pathogenicity Data:: Best Score: 0.15549934; CADD: 0.155 (0.734)

Frequency Data:: gnomAD_G_AFR: 0.6880%; gnomAD_G_AMR: 0.8333%; gnomAD_G_ASJ: 1.2712%; gnomAD_G_EAS: 1.9667%; gnomAD_G_FIN: 1.5904%; gnomAD_G_NFE: 0.8896%; gnomAD_G_OTH: 0.8663%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.118692765A>AGTTATGTAACTTTGCTGAAACCATTAGGAGAGAGGTTACATCTTTTTCTTT [0/1]

Variant score: 0.000

Transcripts:: CEP85L:ENST00000368488.9:c.-28+17270_-28+17271insAAAGAAAAAGATGTAACCTCTCTCCTAATGGTTTCAGCAAAGTTACATAAC:p.(=); CEP85L:ENST00000392500.7:c.-139+17270_-139+17271insAAAGAAAAAGATGTAACCTCTCTCCTAATGGTTTCAGCAAAGTTACATAAC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ATP2A2

Exomiser Score: 0.806

Phenotype Score: 1.000

Variant Score: 0.470

Phenotype matches:

Phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases:: OMIM:101900 Acrokeratosis verruciformis - autosomal dominant; OMIM:124200 Darier disease - autosomal dominant; ORPHA:218 Darier disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.806

Phenotype Score: 1.000

Variant Score: 0.470

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.110319223GAA>G [-/1] rs59623372 (variation viewer)

Variant score: 0.470 CONTRIBUTING VARIANT

Transcripts:: ATP2A2:ENST00000308664.10:c.464-3768_464-3767del:p.(=); ATP2A2:ENST00000539276.7:c.464-3768_464-3767del:p.(=)

Pathogenicity Data:: Best Score: 0.4702146; CADD: 0.470 (2.759)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.019

Phenotype Score: 0.500

Variant Score: 0.452

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.110319223GAA>G [-/1] rs59623372 (variation viewer)

Variant score: 0.470 CONTRIBUTING VARIANT

Transcripts:: ATP2A2:ENST00000308664.10:c.464-3768_464-3767del:p.(=); ATP2A2:ENST00000539276.7:c.464-3768_464-3767del:p.(=)

Pathogenicity Data:: Best Score: 0.4702146; CADD: 0.470 (2.759)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr12:g.110355618C>CA [0/1] rs1027881861 (variation viewer)

Variant score: 0.434 CONTRIBUTING VARIANT

Transcripts:: ATP2A2:ENST00000539276.7::; ATP2A2:ENST00000455511.7::

Pathogenicity Data:: Best Score: 0.44165838; CADD: 0.442 (2.531)

Frequency Data:: TOPMed: 0.0207%; gnomAD_G_AMR: 0.1202%; gnomAD_G_NFE: 0.0068%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.110288101C>CT [1/1] rs71083111 (variation viewer)

Variant score: 0.240

Transcripts:: ATP2A2:ENST00000308664.10:c.220-3919_220-3918insT:p.(=); ATP2A2:ENST00000539276.7:c.220-3919_220-3918insT:p.(=); ATP2A2:ENST00000552636.1:c.-82-3919_-82-3918insT:p.(=)

Pathogenicity Data:: Best Score: 0.24037367; CADD: 0.240 (1.194)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.110293824ATATGTG>A [1|1] rs1371975078 (variation viewer)

Variant score: 0.153

Transcripts:: ATP2A2:ENST00000308664.10:c.324+1701_324+1706del:p.(=); ATP2A2:ENST00000539276.7:c.324+1701_324+1706del:p.(=); ATP2A2:ENST00000552636.1:c.23+1701_23+1706del:p.(=)

Pathogenicity Data:: Best Score: 0.15879858; CADD: 0.159 (0.751)

Frequency Data:: gnomAD_G_AFR: 0.0773%; gnomAD_G_FIN: 0.0358%; gnomAD_G_NFE: 0.2354%; gnomAD_G_OTH: 0.1144%

TLE3

Exomiser Score: 0.761

Phenotype Score: 0.514

Variant Score: 0.991

Phenotype matches:

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.761

Phenotype Score: 0.514

Variant Score: 0.991

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.70092190G>A [0/1]

Variant score: 0.991 CONTRIBUTING VARIANT

Transcripts:: TLE3:ENST00000317509.12:c.234+2342C>T:p.(=); TLE3:ENST00000440567.7:c.213+2342C>T:p.(=); TLE3:ENST00000451782.6:c.234+2342C>T:p.(=); TLE3:ENST00000539550.6:c.36+2342C>T:p.(=); TLE3:ENST00000557907.5:c.234+2342C>T:p.(=); TLE3:ENST00000557997.5:c.234+2342C>T:p.(=); TLE3:ENST00000558201.5:c.252+2342C>T:p.(=); TLE3:ENST00000558379.5:c.234+2342C>T:p.(=); TLE3:ENST00000558939.5:c.234+2342C>T:p.(=); TLE3:ENST00000559048.5:c.252+2342C>T:p.(=); TLE3:ENST00000559929.5:c.234+2342C>T:p.(=); TLE3:ENST00000560589.5:c.66+2342C>T:p.(=); TLE3:ENST00000560939.5:c.252+2342C>T:p.(=); TLE3:ENST00000627388.2:c.234+2342C>T:p.(=); TLE3:ENST00000559191.5:c.-44+5468C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9910875; CADD: 0.991 (20.500)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.110

Phenotype Score: 0.514

Variant Score: 0.638

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.70092190G>A [0/1]

Variant score: 0.991 CONTRIBUTING VARIANT

Transcripts:: TLE3:ENST00000317509.12:c.234+2342C>T:p.(=); TLE3:ENST00000440567.7:c.213+2342C>T:p.(=); TLE3:ENST00000451782.6:c.234+2342C>T:p.(=); TLE3:ENST00000539550.6:c.36+2342C>T:p.(=); TLE3:ENST00000557907.5:c.234+2342C>T:p.(=); TLE3:ENST00000557997.5:c.234+2342C>T:p.(=); TLE3:ENST00000558201.5:c.252+2342C>T:p.(=); TLE3:ENST00000558379.5:c.234+2342C>T:p.(=); TLE3:ENST00000558939.5:c.234+2342C>T:p.(=); TLE3:ENST00000559048.5:c.252+2342C>T:p.(=); TLE3:ENST00000559929.5:c.234+2342C>T:p.(=); TLE3:ENST00000560589.5:c.66+2342C>T:p.(=); TLE3:ENST00000560939.5:c.252+2342C>T:p.(=); TLE3:ENST00000627388.2:c.234+2342C>T:p.(=); TLE3:ENST00000559191.5:c.-44+5468C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9910875; CADD: 0.991 (20.500)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.70069233G>T [0/1] rs533179079 (variation viewer)

Variant score: 0.285 CONTRIBUTING VARIANT

Transcripts:: TLE3:ENST00000317509.12:c.373-3015C>A:p.(=); TLE3:ENST00000440567.7:c.352-3015C>A:p.(=); TLE3:ENST00000451782.6:c.373-3015C>A:p.(=); TLE3:ENST00000539550.6:c.205-3015C>A:p.(=); TLE3:ENST00000557907.5:c.373-3015C>A:p.(=); TLE3:ENST00000557997.5:c.373-3015C>A:p.(=); TLE3:ENST00000558201.5:c.391-3015C>A:p.(=); TLE3:ENST00000558379.5:c.373-3015C>A:p.(=); TLE3:ENST00000558939.5:c.373-3015C>A:p.(=); TLE3:ENST00000559048.5:c.391-3018C>A:p.(=); TLE3:ENST00000559929.5:c.403-3015C>A:p.(=); TLE3:ENST00000560589.5:c.205-3015C>A:p.(=); TLE3:ENST00000560939.5:c.391-3018C>A:p.(=); TLE3:ENST00000627388.2:c.373-3015C>A:p.(=); TLE3:ENST00000559191.5:c.-43-11714C>A:p.(=)

Pathogenicity Data:: Best Score: 0.2856682; CADD: 0.286 (1.461)

Frequency Data:: TOPMed: 0.0159%; gnomAD_G_NFE: 0.0067%

Other passed variants:

REGULATORY_REGION_VARIANT chr15:g.70142619C>T [0/1] rs548853341 (variation viewer)

Variant score: 0.012

Transcripts:: TLE3:ENST00000558939.5::; TLE3:ENST00000558111.2::

Pathogenicity Data:: Best Score: 0.012584388; CADD: 0.013 (0.055)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0159%; gnomAD_G_AFR: 0.0572%

UGT2B11

Exomiser Score: 0.758

Phenotype Score: 0.504

Variant Score: 1.000

Phenotype matches:

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.758

Phenotype Score: 0.504

Variant Score: 1.000

Variants contributing to score:

FRAMESHIFT_TRUNCATION chr4:g.69214299CTT>C [0/1]

Variant score: 1.000 CONTRIBUTING VARIANT

Transcripts:: UGT2B11:ENST00000446444.2:c.422_423del:p.(Gln141Argfs*5)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.031

Phenotype Score: 0.504

Variant Score: 0.501

Variants contributing to score:

FRAMESHIFT_TRUNCATION chr4:g.69214299CTT>C [0/1]

Variant score: 1.000 CONTRIBUTING VARIANT

Transcripts:: UGT2B11:ENST00000446444.2:c.422_423del:p.(Gln141Argfs*5)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.69208845C>A [0/1] rs556757363 (variation viewer)

Variant score: 0.002 CONTRIBUTING VARIANT

Transcripts:: UGT2B11:ENST00000446444.2:c.871-363G>T:p.(=)

Pathogenicity Data:: Best Score: 0.003906727; CADD: 0.004 (0.017)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.7677%; gnomAD_G_AFR: 0.1983%; gnomAD_G_AMR: 0.1232%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_EAS: 0.0657%; gnomAD_G_FIN: 1.1723%; gnomAD_G_NFE: 1.3557%; gnomAD_G_OTH: 0.9202%

Other passed variants:

EP300

Exomiser Score: 0.757

Phenotype Score: 0.507

Variant Score: 0.996

Phenotype matches:

Phenotypic similarity 0.507 to Rubinstein-Taybi syndrome due to EP300 haploinsufficiency associated with EP300.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000756, Agoraphobia

Known diseases:: OMIM:114500 Colorectal cancer, somatic - autosomal dominant; OMIM:613684 Rubinstein-Taybi syndrome 2 - autosomal dominant; OMIM:618333 Menke-Hennekam syndrome 2 - autosomal dominant; ORPHA:353284 Rubinstein-Taybi syndrome due to EP300 haploinsufficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.757

Phenotype Score: 0.507

Variant Score: 0.996

Variants contributing to score:

MISSENSE_VARIANT chr22:g.41172657C>A [0/1] rs1303397164 (variation viewer)

Variant score: 0.996 CONTRIBUTING VARIANT

Transcripts:: EP300:ENST00000263253.9:c.4611C>A:p.(Ser1537Arg); EP300:ENST00000674155.1:c.4533C>A:p.(Ser1511Arg)

Pathogenicity Data:: Best Score: 0.999; Polyphen2: 0.999 (D); Mutation Taster: 0.994 (P); SIFT: 0.033 (D); CADD: 0.995 (23.200)

Frequency Data:: gnomAD_E_OTH: 0.0184%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.028

Phenotype Score: 0.254

Variant Score: 0.773

Variants contributing to score:

MISSENSE_VARIANT chr22:g.41172657C>A [0/1] rs1303397164 (variation viewer)

Variant score: 0.996 CONTRIBUTING VARIANT

Transcripts:: EP300:ENST00000263253.9:c.4611C>A:p.(Ser1537Arg); EP300:ENST00000674155.1:c.4533C>A:p.(Ser1511Arg)

Pathogenicity Data:: Best Score: 0.999; Polyphen2: 0.999 (D); Mutation Taster: 0.994 (P); SIFT: 0.033 (D); CADD: 0.995 (23.200)

Frequency Data:: gnomAD_E_OTH: 0.0184%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41167602A>G [-/1] rs1428155357 (variation viewer)

Variant score: 0.550 CONTRIBUTING VARIANT

Transcripts:: EP300:ENST00000263253.9:c.3875-847A>G:p.(=); EP300:ENST00000674155.1:c.3797-847A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5930885; CADD: 0.593 (3.905)

Frequency Data:: gnomAD_G_AFR: 0.3119%; gnomAD_G_AMR: 0.4310%; gnomAD_G_NFE: 0.1492%; gnomAD_G_OTH: 0.2618%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41105081C>T [0|1] rs373168662 (variation viewer)

Variant score: 0.283

Transcripts:: EP300:ENST00000263253.9:c.94+11983C>T:p.(=); EP300:ENST00000674155.1:c.94+11983C>T:p.(=)

Pathogenicity Data:: Best Score: 0.50065583; CADD: 0.501 (3.016)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4802%; gnomAD_G_AFR: 0.1382%; gnomAD_G_AMR: 0.6083%; gnomAD_G_ASJ: 1.4388%; gnomAD_G_FIN: 0.0581%; gnomAD_G_NFE: 0.4977%; gnomAD_G_OTH: 0.2105%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41105095G>C [0|1] rs538437271 (variation viewer)

Variant score: 0.258

Transcripts:: EP300:ENST00000263253.9:c.94+11997G>C:p.(=); EP300:ENST00000674155.1:c.94+11997G>C:p.(=)

Pathogenicity Data:: Best Score: 0.43480277; CADD: 0.435 (2.478)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4818%; gnomAD_G_AFR: 0.1271%; gnomAD_G_AMR: 0.6068%; gnomAD_G_ASJ: 1.3889%; gnomAD_G_FIN: 0.0583%; gnomAD_G_NFE: 0.5044%; gnomAD_G_OTH: 0.2088%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41126729C>CT [1/1] rs71328775 (variation viewer)

Variant score: 0.231

Transcripts:: EP300:ENST00000263253.9:c.906+689_906+690insT:p.(=); EP300:ENST00000674155.1:c.906+689_906+690insT:p.(=)

Pathogenicity Data:: Best Score: 0.23069245; CADD: 0.231 (1.139)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41098040G>A [0/1] rs142021682 (variation viewer)

Variant score: 0.221

Transcripts:: EP300:ENST00000263253.9:c.94+4942G>A:p.(=); EP300:ENST00000674155.1:c.94+4942G>A:p.(=)

Pathogenicity Data:: Best Score: 0.51749706; CADD: 0.517 (3.165)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.4778%; UK10K: 0.6480%; gnomAD_G_AFR: 0.1265%; gnomAD_G_AMR: 0.4796%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0587%; gnomAD_G_NFE: 0.5029%; gnomAD_G_OTH: 0.2053%

INTERGENIC_VARIANT chr22:g.41079630C>CAAA [0/1] rs59121693 (variation viewer)

Variant score: 0.171

Transcripts:: EP300:ENST00000263253.9::

Pathogenicity Data:: Best Score: 0.1707223; CADD: 0.171 (0.813)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41102029C>CTTT [0/1] rs5845488 (variation viewer)

Variant score: 0.166

Transcripts:: EP300:ENST00000263253.9:c.94+8931_94+8932insTTT:p.(=); EP300:ENST00000674155.1:c.94+8931_94+8932insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.1659348; CADD: 0.166 (0.788)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41167584GTATATATATATATATA>G [-/1] rs56131556 (variation viewer)

Variant score: 0.160

Transcripts:: EP300:ENST00000263253.9:c.3875-864_3875-849del:p.(=); EP300:ENST00000674155.1:c.3797-864_3797-849del:p.(=)

Pathogenicity Data:: Best Score: 0.15995991; CADD: 0.160 (0.757)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41106990T>C [0/1] rs138022706 (variation viewer)

Variant score: 0.153

Transcripts:: EP300:ENST00000263253.9:c.95-10197T>C:p.(=); EP300:ENST00000674155.1:c.95-10197T>C:p.(=)

Pathogenicity Data:: Best Score: 0.3581996; CADD: 0.358 (1.926)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4874%; UK10K: 0.6876%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.5135%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41134163C>CT [1/1] rs11362436 (variation viewer)

Variant score: 0.119

Transcripts:: EP300:ENST00000263253.9:c.1529-1650_1529-1649insT:p.(=); EP300:ENST00000674155.1:c.1529-1650_1529-1649insT:p.(=)

Pathogenicity Data:: Best Score: 0.118545294; CADD: 0.119 (0.548)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41157512C>CT [0/1] rs1214250106 (variation viewer)

Variant score: 0.114

Transcripts:: EP300:ENST00000263253.9:c.3501+104_3501+105insT:p.(=); EP300:ENST00000674155.1:c.3423+104_3423+105insT:p.(=)

Pathogenicity Data:: Best Score: 0.114068806; CADD: 0.114 (0.526)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41167193T>G [0/1] rs150826248 (variation viewer)

Variant score: 0.106

Transcripts:: EP300:ENST00000263253.9:c.3874+527T>G:p.(=); EP300:ENST00000674155.1:c.3796+527T>G:p.(=)

Pathogenicity Data:: Best Score: 0.24872315; CADD: 0.249 (1.242)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.4866%; UK10K: 0.6215%; gnomAD_G_AFR: 0.1377%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.5134%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41106797A>G [0/1] rs150441760 (variation viewer)

Variant score: 0.052

Transcripts:: EP300:ENST00000263253.9:c.95-10390A>G:p.(=); EP300:ENST00000674155.1:c.95-10390A>G:p.(=)

Pathogenicity Data:: Best Score: 0.052672803; CADD: 0.053 (0.235)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0040%; gnomAD_G_AFR: 0.0115%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41167826G>T [1/1] rs10222217 (variation viewer)

Variant score: 0.049

Transcripts:: EP300:ENST00000263253.9:c.3875-623G>T:p.(=); EP300:ENST00000674155.1:c.3797-623G>T:p.(=)

Pathogenicity Data:: Best Score: 0.049395204; CADD: 0.049 (0.220)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41105201A>* [-/1]

Variant score: 0.000

Transcripts:: EP300:ENST00000263253.9:c.95-11986A>*:p.(=); EP300:ENST00000674155.1:c.95-11986A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41167584GTATATATATATATATATA>* [-/1]

Variant score: 0.000

Transcripts:: EP300:ENST00000263253.9:c.3875-865_3875-847delGTATATATATATATATATAins*:p.(=); EP300:ENST00000674155.1:c.3797-865_3797-847delGTATATATATATATATATAins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41167602A>* [-/1]

Variant score: 0.000

Transcripts:: EP300:ENST00000263253.9:c.3875-847A>*:p.(=); EP300:ENST00000674155.1:c.3797-847A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NME6

Exomiser Score: 0.755

Phenotype Score: 0.504

Variant Score: 0.999

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.755

Phenotype Score: 0.504

Variant Score: 0.999

Variants contributing to score:

MISSENSE_VARIANT chr3:g.48295128G>C [0/1] rs1213911330 (variation viewer)

Variant score: 0.999 CONTRIBUTING VARIANT

Transcripts:: NME6:ENST00000415053.5:c.341C>G:p.(Ser114Cys); NME6:ENST00000421967.5:c.365C>G:p.(Ser122Cys); NME6:ENST00000426689.6:c.341C>G:p.(Ser114Cys); NME6:ENST00000435684.5:c.301C>G:p.(Leu101Val); NME6:ENST00000442597.5:c.341C>G:p.(Ser114Cys); NME6:ENST00000444069.5:c.47C>G:p.(Ser16Cys); NME6:ENST00000447314.5:c.206C>G:p.(Ser69Cys); NME6:ENST00000451657.6:c.301C>G:p.(Leu101Val); NME6:ENST00000452211.5:c.341C>G:p.(Ser114Cys); NME6:ENST00000642710.1:c.47C>G:p.(Ser16Cys); NME6:ENST00000643011.1:c.125C>G:p.(Ser42Cys); NME6:ENST00000643457.1:c.341C>G:p.(Ser114Cys); NME6:ENST00000412564.5:c.224-3827G>C:p.(=); NME6:ENST00000415644.5:c.194-325C>G:p.(=)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.946 (P); Mutation Taster: 1.000 (P); SIFT: 0.164 (T); CADD: 0.996 (24.200)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.615

Phenotype Score: 0.504

Variant Score: 0.928

Variants contributing to score:

MISSENSE_VARIANT chr3:g.48295128G>C [0/1] rs1213911330 (variation viewer)

Variant score: 0.999 CONTRIBUTING VARIANT

Transcripts:: NME6:ENST00000415053.5:c.341C>G:p.(Ser114Cys); NME6:ENST00000421967.5:c.365C>G:p.(Ser122Cys); NME6:ENST00000426689.6:c.341C>G:p.(Ser114Cys); NME6:ENST00000435684.5:c.301C>G:p.(Leu101Val); NME6:ENST00000442597.5:c.341C>G:p.(Ser114Cys); NME6:ENST00000444069.5:c.47C>G:p.(Ser16Cys); NME6:ENST00000447314.5:c.206C>G:p.(Ser69Cys); NME6:ENST00000451657.6:c.301C>G:p.(Leu101Val); NME6:ENST00000452211.5:c.341C>G:p.(Ser114Cys); NME6:ENST00000642710.1:c.47C>G:p.(Ser16Cys); NME6:ENST00000643011.1:c.125C>G:p.(Ser42Cys); NME6:ENST00000643457.1:c.341C>G:p.(Ser114Cys); NME6:ENST00000412564.5:c.224-3827G>C:p.(=); NME6:ENST00000415644.5:c.194-325C>G:p.(=)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.946 (P); Mutation Taster: 1.000 (P); SIFT: 0.164 (T); CADD: 0.996 (24.200)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48298115T>G [0/1] rs886766536 (variation viewer)

Variant score: 0.856 CONTRIBUTING VARIANT

Transcripts:: NME6:ENST00000415053.5:c.90+312A>C:p.(=)

Pathogenicity Data:: Best Score: 0.8571435; CADD: 0.857 (8.451)

Frequency Data:: TOPMed: 0.0080%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48299841T>C [0/1] rs115292135 (variation viewer)

Variant score: 0.244

Transcripts:: NME6:ENST00000421967.5:c.18-1318A>G:p.(=); NME6:ENST00000643011.1:c.17+1455A>G:p.(=); NME6:ENST00000415053.5:c.-8+686A>G:p.(=); NME6:ENST00000415644.5:c.-7-1318A>G:p.(=); NME6:ENST00000435684.5:c.-7-1318A>G:p.(=); NME6:ENST00000442597.5:c.-7-1318A>G:p.(=); NME6:ENST00000444069.5:c.-62+1438A>G:p.(=); NME6:ENST00000447314.5:c.-46+1512A>G:p.(=); NME6:ENST00000451657.6:c.-7-1318A>G:p.(=); NME6:ENST00000452211.5:c.-8+590A>G:p.(=); NME6:ENST00000642710.1:c.-62+1512A>G:p.(=); NME6:ENST00000643457.1:c.-7-1318A>G:p.(=)

Pathogenicity Data:: Best Score: 0.38482314; CADD: 0.385 (2.110)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.6825%; UK10K: 1.3092%; gnomAD_G_AFR: 0.2407%; gnomAD_G_AMR: 0.9547%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.9128%; gnomAD_G_OTH: 0.4082%

THREE_PRIME_UTR_EXON_VARIANT chr3:g.48291546GTTT>G [0/1] rs560012208 (variation viewer)

Variant score: 0.174

Transcripts:: NME6:ENST00000451657.6:c.*3117_*3119del:p.(=)

Pathogenicity Data:: Best Score: 0.21222901; CADD: 0.212 (1.036)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.6220%; gnomAD_G_AFR: 0.2302%; gnomAD_G_AMR: 0.8413%; gnomAD_G_FIN: 0.1148%; gnomAD_G_NFE: 0.7987%; gnomAD_G_OTH: 0.3099%

NKX2-6

Exomiser Score: 0.754

Phenotype Score: 0.514

Variant Score: 0.987

Phenotype matches:

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases:: OMIM:217095 Persistent truncus arteriosus - autosomal recessive; ORPHA:3303 Tetralogy of Fallot

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.754

Phenotype Score: 0.514

Variant Score: 0.987

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr8:g.23698899T>A [0/1]

Variant score: 0.987 CONTRIBUTING VARIANT

Transcripts:: NKX2-6:ENST00000325017.3::; NKX2-6:ENST00000380871.5::

Pathogenicity Data:: Best Score: 0.98705804; CADD: 0.987 (18.880)

Frequency Data:: No frequency data

Other passed variants:

ASAH2

Exomiser Score: 0.753

Phenotype Score: 0.505

Variant Score: 0.997

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.753

Phenotype Score: 0.505

Variant Score: 0.997

Variants contributing to score:

MISSENSE_VARIANT chr10:g.50189586G>T [0/1] rs1279780267 (variation viewer)

Variant score: 0.997 CONTRIBUTING VARIANT

Transcripts:: ASAH2:ENST00000329428.10:c.1904C>A:p.(Thr635Asn); ASAH2:ENST00000395526.9:c.2066C>A:p.(Thr689Asn); ASAH2:ENST00000443575.5:c.1592C>A:p.(Thr531Asn); ASAH2:ENST00000447815.5:c.1961C>A:p.(Thr654Asn); ASAH2:ENST00000656090.1:c.2066C>A:p.(Thr689Asn)

Pathogenicity Data:: Best Score: 0.996965; Polyphen2: 0.787 (P); Mutation Taster: 0.997 (P); SIFT: 0.007 (D); CADD: 0.996 (23.700)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.734

Phenotype Score: 0.505

Variant Score: 0.986

Variants contributing to score:

MISSENSE_VARIANT chr10:g.50189586G>T [0/1] rs1279780267 (variation viewer)

Variant score: 0.997 CONTRIBUTING VARIANT

Transcripts:: ASAH2:ENST00000329428.10:c.1904C>A:p.(Thr635Asn); ASAH2:ENST00000395526.9:c.2066C>A:p.(Thr689Asn); ASAH2:ENST00000443575.5:c.1592C>A:p.(Thr531Asn); ASAH2:ENST00000447815.5:c.1961C>A:p.(Thr654Asn); ASAH2:ENST00000656090.1:c.2066C>A:p.(Thr689Asn)

Pathogenicity Data:: Best Score: 0.996965; Polyphen2: 0.787 (P); Mutation Taster: 0.997 (P); SIFT: 0.007 (D); CADD: 0.996 (23.700)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50189387T>C [0/1] rs1199399098 (variation viewer)

Variant score: 0.975 CONTRIBUTING VARIANT

Transcripts:: ASAH2:ENST00000329428.10:c.1991+112A>G:p.(=); ASAH2:ENST00000395526.9:c.2153+112A>G:p.(=); ASAH2:ENST00000443575.5:c.1679+112A>G:p.(=); ASAH2:ENST00000447815.5:c.2048+112A>G:p.(=); ASAH2:ENST00000656090.1:c.2153+112A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9752828; CADD: 0.975 (16.070)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50197370T>C [0/1] rs71203959 (variation viewer)

Variant score: 0.948

Transcripts:: ASAH2:ENST00000329428.10:c.1696-451A>G:p.(=); ASAH2:ENST00000395526.9:c.1858-451A>G:p.(=); ASAH2:ENST00000443575.5:c.1384-451A>G:p.(=); ASAH2:ENST00000447815.5:c.1753-451A>G:p.(=); ASAH2:ENST00000656090.1:c.1858-451A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9478805; CADD: 0.948 (12.830)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50191260T>C [1/1] rs1437638588 (variation viewer)

Variant score: 0.933

Transcripts:: ASAH2:ENST00000329428.10:c.1902+1393A>G:p.(=); ASAH2:ENST00000395526.9:c.2064+1393A>G:p.(=); ASAH2:ENST00000443575.5:c.1590+1393A>G:p.(=); ASAH2:ENST00000447815.5:c.1959+1393A>G:p.(=); ASAH2:ENST00000656090.1:c.2064+1393A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9325472; CADD: 0.933 (11.710)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50189460G>A [0/1] rs1273378765 (variation viewer)

Variant score: 0.891

Transcripts:: ASAH2:ENST00000329428.10:c.1991+39C>T:p.(=); ASAH2:ENST00000395526.9:c.2153+39C>T:p.(=); ASAH2:ENST00000443575.5:c.1679+39C>T:p.(=); ASAH2:ENST00000447815.5:c.2048+39C>T:p.(=); ASAH2:ENST00000656090.1:c.2153+39C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8912824; CADD: 0.891 (9.637)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50180793A>G [1/1] rs1192529498 (variation viewer)

Variant score: 0.876

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.8756058; CADD: 0.876 (9.052)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50190959G>A [0/1] rs11527284 (variation viewer)

Variant score: 0.857

Transcripts:: ASAH2:ENST00000329428.10:c.1903-1372C>T:p.(=); ASAH2:ENST00000395526.9:c.2065-1372C>T:p.(=); ASAH2:ENST00000443575.5:c.1591-1372C>T:p.(=); ASAH2:ENST00000447815.5:c.1960-1372C>T:p.(=); ASAH2:ENST00000656090.1:c.2065-1372C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8570777; CADD: 0.857 (8.449)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50180820T>G [1|1] rs1347670265 (variation viewer)

Variant score: 0.837

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.83677; CADD: 0.837 (7.872)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50180819T>A [1|1] rs1301351985 (variation viewer)

Variant score: 0.832

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.8316938; CADD: 0.832 (7.739)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50182482A>T [0/1] rs2813185 (variation viewer)

Variant score: 0.829

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.82915586; CADD: 0.829 (7.674)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50192749C>A [1|1] rs3867224 (variation viewer)

Variant score: 0.828

Transcripts:: ASAH2:ENST00000329428.10:c.1843-37G>T:p.(=); ASAH2:ENST00000395526.9:c.2005-37G>T:p.(=); ASAH2:ENST00000443575.5:c.1531-37G>T:p.(=); ASAH2:ENST00000447815.5:c.1900-37G>T:p.(=); ASAH2:ENST00000656090.1:c.2005-37G>T:p.(=)

Pathogenicity Data:: Best Score: 0.8283278; CADD: 0.828 (7.653)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50196216A>T [0/1] rs35255958 (variation viewer)

Variant score: 0.757

Transcripts:: ASAH2:ENST00000329428.10:c.1842+557T>A:p.(=); ASAH2:ENST00000395526.9:c.2004+557T>A:p.(=); ASAH2:ENST00000443575.5:c.1530+557T>A:p.(=); ASAH2:ENST00000447815.5:c.1899+557T>A:p.(=); ASAH2:ENST00000656090.1:c.2004+557T>A:p.(=)

Pathogenicity Data:: Best Score: 0.7571713; CADD: 0.757 (6.147)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50179893T>C [1/1] rs11004404 (variation viewer)

Variant score: 0.747

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.7543029; CADD: 0.754 (6.096)

Frequency Data:: gnomAD_G_AFR: 0.0707%

DOWNSTREAM_GENE_VARIANT chr10:g.50179993T>C [1|1] rs1364367779 (variation viewer)

Variant score: 0.711

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.7180968; CADD: 0.718 (5.499)

Frequency Data:: gnomAD_G_NFE: 0.0711%

DOWNSTREAM_GENE_VARIANT chr10:g.50180342T>G [1/1] rs189839166 (variation viewer)

Variant score: 0.682

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.6818734; CADD: 0.682 (4.974)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50179996C>G [1|1] rs566824612 (variation viewer)

Variant score: 0.667

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.66711056; CADD: 0.667 (4.777)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50180822G>A [1|1] rs1271366104 (variation viewer)

Variant score: 0.666

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.6660358; CADD: 0.666 (4.763)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50179847G>T [1|1] rs11004403 (variation viewer)

Variant score: 0.624

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.62381625; CADD: 0.624 (4.246)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50235783G>A [0|1]

Variant score: 0.596

Transcripts:: ASAH2:ENST00000329428.10:c.630+105C>T:p.(=); ASAH2:ENST00000395526.9:c.687+105C>T:p.(=); ASAH2:ENST00000443575.5:c.213+105C>T:p.(=); ASAH2:ENST00000447815.5:c.687+105C>T:p.(=); ASAH2:ENST00000656090.1:c.687+105C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5959827; CADD: 0.596 (3.936)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50187118TCACACACA>T [-/1] rs1171385681 (variation viewer)

Variant score: 0.586

Transcripts:: ASAH2:ENST00000395526.9:c.*189_*196del:p.(=)

Pathogenicity Data:: Best Score: 0.58609563; CADD: 0.586 (3.831)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50235784C>A [0|1]

Variant score: 0.570

Transcripts:: ASAH2:ENST00000329428.10:c.630+104G>T:p.(=); ASAH2:ENST00000395526.9:c.687+104G>T:p.(=); ASAH2:ENST00000443575.5:c.213+104G>T:p.(=); ASAH2:ENST00000447815.5:c.687+104G>T:p.(=); ASAH2:ENST00000656090.1:c.687+104G>T:p.(=)

Pathogenicity Data:: Best Score: 0.57026577; CADD: 0.570 (3.668)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50203577AGG>A [0|1] rs1488626150 (variation viewer)

Variant score: 0.549

Transcripts:: ASAH2:ENST00000329428.10:c.1503+61_1503+62del:p.(=); ASAH2:ENST00000395526.9:c.1665+61_1665+62del:p.(=); ASAH2:ENST00000443575.5:c.1191+61_1191+62del:p.(=); ASAH2:ENST00000447815.5:c.1560+61_1560+62del:p.(=); ASAH2:ENST00000656090.1:c.1665+61_1665+62del:p.(=)

Pathogenicity Data:: Best Score: 0.54939085; CADD: 0.549 (3.462)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181292G>A [1|1] rs1272581090 (variation viewer)

Variant score: 0.517

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.51727474; CADD: 0.517 (3.163)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50183230T>C [1/1] rs57545547 (variation viewer)

Variant score: 0.503

Transcripts:: ASAH2:ENST00000395526.9:c.*4085A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5029501; CADD: 0.503 (3.036)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181178G>A [1/1] rs1227319887 (variation viewer)

Variant score: 0.499

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.49869734; CADD: 0.499 (2.999)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50190807G>A [0/1] rs10909590 (variation viewer)

Variant score: 0.496

Transcripts:: ASAH2:ENST00000329428.10:c.1903-1220C>T:p.(=); ASAH2:ENST00000395526.9:c.2065-1220C>T:p.(=); ASAH2:ENST00000443575.5:c.1591-1220C>T:p.(=); ASAH2:ENST00000447815.5:c.1960-1220C>T:p.(=); ASAH2:ENST00000656090.1:c.2065-1220C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4956872; CADD: 0.496 (2.973)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50180052A>T [1/1] rs11004405 (variation viewer)

Variant score: 0.486

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.48560113; CADD: 0.486 (2.887)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50184127TAAG>T [1/1] rs1284997521 (variation viewer)

Variant score: 0.475

Transcripts:: ASAH2:ENST00000395526.9:c.*3185_*3187del:p.(=)

Pathogenicity Data:: Best Score: 0.4749508; CADD: 0.475 (2.798)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50182577T>C [1/1] rs74879970 (variation viewer)

Variant score: 0.453

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.45260602; CADD: 0.453 (2.617)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181462C>T [1|1] rs1228149573 (variation viewer)

Variant score: 0.447

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.44677728; CADD: 0.447 (2.571)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50198991TACACAC>T [0|1] rs1264348423 (variation viewer)

Variant score: 0.446

Transcripts:: ASAH2:ENST00000329428.10:c.1695+54_1695+59del:p.(=); ASAH2:ENST00000395526.9:c.1857+54_1857+59del:p.(=); ASAH2:ENST00000443575.5:c.1383+54_1383+59del:p.(=); ASAH2:ENST00000447815.5:c.1752+54_1752+59del:p.(=); ASAH2:ENST00000656090.1:c.1857+54_1857+59del:p.(=)

Pathogenicity Data:: Best Score: 0.44614; CADD: 0.446 (2.566)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181379T>G [1/1] rs1179011364 (variation viewer)

Variant score: 0.437

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.43869358; CADD: 0.439 (2.508)

Frequency Data:: gnomAD_G_NFE: 0.0354%

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50187118TCACACA>T [-/1] rs1171385681 (variation viewer)

Variant score: 0.435

Transcripts:: ASAH2:ENST00000395526.9:c.*191_*196del:p.(=)

Pathogenicity Data:: Best Score: 0.43519306; CADD: 0.435 (2.481)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181167A>G [1/1] rs1340271038 (variation viewer)

Variant score: 0.417

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.41668922; CADD: 0.417 (2.341)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50192738T>C [1/1] rs1332962816 (variation viewer)

Variant score: 0.384

Transcripts:: ASAH2:ENST00000329428.10:c.1843-26A>G:p.(=); ASAH2:ENST00000395526.9:c.2005-26A>G:p.(=); ASAH2:ENST00000443575.5:c.1531-26A>G:p.(=); ASAH2:ENST00000447815.5:c.1900-26A>G:p.(=); ASAH2:ENST00000656090.1:c.2005-26A>G:p.(=)

Pathogenicity Data:: Best Score: 0.38411444; CADD: 0.384 (2.105)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181644T>G [1/1] rs201545652 (variation viewer)

Variant score: 0.378

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.43921036; CADD: 0.439 (2.512)

Frequency Data:: gnomAD_G_AFR: 0.0481%; gnomAD_G_EAS: 0.2203%; gnomAD_G_FIN: 0.7042%; gnomAD_G_NFE: 0.0395%

DOWNSTREAM_GENE_VARIANT chr10:g.50181449C>T [1/1] rs374635317 (variation viewer)

Variant score: 0.366

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.3674425; CADD: 0.367 (1.989)

Frequency Data:: gnomAD_G_NFE: 0.0360%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50254176C>CA [0/1] rs981796928 (variation viewer)

Variant score: 0.364

Transcripts:: ASAH2:ENST00000395526.9:c.-153-2666_-153-2665insT:p.(=)

Pathogenicity Data:: Best Score: 0.3795597; CADD: 0.380 (2.073)

Frequency Data:: gnomAD_G_AFR: 0.0998%; gnomAD_G_AMR: 0.1437%; gnomAD_G_EAS: 0.0638%; gnomAD_G_NFE: 0.1595%; gnomAD_G_OTH: 0.2646%

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50185645A>G [0|1] rs796311126 (variation viewer)

Variant score: 0.357

Transcripts:: ASAH2:ENST00000395526.9:c.*1670T>C:p.(=)

Pathogenicity Data:: Best Score: 0.3568682; CADD: 0.357 (1.917)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50179822G>T [1|1] rs1345808761 (variation viewer)

Variant score: 0.337

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.336868; CADD: 0.337 (1.784)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50207633TA>T [0/1] rs34303021 (variation viewer)

Variant score: 0.322

Transcripts:: ASAH2:ENST00000329428.10:c.1253-1537del:p.(=); ASAH2:ENST00000395526.9:c.1415-1537del:p.(=); ASAH2:ENST00000443575.5:c.941-1537del:p.(=); ASAH2:ENST00000447815.5:c.1310-1537del:p.(=); ASAH2:ENST00000656090.1:c.1415-1537del:p.(=)

Pathogenicity Data:: Best Score: 0.32220244; CADD: 0.322 (1.689)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50190756G>A [0/1] rs10909586 (variation viewer)

Variant score: 0.318

Transcripts:: ASAH2:ENST00000329428.10:c.1903-1169C>T:p.(=); ASAH2:ENST00000395526.9:c.2065-1169C>T:p.(=); ASAH2:ENST00000443575.5:c.1591-1169C>T:p.(=); ASAH2:ENST00000447815.5:c.1960-1169C>T:p.(=); ASAH2:ENST00000656090.1:c.2065-1169C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3176613; CADD: 0.318 (1.660)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181332G>A [1/1] rs1171330872 (variation viewer)

Variant score: 0.295

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.29579353; CADD: 0.296 (1.523)

Frequency Data:: gnomAD_G_AFR: 0.0222%

DOWNSTREAM_GENE_VARIANT chr10:g.50181463A>G [1|1] rs1377400095 (variation viewer)

Variant score: 0.282

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.28154427; CADD: 0.282 (1.436)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50209445T>G [0|1] rs2842101 (variation viewer)

Variant score: 0.277

Transcripts:: ASAH2:ENST00000329428.10:c.1252+1378A>C:p.(=); ASAH2:ENST00000395526.9:c.1414+1378A>C:p.(=); ASAH2:ENST00000443575.5:c.940+1378A>C:p.(=); ASAH2:ENST00000447815.5:c.1309+1378A>C:p.(=); ASAH2:ENST00000656090.1:c.1414+1378A>C:p.(=)

Pathogenicity Data:: Best Score: 0.30015802; CADD: 0.300 (1.550)

Frequency Data:: gnomAD_G_AFR: 0.3156%; gnomAD_G_OTH: 0.4464%

DOWNSTREAM_GENE_VARIANT chr10:g.50180163C>T [1/1] rs1443823932 (variation viewer)

Variant score: 0.267

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.26650017; CADD: 0.267 (1.346)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50221627T>TTG [0/1] rs1364076496 (variation viewer)

Variant score: 0.264

Transcripts:: ASAH2:ENST00000329428.10:c.837-2998_837-2997insCA:p.(=); ASAH2:ENST00000395526.9:c.894-2998_894-2997insCA:p.(=); ASAH2:ENST00000443575.5:c.420-2998_420-2997insCA:p.(=); ASAH2:ENST00000447815.5:c.894-2998_894-2997insCA:p.(=); ASAH2:ENST00000656090.1:c.894-2998_894-2997insCA:p.(=)

Pathogenicity Data:: Best Score: 0.26430124; CADD: 0.264 (1.333)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50203581T>TCCTATGGTGAAGAGGG [0|1] rs1224226418 (variation viewer)

Variant score: 0.250

Transcripts:: ASAH2:ENST00000329428.10:c.1503+58_1503+59insCCCTCTTCACCATAGG:p.(=); ASAH2:ENST00000395526.9:c.1665+58_1665+59insCCCTCTTCACCATAGG:p.(=); ASAH2:ENST00000443575.5:c.1191+58_1191+59insCCCTCTTCACCATAGG:p.(=); ASAH2:ENST00000447815.5:c.1560+58_1560+59insCCCTCTTCACCATAGG:p.(=); ASAH2:ENST00000656090.1:c.1665+58_1665+59insCCCTCTTCACCATAGG:p.(=)

Pathogenicity Data:: Best Score: 0.2495876; CADD: 0.250 (1.247)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50185960G>C [0/1] rs1244999095 (variation viewer)

Variant score: 0.243

Transcripts:: ASAH2:ENST00000395526.9:c.*1355C>G:p.(=)

Pathogenicity Data:: Best Score: 0.25062364; CADD: 0.251 (1.253)

Frequency Data:: gnomAD_G_FIN: 0.1949%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50239828ATTT>A [0/1] rs1208518684 (variation viewer)

Variant score: 0.217

Transcripts:: ASAH2:ENST00000329428.10:c.453+3371_453+3373del:p.(=); ASAH2:ENST00000395526.9:c.510+3371_510+3373del:p.(=); ASAH2:ENST00000443575.5:c.36+681_36+683del:p.(=); ASAH2:ENST00000447815.5:c.510+3371_510+3373del:p.(=); ASAH2:ENST00000656090.1:c.510+3371_510+3373del:p.(=)

Pathogenicity Data:: Best Score: 0.21657032; CADD: 0.217 (1.060)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50217229C>CT [0/1] rs878958733 (variation viewer)

Variant score: 0.199

Transcripts:: ASAH2:ENST00000329428.10:c.957+1280_957+1281insA:p.(=); ASAH2:ENST00000395526.9:c.1014+1280_1014+1281insA:p.(=); ASAH2:ENST00000443575.5:c.540+1280_540+1281insA:p.(=); ASAH2:ENST00000447815.5:c.1014+1280_1014+1281insA:p.(=); ASAH2:ENST00000656090.1:c.1014+1280_1014+1281insA:p.(=)

Pathogenicity Data:: Best Score: 0.19869107; CADD: 0.199 (0.962)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50192751GT>G [1|1] rs1308764689 (variation viewer)

Variant score: 0.194

Transcripts:: ASAH2:ENST00000329428.10:c.1843-40del:p.(=); ASAH2:ENST00000395526.9:c.2005-40del:p.(=); ASAH2:ENST00000443575.5:c.1531-40del:p.(=); ASAH2:ENST00000447815.5:c.1900-40del:p.(=); ASAH2:ENST00000656090.1:c.2005-40del:p.(=)

Pathogenicity Data:: Best Score: 0.19387943; CADD: 0.194 (0.936)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181813C>A [1/1] rs2813188 (variation viewer)

Variant score: 0.188

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.18829167; CADD: 0.188 (0.906)

Frequency Data:: gnomAD_G_AFR: 0.0225%

DOWNSTREAM_GENE_VARIANT chr10:g.50182715T>G [1/1] rs1398704 (variation viewer)

Variant score: 0.180

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.18021494; CADD: 0.180 (0.863)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181072A>G [1/1] rs1387176303 (variation viewer)

Variant score: 0.177

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.17718917; CADD: 0.177 (0.847)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50227349T>TA [1|1] rs1321747642 (variation viewer)

Variant score: 0.143

Transcripts:: ASAH2:ENST00000329428.10:c.836+5834_836+5835insT:p.(=); ASAH2:ENST00000395526.9:c.893+5834_893+5835insT:p.(=); ASAH2:ENST00000443575.5:c.419+5834_419+5835insT:p.(=); ASAH2:ENST00000447815.5:c.893+5834_893+5835insT:p.(=); ASAH2:ENST00000656090.1:c.893+5834_893+5835insT:p.(=)

Pathogenicity Data:: Best Score: 0.14315951; CADD: 0.143 (0.671)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50178080G>A [0/1] rs1215082096 (variation viewer)

Variant score: 0.128

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.12923694; CADD: 0.129 (0.601)

Frequency Data:: TOPMed: 0.0932%; gnomAD_G_NFE: 0.0602%

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50186039G>A [0/1]

Variant score: 0.123

Transcripts:: ASAH2:ENST00000395526.9:c.*1276C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12299919; CADD: 0.123 (0.570)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.50181290C>T [1|1] rs1417417379 (variation viewer)

Variant score: 0.115

Transcripts:: ASAH2:ENST00000395526.9::; ASAH2:ENST00000426317.1::

Pathogenicity Data:: Best Score: 0.11549562; CADD: 0.115 (0.533)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50220497GCT>G [1|1] rs1296542532 (variation viewer)

Variant score: 0.113

Transcripts:: ASAH2:ENST00000329428.10:c.837-1869_837-1868del:p.(=); ASAH2:ENST00000395526.9:c.894-1869_894-1868del:p.(=); ASAH2:ENST00000443575.5:c.420-1869_420-1868del:p.(=); ASAH2:ENST00000447815.5:c.894-1869_894-1868del:p.(=); ASAH2:ENST00000656090.1:c.894-1869_894-1868del:p.(=)

Pathogenicity Data:: Best Score: 0.11345661; CADD: 0.113 (0.523)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50212464C>A [1/1] rs796402125 (variation viewer)

Variant score: 0.108

Transcripts:: ASAH2:ENST00000329428.10:c.1170+508G>T:p.(=); ASAH2:ENST00000395526.9:c.1227+508G>T:p.(=); ASAH2:ENST00000443575.5:c.753+508G>T:p.(=); ASAH2:ENST00000447815.5:c.1227+508G>T:p.(=); ASAH2:ENST00000656090.1:c.1227+508G>T:p.(=)

Pathogenicity Data:: Best Score: 0.107516885; CADD: 0.108 (0.494)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50227341T>TGG [1|1] rs1226507226 (variation viewer)

Variant score: 0.106

Transcripts:: ASAH2:ENST00000329428.10:c.836+5842_836+5843insCC:p.(=); ASAH2:ENST00000395526.9:c.893+5842_893+5843insCC:p.(=); ASAH2:ENST00000443575.5:c.419+5842_419+5843insCC:p.(=); ASAH2:ENST00000447815.5:c.893+5842_893+5843insCC:p.(=); ASAH2:ENST00000656090.1:c.893+5842_893+5843insCC:p.(=)

Pathogenicity Data:: Best Score: 0.10587138; CADD: 0.106 (0.486)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50227344TG>T [1|1] rs1311451222 (variation viewer)

Variant score: 0.101

Transcripts:: ASAH2:ENST00000329428.10:c.836+5839del:p.(=); ASAH2:ENST00000395526.9:c.893+5839del:p.(=); ASAH2:ENST00000443575.5:c.419+5839del:p.(=); ASAH2:ENST00000447815.5:c.893+5839del:p.(=); ASAH2:ENST00000656090.1:c.893+5839del:p.(=)

Pathogenicity Data:: Best Score: 0.100916564; CADD: 0.101 (0.462)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50220836CAAAA>C [-/1] rs1206033397 (variation viewer)

Variant score: 0.100

Transcripts:: ASAH2:ENST00000329428.10:c.837-2210_837-2207del:p.(=); ASAH2:ENST00000395526.9:c.894-2210_894-2207del:p.(=); ASAH2:ENST00000443575.5:c.420-2210_420-2207del:p.(=); ASAH2:ENST00000447815.5:c.894-2210_894-2207del:p.(=); ASAH2:ENST00000656090.1:c.894-2210_894-2207del:p.(=)

Pathogenicity Data:: Best Score: 0.09967357; CADD: 0.100 (0.456)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50227343T>C [1|1] rs1192968381 (variation viewer)

Variant score: 0.095

Transcripts:: ASAH2:ENST00000329428.10:c.836+5841A>G:p.(=); ASAH2:ENST00000395526.9:c.893+5841A>G:p.(=); ASAH2:ENST00000443575.5:c.419+5841A>G:p.(=); ASAH2:ENST00000447815.5:c.893+5841A>G:p.(=); ASAH2:ENST00000656090.1:c.893+5841A>G:p.(=)

Pathogenicity Data:: Best Score: 0.095309556; CADD: 0.095 (0.435)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50274765A>AAATAATAATAATAATAATAATAAT [-/1] rs10627167 (variation viewer)

Variant score: 0.093

Transcripts:: ASAH2:ENST00000395526.9:c.-154+4817_-154+4818insATTATTATTATTATTATTATTATT:p.(=)

Pathogenicity Data:: Best Score: 0.09322405; CADD: 0.093 (0.425)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50220502ATTTG>A [1|1] rs1399105184 (variation viewer)

Variant score: 0.084

Transcripts:: ASAH2:ENST00000329428.10:c.837-1876_837-1873del:p.(=); ASAH2:ENST00000395526.9:c.894-1876_894-1873del:p.(=); ASAH2:ENST00000443575.5:c.420-1876_420-1873del:p.(=); ASAH2:ENST00000447815.5:c.894-1876_894-1873del:p.(=); ASAH2:ENST00000656090.1:c.894-1876_894-1873del:p.(=)

Pathogenicity Data:: Best Score: 0.08441222; CADD: 0.084 (0.383)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50209442C>T [0|1] rs992902876 (variation viewer)

Variant score: 0.076

Transcripts:: ASAH2:ENST00000329428.10:c.1252+1381G>A:p.(=); ASAH2:ENST00000395526.9:c.1414+1381G>A:p.(=); ASAH2:ENST00000443575.5:c.940+1381G>A:p.(=); ASAH2:ENST00000447815.5:c.1309+1381G>A:p.(=); ASAH2:ENST00000656090.1:c.1414+1381G>A:p.(=)

Pathogenicity Data:: Best Score: 0.07594037; CADD: 0.076 (0.343)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50227340T>A [1|1] rs1167562316 (variation viewer)

Variant score: 0.076

Transcripts:: ASAH2:ENST00000329428.10:c.836+5844A>T:p.(=); ASAH2:ENST00000395526.9:c.893+5844A>T:p.(=); ASAH2:ENST00000443575.5:c.419+5844A>T:p.(=); ASAH2:ENST00000447815.5:c.893+5844A>T:p.(=); ASAH2:ENST00000656090.1:c.893+5844A>T:p.(=)

Pathogenicity Data:: Best Score: 0.07572758; CADD: 0.076 (0.342)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50197154C>T [0/1] rs2669791 (variation viewer)

Variant score: 0.067

Transcripts:: ASAH2:ENST00000329428.10:c.1696-235G>A:p.(=); ASAH2:ENST00000395526.9:c.1858-235G>A:p.(=); ASAH2:ENST00000443575.5:c.1384-235G>A:p.(=); ASAH2:ENST00000447815.5:c.1753-235G>A:p.(=); ASAH2:ENST00000656090.1:c.1858-235G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0667457; CADD: 0.067 (0.300)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50278083C>CAAAAAA [1/1] rs71029305 (variation viewer)

Variant score: 0.053

Transcripts:: ASAH2:ENST00000395526.9:c.-154+1499_-154+1500insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.053326964; CADD: 0.053 (0.238)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr10:g.50183093G>A [1/1] rs58534734 (variation viewer)

Variant score: 0.053

Transcripts:: ASAH2:ENST00000395526.9:c.*4222C>T:p.(=)

Pathogenicity Data:: Best Score: 0.053326964; CADD: 0.053 (0.238)

Frequency Data:: gnomAD_G_AFR: 0.0362%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.50227350G>C [1|1] rs1288847125 (variation viewer)

Variant score: 0.044

Transcripts:: ASAH2:ENST00000329428.10:c.836+5834C>G:p.(=); ASAH2:ENST00000395526.9:c.893+5834C>G:p.(=); ASAH2:ENST00000443575.5:c.419+5834C>G:p.(=); ASAH2:ENST00000447815.5:c.893+5834C>G:p.(=); ASAH2:ENST00000656090.1:c.893+5834C>G:p.(=)

Pathogenicity Data:: Best Score: 0.043687105; CADD: 0.044 (0.194)

Frequency Data:: No frequency data

FAT1

Exomiser Score: 0.750

Phenotype Score: 0.503

Variant Score: 0.997

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.750

Phenotype Score: 0.503

Variant Score: 0.997

Variants contributing to score:

MISSENSE_VARIANT chr4:g.186588714C>T [0/1] rs371451914 (variation viewer)

Variant score: 0.997 CONTRIBUTING VARIANT

Transcripts:: FAT1:ENST00000441802.7:c.13645G>A:p.(Val4549Met); FAT1:ENST00000614102.4:c.13651G>A:p.(Val4551Met)

Pathogenicity Data:: Best Score: 0.999877; Polyphen2: 0.050 (B); Mutation Taster: 1.000 (P); SIFT: 0.307 (T); CADD: 0.978 (16.480)

Frequency Data:: TOPMed: 0.0111%; ESP EA: 0.0118%; ESP All: 0.0078%; ExAC NFE: 0.0015%; gnomAD_E_NFE: 0.0027%; gnomAD_E_OTH: 0.0183%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.095

Phenotype Score: 0.503

Variant Score: 0.632

Variants contributing to score:

MISSENSE_VARIANT chr4:g.186588714C>T [0/1] rs371451914 (variation viewer)

Variant score: 0.997 CONTRIBUTING VARIANT

Transcripts:: FAT1:ENST00000441802.7:c.13645G>A:p.(Val4549Met); FAT1:ENST00000614102.4:c.13651G>A:p.(Val4551Met)

Pathogenicity Data:: Best Score: 0.999877; Polyphen2: 0.050 (B); Mutation Taster: 1.000 (P); SIFT: 0.307 (T); CADD: 0.978 (16.480)

Frequency Data:: TOPMed: 0.0111%; ESP EA: 0.0118%; ESP All: 0.0078%; ExAC NFE: 0.0015%; gnomAD_E_NFE: 0.0027%; gnomAD_E_OTH: 0.0183%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186645366CATATATATATATAT>C [-/1] rs70964973 (variation viewer)

Variant score: 0.266 CONTRIBUTING VARIANT

Transcripts:: FAT1:ENST00000441802.7:c.3581-5597_3581-5584del:p.(=); FAT1:ENST00000614102.4:c.3581-5597_3581-5584del:p.(=)

Pathogenicity Data:: Best Score: 0.26599336; CADD: 0.266 (1.343)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr4:g.186587748T>C [0/1] rs141508758 (variation viewer)

Variant score: 0.253

Transcripts:: FAT1:ENST00000441802.7::; FAT1:ENST00000307161.5::

Pathogenicity Data:: Best Score: 0.37698287; CADD: 0.377 (2.055)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.5790%; UK10K: 1.1637%; gnomAD_G_AFR: 0.1832%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.2307%; gnomAD_G_NFE: 1.0189%; gnomAD_G_OTH: 1.2245%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186697470G>A [0/1] rs1262625983 (variation viewer)

Variant score: 0.100

Transcripts:: FAT1:ENST00000441802.7:c.3265+9093C>T:p.(=); FAT1:ENST00000614102.4:c.3265+9093C>T:p.(=)

Pathogenicity Data:: Best Score: 0.100916564; CADD: 0.101 (0.462)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_AFR: 0.0115%; gnomAD_G_EAS: 0.0617%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186659931C>T [0/1] rs144056917 (variation viewer)

Variant score: 0.044

Transcripts:: FAT1:ENST00000441802.7:c.3580+3368G>A:p.(=); FAT1:ENST00000614102.4:c.3580+3368G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0557217; CADD: 0.056 (0.249)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.2396%; UK10K: 0.9389%; gnomAD_G_AFR: 0.1493%; gnomAD_G_AMR: 0.1202%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.8611%; gnomAD_G_NFE: 0.8299%; gnomAD_G_OTH: 0.7172%

USH2A

Exomiser Score: 0.749

Phenotype Score: 0.512

Variant Score: 0.986

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 2 associated with USH2A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.512 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.512 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:276901 Usher syndrome, type 2A - autosomal recessive; OMIM:613809 Retinitis pigmentosa 39 - autosomal recessive; ORPHA:231178 Usher syndrome type 2; ORPHA:791 Retinitis pigmentosa

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.174

Phenotype Score: 0.256

Variant Score: 0.987

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215940018C>T [0/1]

Variant score: 0.987 CONTRIBUTING VARIANT

Transcripts:: USH2A:ENST00000307340.8:c.7121-5223G>A:p.(=); USH2A:ENST00000674083.1:c.7121-5223G>A:p.(=)

Pathogenicity Data:: Best Score: 0.98705804; CADD: 0.987 (18.880)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.749

Phenotype Score: 0.512

Variant Score: 0.986

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215940018C>T [0/1]

Variant score: 0.987 CONTRIBUTING VARIANT

Transcripts:: USH2A:ENST00000307340.8:c.7121-5223G>A:p.(=); USH2A:ENST00000674083.1:c.7121-5223G>A:p.(=)

Pathogenicity Data:: Best Score: 0.98705804; CADD: 0.987 (18.880)

Frequency Data:: No frequency data

MISSENSE_VARIANT chr1:g.215648591A>G [0/1] rs143275144 (variation viewer)

ClinVar: UNCERTAIN_SIGNIFICANCE (criteria_provided,_multiple_submitters,_no_conflicts)

Variant score: 0.985 CONTRIBUTING VARIANT

Transcripts:: USH2A:ENST00000307340.8:c.14519T>C:p.(Leu4840Pro); USH2A:ENST00000674083.1:c.14519T>C:p.(Leu4840Pro)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.952 (P); Mutation Taster: 1.000 (P); SIFT: 0.010 (D); CADD: 0.994 (22.400)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0374%; UK10K: 0.0529%; ESP AA: 0.0227%; ESP EA: 0.0349%; ESP All: 0.0308%; ExAC AMR: 0.0259%; ExAC NFE: 0.0420%; ExAC SAS: 0.0182%; gnomAD_E_AFR: 0.0065%; gnomAD_E_AMR: 0.0387%; gnomAD_E_ASJ: 0.0305%; gnomAD_E_NFE: 0.0439%; gnomAD_E_OTH: 0.0912%; gnomAD_E_SAS: 0.0065%; gnomAD_G_AFR: 0.0114%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215755594T>G [0/1] rs75124783 (variation viewer)

Variant score: 0.873

Transcripts:: USH2A:ENST00000307340.8:c.11389+3001A>C:p.(=); USH2A:ENST00000674083.1:c.11389+3001A>C:p.(=)

Pathogenicity Data:: Best Score: 0.9733927; CADD: 0.973 (15.750)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.3823%; UK10K: 0.5686%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.5330%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215678462G>A [0/1] rs146196989 (variation viewer)

Variant score: 0.829

Transcripts:: USH2A:ENST00000307340.8:c.12294+1687C>T:p.(=); USH2A:ENST00000674083.1:c.12294+1687C>T:p.(=)

Pathogenicity Data:: Best Score: 0.90645945; CADD: 0.906 (10.290)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.3631%; UK10K: 0.4893%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.4664%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215728777T>C [0/1] rs1025384130 (variation viewer)

Variant score: 0.786

Transcripts:: USH2A:ENST00000307340.8:c.11712-393A>G:p.(=); USH2A:ENST00000674083.1:c.11712-393A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7882614; CADD: 0.788 (6.742)

Frequency Data:: TOPMed: 0.0127%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216419637A>G [0/1] rs756643079 (variation viewer)

Variant score: 0.696

Transcripts:: USH2A:ENST00000307340.8:c.486-958T>C:p.(=); USH2A:ENST00000366942.3:c.486-958T>C:p.(=); USH2A:ENST00000674083.1:c.486-958T>C:p.(=)

Pathogenicity Data:: Best Score: 0.69716924; CADD: 0.697 (5.188)

Frequency Data:: TOPMed: 0.0016%; UK10K: 0.0132%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215983909A>T [0/1] rs116365079 (variation viewer)

Variant score: 0.668

Transcripts:: USH2A:ENST00000307340.8:c.6805+9111T>A:p.(=); USH2A:ENST00000674083.1:c.6805+9111T>A:p.(=)

Pathogenicity Data:: Best Score: 0.8061794; CADD: 0.806 (7.126)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5296%; UK10K: 0.8199%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.6993%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216120219CAAAAAAAAAAAAAAA>C [-/1] rs10525093 (variation viewer)

Variant score: 0.632

Transcripts:: USH2A:ENST00000307340.8:c.4628-23021_4628-23007del:p.(=); USH2A:ENST00000674083.1:c.4628-23021_4628-23007del:p.(=)

Pathogenicity Data:: Best Score: 0.63195574; CADD: 0.632 (4.341)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215691497G>T [0/1] rs905467830 (variation viewer)

Variant score: 0.580

Transcripts:: USH2A:ENST00000307340.8:c.12067-11121C>A:p.(=); USH2A:ENST00000674083.1:c.12067-11121C>A:p.(=)

Pathogenicity Data:: Best Score: 0.58101356; CADD: 0.581 (3.778)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215728582G>GACAC [-/1] rs1311988583 (variation viewer)

Variant score: 0.541

Transcripts:: USH2A:ENST00000307340.8:c.11712-199_11712-198insGTGT:p.(=); USH2A:ENST00000674083.1:c.11712-199_11712-198insGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.5410134; CADD: 0.541 (3.382)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216268821G>A [0/1] rs144110432 (variation viewer)

Variant score: 0.456

Transcripts:: USH2A:ENST00000307340.8:c.1972-17723C>T:p.(=); USH2A:ENST00000366942.3:c.1972-17723C>T:p.(=); USH2A:ENST00000674083.1:c.1972-17723C>T:p.(=)

Pathogenicity Data:: Best Score: 0.665805; CADD: 0.666 (4.760)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.6610%; UK10K: 1.0976%; gnomAD_G_AFR: 0.1607%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.2034%; gnomAD_G_NFE: 1.0870%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215719362C>CA [0/1] rs375176415 (variation viewer)

Variant score: 0.449

Transcripts:: USH2A:ENST00000307340.8:c.12066+8667_12066+8668insT:p.(=); USH2A:ENST00000674083.1:c.12066+8667_12066+8668insT:p.(=)

Pathogenicity Data:: Best Score: 0.44868475; CADD: 0.449 (2.586)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215732216G>C [0/1] rs768442665 (variation viewer)

Variant score: 0.435

Transcripts:: USH2A:ENST00000307340.8:c.11712-3832C>G:p.(=); USH2A:ENST00000674083.1:c.11712-3832C>G:p.(=)

Pathogenicity Data:: Best Score: 0.4361027; CADD: 0.436 (2.488)

Frequency Data:: TOPMed: 0.0191%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216067325T>G [0/1] rs183227623 (variation viewer)

Variant score: 0.426

Transcripts:: USH2A:ENST00000307340.8:c.6049+2776A>C:p.(=); USH2A:ENST00000674083.1:c.6049+2776A>C:p.(=)

Pathogenicity Data:: Best Score: 0.44011354; CADD: 0.440 (2.519)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1513%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0231%; gnomAD_G_NFE: 0.1687%; gnomAD_G_OTH: 0.2075%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216174317T>C [0/1]

Variant score: 0.424

Transcripts:: USH2A:ENST00000307340.8:c.4627+935A>G:p.(=); USH2A:ENST00000674083.1:c.4627+935A>G:p.(=); USH2A:ENST00000366942.3:c.*921A>G:p.(=)

Pathogenicity Data:: Best Score: 0.42416245; CADD: 0.424 (2.397)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216130091A>C [0/1] rs750126792 (variation viewer)

Variant score: 0.406

Transcripts:: USH2A:ENST00000307340.8:c.4628-32878T>G:p.(=); USH2A:ENST00000674083.1:c.4628-32878T>G:p.(=)

Pathogenicity Data:: Best Score: 0.9505689; CADD: 0.951 (13.060)

Frequency Data:: TOPMed: 0.0534%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3597%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215753360A>T [0/1] rs770213083 (variation viewer)

Variant score: 0.398

Transcripts:: USH2A:ENST00000307340.8:c.11389+5235T>A:p.(=); USH2A:ENST00000674083.1:c.11389+5235T>A:p.(=)

Pathogenicity Data:: Best Score: 0.3992414; CADD: 0.399 (2.213)

Frequency Data:: TOPMed: 0.0191%; gnomAD_G_AFR: 0.0230%; gnomAD_G_NFE: 0.0210%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216281865G>GT [0/1] rs766030449 (variation viewer)

Variant score: 0.374

Transcripts:: USH2A:ENST00000307340.8:c.1971+7414_1971+7415insA:p.(=); USH2A:ENST00000366942.3:c.1971+7414_1971+7415insA:p.(=); USH2A:ENST00000674083.1:c.1971+7414_1971+7415insA:p.(=)

Pathogenicity Data:: Best Score: 0.37367463; CADD: 0.374 (2.032)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216023459CAAAAAA>C [-/1] rs60280432 (variation viewer)

Variant score: 0.327

Transcripts:: USH2A:ENST00000307340.8:c.6326-22903_6326-22898del:p.(=); USH2A:ENST00000674083.1:c.6326-22903_6326-22898del:p.(=)

Pathogenicity Data:: Best Score: 0.3271783; CADD: 0.327 (1.721)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215686000C>G [0/1] rs145367403 (variation viewer)

Variant score: 0.318

Transcripts:: USH2A:ENST00000307340.8:c.12067-5624G>C:p.(=); USH2A:ENST00000674083.1:c.12067-5624G>C:p.(=)

Pathogenicity Data:: Best Score: 0.3485216; CADD: 0.349 (1.861)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.3735%; UK10K: 0.5025%; gnomAD_G_AFR: 0.0801%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.4873%; gnomAD_G_OTH: 0.2049%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215836565A>T [1/1] rs368595557 (variation viewer)

Variant score: 0.288

Transcripts:: USH2A:ENST00000307340.8:c.9371+1426T>A:p.(=); USH2A:ENST00000674083.1:c.9371+1426T>A:p.(=)

Pathogenicity Data:: Best Score: 0.2879672; CADD: 0.288 (1.475)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216050019C>T [0/1] rs533663677 (variation viewer)

Variant score: 0.261

Transcripts:: USH2A:ENST00000307340.8:c.6050-1372G>A:p.(=); USH2A:ENST00000674083.1:c.6050-1372G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2740612; CADD: 0.274 (1.391)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2262%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0573%; gnomAD_G_NFE: 0.2931%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216128081C>T [0/1] rs560579180 (variation viewer)

Variant score: 0.215

Transcripts:: USH2A:ENST00000307340.8:c.4628-30868G>A:p.(=); USH2A:ENST00000674083.1:c.4628-30868G>A:p.(=)

Pathogenicity Data:: Best Score: 0.50489193; CADD: 0.505 (3.053)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0534%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215856832G>GGTGT [0/1] rs71159889 (variation viewer)

Variant score: 0.210

Transcripts:: USH2A:ENST00000307340.8:c.8845+10174_8845+10175insACAC:p.(=); USH2A:ENST00000674083.1:c.8845+10174_8845+10175insACAC:p.(=)

Pathogenicity Data:: Best Score: 0.20986736; CADD: 0.210 (1.023)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215850479A>G [0/1] rs150545749 (variation viewer)

Variant score: 0.202

Transcripts:: USH2A:ENST00000307340.8:c.8846-4446T>C:p.(=); USH2A:ENST00000674083.1:c.8846-4446T>C:p.(=)

Pathogenicity Data:: Best Score: 0.23405075; CADD: 0.234 (1.158)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5017%; UK10K: 0.7009%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.6607%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216340536C>CAAAA [-/1] rs370374592 (variation viewer)

Variant score: 0.196

Transcripts:: USH2A:ENST00000307340.8:c.785-12883_785-12882insTTTT:p.(=); USH2A:ENST00000366942.3:c.785-12883_785-12882insTTTT:p.(=); USH2A:ENST00000674083.1:c.785-12883_785-12882insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.21927154; CADD: 0.219 (1.075)

Frequency Data:: gnomAD_G_AFR: 0.2126%; gnomAD_G_AMR: 0.5848%; gnomAD_G_ASJ: 0.4950%; gnomAD_G_EAS: 0.4303%; gnomAD_G_NFE: 0.3146%; gnomAD_G_OTH: 0.3922%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215840163CAAAAAA>C [0/1] rs60766928 (variation viewer)

Variant score: 0.153

Transcripts:: USH2A:ENST00000307340.8:c.9259-2066_9259-2061del:p.(=); USH2A:ENST00000674083.1:c.9259-2066_9259-2061del:p.(=)

Pathogenicity Data:: Best Score: 0.15296763; CADD: 0.153 (0.721)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216231249T>TTA [0/1] rs367785093 (variation viewer)

Variant score: 0.142

Transcripts:: USH2A:ENST00000307340.8:c.2993+703_2993+704insTA:p.(=); USH2A:ENST00000366942.3:c.2993+703_2993+704insTA:p.(=); USH2A:ENST00000674083.1:c.2993+703_2993+704insTA:p.(=)

Pathogenicity Data:: Best Score: 0.14236993; CADD: 0.142 (0.667)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215768957C>G [0/1] rs184711939 (variation viewer)

Variant score: 0.141

Transcripts:: USH2A:ENST00000307340.8:c.10940-2169G>C:p.(=); USH2A:ENST00000674083.1:c.10940-2169G>C:p.(=)

Pathogenicity Data:: Best Score: 0.17945957; CADD: 0.179 (0.859)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4659%; UK10K: 0.3967%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1717%; gnomAD_G_NFE: 0.4799%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216156295CTTT>C [1/1] rs35698520 (variation viewer)

Variant score: 0.097

Transcripts:: USH2A:ENST00000307340.8:c.4627+18954_4627+18956del:p.(=); USH2A:ENST00000674083.1:c.4627+18954_4627+18956del:p.(=)

Pathogenicity Data:: Best Score: 0.09655857; CADD: 0.097 (0.441)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216120219CAA>C [-/1] rs10525093 (variation viewer)

Variant score: 0.096

Transcripts:: USH2A:ENST00000307340.8:c.4628-23008_4628-23007del:p.(=); USH2A:ENST00000674083.1:c.4628-23008_4628-23007del:p.(=)

Pathogenicity Data:: Best Score: 0.09635055; CADD: 0.096 (0.440)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215693116G>GTATATA [-/1] rs1553253927 (variation viewer)

Variant score: 0.096

Transcripts:: USH2A:ENST00000307340.8:c.12067-12741_12067-12740insTATATA:p.(=); USH2A:ENST00000674083.1:c.12067-12741_12067-12740insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.09572607; CADD: 0.096 (0.437)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215693116G>GTATATATATA [-/1] rs1553253927 (variation viewer)

Variant score: 0.088

Transcripts:: USH2A:ENST00000307340.8:c.12067-12741_12067-12740insTATATATATA:p.(=); USH2A:ENST00000674083.1:c.12067-12741_12067-12740insTATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.08819914; CADD: 0.088 (0.401)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215692946C>A [0/1] rs146941613 (variation viewer)

Variant score: 0.087

Transcripts:: USH2A:ENST00000307340.8:c.12067-12570G>T:p.(=); USH2A:ENST00000674083.1:c.12067-12570G>T:p.(=)

Pathogenicity Data:: Best Score: 0.095517874; CADD: 0.096 (0.436)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.3703%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0808%; gnomAD_G_AMR: 0.4938%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.4702%; gnomAD_G_OTH: 0.2058%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215771579CAAAAAAAAAAAAAAAAAAA>C [1/1] rs759067576 (variation viewer)

Variant score: 0.085

Transcripts:: USH2A:ENST00000307340.8:c.10940-4810_10940-4792del:p.(=); USH2A:ENST00000674083.1:c.10940-4810_10940-4792del:p.(=)

Pathogenicity Data:: Best Score: 0.08546567; CADD: 0.085 (0.388)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215947042C>CT [0/1] rs376248926 (variation viewer)

Variant score: 0.083

Transcripts:: USH2A:ENST00000307340.8:c.7121-12248_7121-12247insA:p.(=); USH2A:ENST00000674083.1:c.7121-12248_7121-12247insA:p.(=)

Pathogenicity Data:: Best Score: 0.11590284; CADD: 0.116 (0.535)

Frequency Data:: gnomAD_G_AFR: 0.1838%; gnomAD_G_AMR: 0.6135%; gnomAD_G_FIN: 1.1322%; gnomAD_G_NFE: 0.7865%; gnomAD_G_OTH: 0.7264%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216159537TACACAC>T [0/1] rs60343349 (variation viewer)

Variant score: 0.082

Transcripts:: USH2A:ENST00000307340.8:c.4627+15709_4627+15714del:p.(=); USH2A:ENST00000674083.1:c.4627+15709_4627+15714del:p.(=)

Pathogenicity Data:: Best Score: 0.08187884; CADD: 0.082 (0.371)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216377748AAAG>A [0/1] rs1339879003 (variation viewer)

Variant score: 0.068

Transcripts:: USH2A:ENST00000307340.8:c.652-12666_652-12664del:p.(=); USH2A:ENST00000366942.3:c.652-12666_652-12664del:p.(=); USH2A:ENST00000674083.1:c.652-12666_652-12664del:p.(=)

Pathogenicity Data:: Best Score: 0.06953508; CADD: 0.070 (0.313)

Frequency Data:: gnomAD_G_AFR: 0.0245%; gnomAD_G_FIN: 0.0422%; gnomAD_G_NFE: 0.0225%; gnomAD_G_OTH: 0.1238%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215926614C>CTTT [1/1] rs10673615 (variation viewer)

Variant score: 0.058

Transcripts:: USH2A:ENST00000307340.8:c.7300+8001_7300+8002insAAA:p.(=); USH2A:ENST00000674083.1:c.7300+8001_7300+8002insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.057676554; CADD: 0.058 (0.258)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215726223T>A [0/1] rs770458414 (variation viewer)

Variant score: 0.057

Transcripts:: USH2A:ENST00000307340.8:c.12066+1807A>T:p.(=); USH2A:ENST00000674083.1:c.12066+1807A>T:p.(=)

Pathogenicity Data:: Best Score: 0.057676554; CADD: 0.058 (0.258)

Frequency Data:: TOPMed: 0.0175%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215973656C>CT [0/1] rs750306238 (variation viewer)

Variant score: 0.053

Transcripts:: USH2A:ENST00000307340.8:c.6806-2881_6806-2880insA:p.(=); USH2A:ENST00000674083.1:c.6806-2881_6806-2880insA:p.(=)

Pathogenicity Data:: Best Score: 0.053326964; CADD: 0.053 (0.238)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216339681C>A [0/1] rs149358084 (variation viewer)

Variant score: 0.042

Transcripts:: USH2A:ENST00000307340.8:c.785-12027G>T:p.(=); USH2A:ENST00000366942.3:c.785-12027G>T:p.(=); USH2A:ENST00000674083.1:c.785-12027G>T:p.(=)

Pathogenicity Data:: Best Score: 0.05876082; CADD: 0.059 (0.263)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5790%; UK10K: 1.0315%; gnomAD_G_AFR: 0.1492%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 1.1474%; gnomAD_G_NFE: 0.9813%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216023459C>CAAAAAAAAAA [-/1] rs60280432 (variation viewer)

Variant score: 0.017

Transcripts:: USH2A:ENST00000307340.8:c.6326-22898_6326-22897insTTTTTTTTTT:p.(=); USH2A:ENST00000674083.1:c.6326-22898_6326-22897insTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.01666838; CADD: 0.017 (0.073)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215817760A>G [0/1] rs141909166 (variation viewer)

Variant score: 0.015

Transcripts:: USH2A:ENST00000307340.8:c.9372-565T>C:p.(=); USH2A:ENST00000674083.1:c.9372-565T>C:p.(=)

Pathogenicity Data:: Best Score: 0.035727024; CADD: 0.036 (0.158)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.6021%; UK10K: 0.8067%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.9639%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.9737%; gnomAD_G_NFE: 0.8016%; gnomAD_G_OTH: 0.6135%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216330665C>T [0/1] rs79788220 (variation viewer)

Variant score: 0.010

Transcripts:: USH2A:ENST00000307340.8:c.785-3011G>A:p.(=); USH2A:ENST00000366942.3:c.785-3011G>A:p.(=); USH2A:ENST00000674083.1:c.785-3011G>A:p.(=)

Pathogenicity Data:: Best Score: 0.013947606; CADD: 0.014 (0.061)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5774%; UK10K: 1.0315%; gnomAD_G_AFR: 0.1492%; gnomAD_G_AMR: 0.2404%; gnomAD_G_FIN: 1.1741%; gnomAD_G_NFE: 0.9746%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216329455A>G [0/1] rs778797926 (variation viewer)

Variant score: 0.007

Transcripts:: USH2A:ENST00000307340.8:c.785-1801T>C:p.(=); USH2A:ENST00000366942.3:c.785-1801T>C:p.(=); USH2A:ENST00000674083.1:c.785-1801T>C:p.(=)

Pathogenicity Data:: Best Score: 0.010763824; CADD: 0.011 (0.047)

Frequency Data:: TOPMed: 0.0645%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215685354GT>* [-/1]

Variant score: 0.000

Transcripts:: USH2A:ENST00000307340.8:c.12067-4979_12067-4978delACins:p.(=); USH2A:ENST00000674083.1:c.12067-4979_12067-4978delACins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.215912512C>* [-/1]

Variant score: 0.000

Transcripts:: USH2A:ENST00000307340.8:c.7301-11607G>:p.(=); USH2A:ENST00000674083.1:c.7301-11607G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216030438T>* [-/1]

Variant score: 0.000

Transcripts:: USH2A:ENST00000307340.8:c.6325+15993A>:p.(=); USH2A:ENST00000674083.1:c.6325+15993A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.216135179T>* [-/1]

Variant score: 0.000

Transcripts:: USH2A:ENST00000307340.8:c.4628-37966A>:p.(=); USH2A:ENST00000674083.1:c.4628-37966A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

IRAK1

Exomiser Score: 0.748

Phenotype Score: 0.519

Variant Score: 0.978

Phenotype matches:

Proximity score 0.519 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.748

Phenotype Score: 0.519

Variant Score: 0.978

Variants contributing to score:

MISSENSE_VARIANT chr23:g.154016567C>T [1/1] rs145385375 (variation viewer)

Variant score: 0.978 CONTRIBUTING VARIANT

Transcripts:: IRAK1:ENST00000369974.6:c.1106G>A:p.(Gly369Glu); IRAK1:ENST00000369980.8:c.1106G>A:p.(Gly369Glu); IRAK1:ENST00000393687.6:c.1106G>A:p.(Gly369Glu); IRAK1:ENST00000429936.6:c.1184G>A:p.(Gly395Glu)

Pathogenicity Data:: Best Score: 0.98811495; Polyphen2: 0.820 (P); SIFT: 0.023 (D); CADD: 0.988 (19.250)

Frequency Data:: TOPMed: 0.0120%; ESP EA: 0.0595%; ESP All: 0.0379%; ExAC NFE: 0.0319%; ExAC SAS: 0.0202%; gnomAD_E_AMR: 0.0038%; gnomAD_E_NFE: 0.0226%; gnomAD_E_OTH: 0.0742%; gnomAD_E_SAS: 0.0209%; gnomAD_G_NFE: 0.0379%

X_DOMINANT

Exomiser Score: 0.748

Phenotype Score: 0.519

Variant Score: 0.978

Variants contributing to score:

MISSENSE_VARIANT chr23:g.154016567C>T [1/1] rs145385375 (variation viewer)

Variant score: 0.978 CONTRIBUTING VARIANT

Transcripts:: IRAK1:ENST00000369974.6:c.1106G>A:p.(Gly369Glu); IRAK1:ENST00000369980.8:c.1106G>A:p.(Gly369Glu); IRAK1:ENST00000393687.6:c.1106G>A:p.(Gly369Glu); IRAK1:ENST00000429936.6:c.1184G>A:p.(Gly395Glu)

Pathogenicity Data:: Best Score: 0.98811495; Polyphen2: 0.820 (P); SIFT: 0.023 (D); CADD: 0.988 (19.250)

Frequency Data:: TOPMed: 0.0120%; ESP EA: 0.0595%; ESP All: 0.0379%; ExAC NFE: 0.0319%; ExAC SAS: 0.0202%; gnomAD_E_AMR: 0.0038%; gnomAD_E_NFE: 0.0226%; gnomAD_E_OTH: 0.0742%; gnomAD_E_SAS: 0.0209%; gnomAD_G_NFE: 0.0379%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154017824AAAT>A [1/1] rs1433094441 (variation viewer)

Variant score: 0.104

Transcripts:: IRAK1:ENST00000369974.6:c.909+179_909+181del:p.(=); IRAK1:ENST00000369980.8:c.909+179_909+181del:p.(=); IRAK1:ENST00000393687.6:c.909+179_909+181del:p.(=); IRAK1:ENST00000429936.6:c.987+179_987+181del:p.(=)

Pathogenicity Data:: Best Score: 0.10360384; CADD: 0.104 (0.475)

Frequency Data:: No frequency data

IRS1

Exomiser Score: 0.744

Phenotype Score: 0.506

Variant Score: 0.990

Phenotype matches:

Proximity score 0.506 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:125853 Type 2 diabetes mellitus, susceptibility to (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.744

Phenotype Score: 0.506

Variant Score: 0.990

Variants contributing to score:

REGULATORY_REGION_VARIANT chr2:g.226801649C>A [0/1]

Variant score: 0.990 CONTRIBUTING VARIANT

Transcripts:: IRS1:ENST00000305123.5::; IRS1:ENST00000341329.7::

Pathogenicity Data:: Best Score: 0.98997694; CADD: 0.990 (19.990)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.144

Phenotype Score: 0.253

Variant Score: 0.967

Variants contributing to score:

REGULATORY_REGION_VARIANT chr2:g.226801649C>A [0/1]

Variant score: 0.990 CONTRIBUTING VARIANT

Transcripts:: IRS1:ENST00000305123.5::; IRS1:ENST00000341329.7::

Pathogenicity Data:: Best Score: 0.98997694; CADD: 0.990 (19.990)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr2:g.226735281G>A [0/1] rs1049313529 (variation viewer)

Variant score: 0.943 CONTRIBUTING VARIANT

Transcripts:: IRS1:ENST00000305123.5:c.*991C>T:p.(=)

Pathogenicity Data:: Best Score: 0.957342; CADD: 0.957 (13.700)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0133%; gnomAD_G_OTH: 0.1018%

Other passed variants:

REGULATORY_REGION_VARIANT chr2:g.226423799G>A [0/1] rs1320740210 (variation viewer)

Variant score: 0.815

Transcripts:: IRS1:ENST00000305123.5::; IRS1:ENST00000412635.1::

Pathogenicity Data:: Best Score: 0.81604993; CADD: 0.816 (7.353)

Frequency Data:: gnomAD_G_NFE: 0.0067%

THREE_PRIME_UTR_INTRON_VARIANT chr2:g.226736490C>T [0/1] rs567702851 (variation viewer)

Variant score: 0.515

Transcripts:: IRS1:ENST00000305123.5:c.*22-240G>A:p.(=)

Pathogenicity Data:: Best Score: 0.523569; CADD: 0.524 (3.220)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0502%; gnomAD_G_AFR: 0.1146%; gnomAD_G_OTH: 0.1018%

DOWNSTREAM_GENE_VARIANT chr2:g.226728076G>GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT [-/1] rs3053727 (variation viewer)

Variant score: 0.244

Transcripts:: IRS1:ENST00000305123.5::; IRS1:ENST00000412635.1::

Pathogenicity Data:: Best Score: 0.24386382; CADD: 0.244 (1.214)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr2:g.226729876C>T [0/1] rs578095367 (variation viewer)

Variant score: 0.087

Transcripts:: IRS1:ENST00000305123.5::; IRS1:ENST00000412635.1::

Pathogenicity Data:: Best Score: 0.08819914; CADD: 0.088 (0.401)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0502%; gnomAD_G_AFR: 0.1146%; gnomAD_G_OTH: 0.1018%

THREE_PRIME_UTR_INTRON_VARIANT chr2:g.226747768T>C [0/1] rs78911336 (variation viewer)

Variant score: 0.044

Transcripts:: IRS1:ENST00000305123.5:c.*22-11518A>G:p.(=)

Pathogenicity Data:: Best Score: 0.08483374; CADD: 0.085 (0.385)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.6650%; UK10K: 1.0976%; gnomAD_G_AFR: 0.2521%; gnomAD_G_FIN: 0.6869%; gnomAD_G_NFE: 1.5071%; gnomAD_G_OTH: 1.1202%

THREE_PRIME_UTR_INTRON_VARIANT chr2:g.226766161ATAT>A [1/1] rs1288778285 (variation viewer)

Variant score: 0.031

Transcripts:: IRS1:ENST00000305123.5:c.*21+28825_*21+28827del:p.(=)

Pathogenicity Data:: Best Score: 0.031276107; CADD: 0.031 (0.138)

Frequency Data:: No frequency data

RAP1A

Exomiser Score: 0.729

Phenotype Score: 0.507

Variant Score: 0.981

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.729

Phenotype Score: 0.507

Variant Score: 0.981

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111606578T>C [0/1] rs1259694932 (variation viewer)

Variant score: 0.981 CONTRIBUTING VARIANT

Transcripts:: RAP1A:ENST00000356415.5:c.-28+64069T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9814647; CADD: 0.981 (17.320)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.119

Phenotype Score: 0.507

Variant Score: 0.655

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111606578T>C [0/1] rs1259694932 (variation viewer)

Variant score: 0.981 CONTRIBUTING VARIANT

Transcripts:: RAP1A:ENST00000356415.5:c.-28+64069T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9814647; CADD: 0.981 (17.320)

Frequency Data:: TOPMed: 0.0008%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111546272C>G [0/1] rs549839393 (variation viewer)

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: RAP1A:ENST00000356415.5:c.-28+3763C>G:p.(=)

Pathogenicity Data:: Best Score: 0.34021872; CADD: 0.340 (1.806)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0382%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1196%; gnomAD_G_FIN: 0.1720%; gnomAD_G_NFE: 0.2206%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr1:g.111715173C>T [0|1] rs1191936332 (variation viewer)

Variant score: 0.267

Transcripts:: RAP1A:ENST00000369709.3:c.*2772C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2668379; CADD: 0.267 (1.348)

Frequency Data:: TOPMed: 0.0056%; gnomAD_G_NFE: 0.0067%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111577401C>CA [0/1] rs56156855 (variation viewer)

Variant score: 0.265

Transcripts:: RAP1A:ENST00000356415.5:c.-28+34892_-28+34893insA:p.(=)

Pathogenicity Data:: Best Score: 0.2651478; CADD: 0.265 (1.338)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.111707318C>T [0/1] rs192819279 (variation viewer)

Variant score: 0.179

Transcripts:: RAP1A:ENST00000356415.5:c.469-1831C>T:p.(=); RAP1A:ENST00000369709.3:c.469-1831C>T:p.(=)

Pathogenicity Data:: Best Score: 0.18191206; CADD: 0.182 (0.872)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0358%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0400%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111555362T>TA [1/1] rs397981230 (variation viewer)

Variant score: 0.145

Transcripts:: RAP1A:ENST00000356415.5:c.-28+12853_-28+12854insA:p.(=)

Pathogenicity Data:: Best Score: 0.14532697; CADD: 0.145 (0.682)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111686690C>CAA [1/1] rs4020149 (variation viewer)

Variant score: 0.105

Transcripts:: RAP1A:ENST00000356415.5:c.-27-4644_-27-4643insAA:p.(=); RAP1A:ENST00000369709.3:c.-27-4644_-27-4643insAA:p.(=)

Pathogenicity Data:: Best Score: 0.10525352; CADD: 0.105 (0.483)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.111664373CA>C [0/1] rs57610280 (variation viewer)

Variant score: 0.079

Transcripts:: RAP1A:ENST00000356415.5:c.-27-26960del:p.(=); RAP1A:ENST00000369709.3:c.-27-26960del:p.(=)

Pathogenicity Data:: Best Score: 0.07870227; CADD: 0.079 (0.356)

Frequency Data:: No frequency data

EIF4A1

Exomiser Score: 0.728

Phenotype Score: 0.502

Variant Score: 0.986

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.728

Phenotype Score: 0.502

Variant Score: 0.986

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.7573469C>A [0/1] rs930459211 (variation viewer)

Variant score: 0.986 CONTRIBUTING VARIANT

Transcripts:: EIF4A1:ENST00000293831.13:c.23+605C>A:p.(=); EIF4A1:ENST00000577269.5:c.23+605C>A:p.(=); EIF4A1:ENST00000582746.5:c.23+605C>A:p.(=); EIF4A1:ENST00000614237.1:c.*469+605C>A:p.(=)

Pathogenicity Data:: Best Score: 0.9881696; CADD: 0.988 (19.270)

Frequency Data:: TOPMed: 0.0143%; gnomAD_G_NFE: 0.0135%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.462

Phenotype Score: 0.502

Variant Score: 0.862

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.7573469C>A [0/1] rs930459211 (variation viewer)

Variant score: 0.986 CONTRIBUTING VARIANT

Transcripts:: EIF4A1:ENST00000293831.13:c.23+605C>A:p.(=); EIF4A1:ENST00000577269.5:c.23+605C>A:p.(=); EIF4A1:ENST00000582746.5:c.23+605C>A:p.(=); EIF4A1:ENST00000614237.1:c.*469+605C>A:p.(=)

Pathogenicity Data:: Best Score: 0.9881696; CADD: 0.988 (19.270)

Frequency Data:: TOPMed: 0.0143%; gnomAD_G_NFE: 0.0135%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.7573214C>T [0/1] rs151155828 (variation viewer)

Variant score: 0.739 CONTRIBUTING VARIANT

Transcripts:: EIF4A1:ENST00000293831.13:c.23+350C>T:p.(=); EIF4A1:ENST00000577269.5:c.23+350C>T:p.(=); EIF4A1:ENST00000582746.5:c.23+350C>T:p.(=); EIF4A1:ENST00000614237.1:c.*469+350C>T:p.(=)

Pathogenicity Data:: Best Score: 0.95926195; CADD: 0.959 (13.900)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.4117%; gnomAD_G_AFR: 0.0689%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.5071%; gnomAD_G_OTH: 0.1018%

Other passed variants:

PIAS1

Exomiser Score: 0.714

Phenotype Score: 0.504

Variant Score: 0.976

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.714

Phenotype Score: 0.504

Variant Score: 0.976

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68055541C>G [0/1] rs938151805 (variation viewer)

Variant score: 0.976 CONTRIBUTING VARIANT

Transcripts:: PIAS1:ENST00000249636.10:c.24+1191C>G:p.(=); PIAS1:ENST00000545237.1:c.-85-258C>G:p.(=)

Pathogenicity Data:: Best Score: 0.98418754; CADD: 0.984 (18.010)

Frequency Data:: TOPMed: 0.0175%; gnomAD_G_EAS: 0.0619%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.554

Phenotype Score: 0.504

Variant Score: 0.900

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68055541C>G [0/1] rs938151805 (variation viewer)

Variant score: 0.976 CONTRIBUTING VARIANT

Transcripts:: PIAS1:ENST00000249636.10:c.24+1191C>G:p.(=); PIAS1:ENST00000545237.1:c.-85-258C>G:p.(=)

Pathogenicity Data:: Best Score: 0.98418754; CADD: 0.984 (18.010)

Frequency Data:: TOPMed: 0.0175%; gnomAD_G_EAS: 0.0619%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68106351CA>C [-/1] rs11313083 (variation viewer)

Variant score: 0.824 CONTRIBUTING VARIANT

Transcripts:: PIAS1:ENST00000249636.10:c.469+19602del:p.(=); PIAS1:ENST00000545237.1:c.475+19602del:p.(=)

Pathogenicity Data:: Best Score: 0.82416713; CADD: 0.824 (7.549)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68146745G>C [0|1] rs759611738 (variation viewer)

Variant score: 0.769

Transcripts:: PIAS1:ENST00000249636.10:c.828+45G>C:p.(=); PIAS1:ENST00000545237.1:c.834+45G>C:p.(=)

Pathogenicity Data:: Best Score: 0.84675014; CADD: 0.847 (8.146)

Frequency Data:: TOPMed: 0.0120%; ExAC AMR: 0.0086%; ExAC NFE: 0.0405%; gnomAD_E_AMR: 0.0095%; gnomAD_E_ASJ: 0.5155%; gnomAD_E_NFE: 0.0083%; gnomAD_E_OTH: 0.0378%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68140419A>C [0/1] rs149798289 (variation viewer)

Variant score: 0.753

Transcripts:: PIAS1:ENST00000249636.10:c.470-1527A>C:p.(=); PIAS1:ENST00000545237.1:c.476-1527A>C:p.(=)

Pathogenicity Data:: Best Score: 0.8274162; CADD: 0.827 (7.630)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.1951%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.3532%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68119237C>CAAAA [1/1] rs60879036 (variation viewer)

Variant score: 0.740

Transcripts:: PIAS1:ENST00000249636.10:c.470-22709_470-22708insAAAA:p.(=); PIAS1:ENST00000545237.1:c.476-22709_476-22708insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.73950464; CADD: 0.740 (5.842)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr15:g.68192354G>A [0/1] rs564940546 (variation viewer)

Variant score: 0.542

Transcripts:: PIAS1:ENST00000249636.10:c.*4519G>A:p.(=); PIAS1:ENST00000395465.3:c.*1711C>T:p.(=); PIAS1:ENST00000448060.6:c.*1661C>T:p.(=); PIAS1:ENST00000540479.5:c.*1661C>T:p.(=); PIAS1:ENST00000562767.2:c.*1752C>T:p.(=)

Pathogenicity Data:: Best Score: 0.58149564; CADD: 0.581 (3.783)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2612%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2003%; gnomAD_G_NFE: 0.3399%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68129224G>A [0/1] rs190318479 (variation viewer)

Variant score: 0.520

Transcripts:: PIAS1:ENST00000249636.10:c.470-12722G>A:p.(=); PIAS1:ENST00000545237.1:c.476-12722G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5959827; CADD: 0.596 (3.936)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1848%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.1199%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.2402%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68179564CTTT>C [1/1] rs766344324 (variation viewer)

Variant score: 0.415

Transcripts:: PIAS1:ENST00000249636.10:c.1482-1647_1482-1645del:p.(=); PIAS1:ENST00000545237.1:c.1488-1647_1488-1645del:p.(=)

Pathogenicity Data:: Best Score: 0.41467106; CADD: 0.415 (2.326)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68177278C>CA [1/1] rs3083984 (variation viewer)

Variant score: 0.397

Transcripts:: PIAS1:ENST00000249636.10:c.1481+624_1481+625insA:p.(=); PIAS1:ENST00000545237.1:c.1487+624_1487+625insA:p.(=)

Pathogenicity Data:: Best Score: 0.39716285; CADD: 0.397 (2.198)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68075078CT>C [0/1] rs146114696 (variation viewer)

Variant score: 0.369

Transcripts:: PIAS1:ENST00000249636.10:c.25-11227del:p.(=); PIAS1:ENST00000545237.1:c.31-11227del:p.(=)

Pathogenicity Data:: Best Score: 0.368752; CADD: 0.369 (1.998)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68155449T>TAAAAA [0|1] rs71937461 (variation viewer)

Variant score: 0.314

Transcripts:: PIAS1:ENST00000249636.10:c.934+1754_934+1755insAAAAA:p.(=); PIAS1:ENST00000545237.1:c.940+1754_940+1755insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.31435394; CADD: 0.314 (1.639)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68146739AAGG>A [0|1] rs751528049 (variation viewer)

Variant score: 0.260

Transcripts:: PIAS1:ENST00000249636.10:c.828+40_828+42del:p.(=); PIAS1:ENST00000545237.1:c.834+40_834+42del:p.(=)

Pathogenicity Data:: Best Score: 0.2855037; CADD: 0.286 (1.460)

Frequency Data:: TOPMed: 0.0120%; ESP EA: 0.0256%; ESP All: 0.0177%; ExAC AMR: 0.0086%; ExAC NFE: 0.0405%; gnomAD_E_AMR: 0.0091%; gnomAD_E_ASJ: 0.5008%; gnomAD_E_NFE: 0.0082%; gnomAD_E_OTH: 0.0370%

THREE_PRIME_UTR_EXON_VARIANT chr15:g.68192325A>C [0/1] rs138522637 (variation viewer)

Variant score: 0.250

Transcripts:: PIAS1:ENST00000249636.10:c.*4490A>C:p.(=); PIAS1:ENST00000395465.3:c.*1740T>G:p.(=); PIAS1:ENST00000448060.6:c.*1690T>G:p.(=); PIAS1:ENST00000540479.5:c.*1690T>G:p.(=); PIAS1:ENST00000562767.2:c.*1781T>G:p.(=)

Pathogenicity Data:: Best Score: 0.26835567; CADD: 0.268 (1.357)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2628%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0345%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.3468%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68071795G>T [0/1] rs180682490 (variation viewer)

Variant score: 0.180

Transcripts:: PIAS1:ENST00000249636.10:c.25-14511G>T:p.(=); PIAS1:ENST00000545237.1:c.31-14511G>T:p.(=)

Pathogenicity Data:: Best Score: 0.2067684; CADD: 0.207 (1.006)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1840%; UK10K: 0.3703%; gnomAD_G_AFR: 0.0812%; gnomAD_G_AMR: 0.1199%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0578%; gnomAD_G_NFE: 0.2418%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68090927G>GGTGTGTGTGT [0/1] rs10667510 (variation viewer)

Variant score: 0.124

Transcripts:: PIAS1:ENST00000249636.10:c.469+4177_469+4178insGTGTGTGTGT:p.(=); PIAS1:ENST00000545237.1:c.475+4177_475+4178insGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.1240083; CADD: 0.124 (0.575)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68182425A>AGTGTGTGTGT [-/1] rs10532167 (variation viewer)

Variant score: 0.117

Transcripts:: PIAS1:ENST00000249636.10:c.1624+1071_1624+1072insGTGTGTGTGT:p.(=); PIAS1:ENST00000545237.1:c.1630+1071_1630+1072insGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr15:g.68050450T>TATATATATATTCATATATATATAC [0/1] rs1555420580 (variation viewer)

Variant score: 0.078

Transcripts:: PIAS1:ENST00000249636.10::; PIAS1:ENST00000568867.1::

Pathogenicity Data:: Best Score: 0.07764101; CADD: 0.078 (0.351)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68088176G>GTATATATATATATATA [-/1] rs71455574 (variation viewer)

Variant score: 0.054

Transcripts:: PIAS1:ENST00000249636.10:c.469+1426_469+1427insTATATATATATATATA:p.(=); PIAS1:ENST00000545237.1:c.475+1426_475+1427insTATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.054198503; CADD: 0.054 (0.242)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68088176G>GTGTATATATATATATATATA [-/1] rs150997979 (variation viewer)

Variant score: 0.050

Transcripts:: PIAS1:ENST00000249636.10:c.469+1426_469+1427insTGTATATATATATATATATA:p.(=); PIAS1:ENST00000545237.1:c.475+1426_475+1427insTGTATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.05005163; CADD: 0.050 (0.223)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.68099071C>T [0/1] rs555781346 (variation viewer)

Variant score: 0.014

Transcripts:: PIAS1:ENST00000249636.10:c.469+12321C>T:p.(=); PIAS1:ENST00000545237.1:c.475+12321C>T:p.(=)

Pathogenicity Data:: Best Score: 0.01462847; CADD: 0.015 (0.064)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.1879%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1746%; gnomAD_G_NFE: 0.3476%; gnomAD_G_OTH: 0.4098%

GP5

Exomiser Score: 0.710

Phenotype Score: 0.509

Variant Score: 0.968

Phenotype matches:

Proximity score 0.509 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.710

Phenotype Score: 0.509

Variant Score: 0.968

Variants contributing to score:

REGULATORY_REGION_VARIANT chr3:g.194089713G>A [0/1] rs764012100 (variation viewer)

Variant score: 0.968 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.97135824; CADD: 0.971 (15.430)

Frequency Data:: TOPMed: 0.0024%; UK10K: 0.0264%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.073

Phenotype Score: 0.509

Variant Score: 0.593

Variants contributing to score:

REGULATORY_REGION_VARIANT chr3:g.194089713G>A [0/1] rs764012100 (variation viewer)

Variant score: 0.968 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.97135824; CADD: 0.971 (15.430)

Frequency Data:: TOPMed: 0.0024%; UK10K: 0.0264%

INTERGENIC_VARIANT chr3:g.194389226G>A [0/1] rs146795585 (variation viewer)

Variant score: 0.219 CONTRIBUTING VARIANT

Transcripts:: GP5:ENST00000401815.1::

Pathogenicity Data:: Best Score: 0.2841863; CADD: 0.284 (1.452)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.3369%; UK10K: 0.5025%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.1718%; gnomAD_G_NFE: 0.6665%; gnomAD_G_OTH: 0.3061%

Other passed variants:

INTERGENIC_VARIANT chr3:g.194385355A>T [0|1] rs375522254 (variation viewer)

Variant score: 0.051

Transcripts:: GP5:ENST00000401815.1::

Pathogenicity Data:: Best Score: 0.05158156; CADD: 0.052 (0.230)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0072%; gnomAD_G_EAS: 0.0619%

DIPK2A

Exomiser Score: 0.700

Phenotype Score: 0.505

Variant Score: 0.968

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.700

Phenotype Score: 0.505

Variant Score: 0.968

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.143961452A>G [0/1] rs958134387 (variation viewer)

Variant score: 0.968 CONTRIBUTING VARIANT

Transcripts:: DIPK2A:ENST00000315691.7::; DIPK2A:ENST00000477300.1::

Pathogenicity Data:: Best Score: 0.96808463; CADD: 0.968 (14.960)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.042

Phenotype Score: 0.505

Variant Score: 0.536

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.143961452A>G [0/1] rs958134387 (variation viewer)

Variant score: 0.968 CONTRIBUTING VARIANT

Transcripts:: DIPK2A:ENST00000315691.7::; DIPK2A:ENST00000477300.1::

Pathogenicity Data:: Best Score: 0.96808463; CADD: 0.968 (14.960)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.143998091T>C [0/1] rs763541547 (variation viewer)

Variant score: 0.105 CONTRIBUTING VARIANT

Transcripts:: DIPK2A:ENST00000441925.2::; DIPK2A:ENST00000410846.1::

Pathogenicity Data:: Best Score: 0.10484135; CADD: 0.105 (0.481)

Frequency Data:: TOPMed: 0.0064%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

Other passed variants:

UPSTREAM_GENE_VARIANT chr3:g.143967802G>GTTTTTTTTTTTTTTTTTTT [1|1]

Variant score: 0.142

Transcripts:: DIPK2A:ENST00000315691.7::; DIPK2A:ENST00000477300.1::

Pathogenicity Data:: Best Score: 0.14217246; CADD: 0.142 (0.666)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978616CTA>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5627_657+5629delCTAins*:p.(=); DIPK2A:ENST00000495414.5:c.30+5054_30+5056delCTAins*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4911_-58+4913delCTAins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978622CTATATATATATATA>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5633_657+5647delCTATATATATATATAins*:p.(=); DIPK2A:ENST00000495414.5:c.30+5060_30+5074delCTATATATATATATAins*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4917_-58+4931delCTATATATATATATAins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978644A>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5655A>*:p.(=); DIPK2A:ENST00000495414.5:c.30+5082A>*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4939A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978648A>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5659A>*:p.(=); DIPK2A:ENST00000495414.5:c.30+5086A>*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4943A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978652A>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5663A>*:p.(=); DIPK2A:ENST00000495414.5:c.30+5090A>*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4947A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978656A>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5667A>*:p.(=); DIPK2A:ENST00000495414.5:c.30+5094A>*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4951A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.143978668AGATATATATATATC>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000315691.7:c.657+5679_657+5693delAGATATATATATATCins*:p.(=); DIPK2A:ENST00000495414.5:c.30+5106_30+5120delAGATATATATATATCins*:p.(=); DIPK2A:ENST00000441925.2:c.-58+4963_-58+4977delAGATATATATATATCins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.144003391A>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000441925.2::; DIPK2A:ENST00000410846.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.144003393A>* [-/1]

Variant score: 0.000

Transcripts:: DIPK2A:ENST00000441925.2::; DIPK2A:ENST00000410846.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

RB1

Exomiser Score: 0.696

Phenotype Score: 0.503

Variant Score: 0.967

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:109800 Bladder cancer, somatic - autosomal dominant; OMIM:180200 Retinoblastoma, trilateral - autosomal dominant; OMIM:182280 Small cell cancer of the lung, somatic - autosomal dominant; OMIM:259500 Osteosarcoma, somatic - somatic; ORPHA:1587 Monosomy 13q14; ORPHA:668 Osteosarcoma

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.696

Phenotype Score: 0.503

Variant Score: 0.967

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48365443A>T [0/1] rs1439466944 (variation viewer)

Variant score: 0.967 CONTRIBUTING VARIANT

Transcripts:: RB1:ENST00000267163.5:c.939+472A>T:p.(=); RB1:ENST00000650461.1:c.939+472A>T:p.(=)

Pathogenicity Data:: Best Score: 0.9673412; CADD: 0.967 (14.860)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.033

Phenotype Score: 0.252

Variant Score: 0.793

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48365443A>T [0/1] rs1439466944 (variation viewer)

Variant score: 0.967 CONTRIBUTING VARIANT

Transcripts:: RB1:ENST00000267163.5:c.939+472A>T:p.(=); RB1:ENST00000650461.1:c.939+472A>T:p.(=)

Pathogenicity Data:: Best Score: 0.9673412; CADD: 0.967 (14.860)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48415733A>G [0/1] rs776296967 (variation viewer)

Variant score: 0.620 CONTRIBUTING VARIANT

Transcripts:: RB1:ENST00000267163.5:c.1695+34290A>G:p.(=); RB1:ENST00000650461.1:c.1695+34290A>G:p.(=); RB1:ENST00000345941.2:c.-722T>C:p.(=); RB1:ENST00000378434.8:c.-722T>C:p.(=); RB1:ENST00000620633.4:c.-722T>C:p.(=)

Pathogenicity Data:: Best Score: 0.620685; CADD: 0.621 (4.210)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48464958C>CT [-/1] rs553094345 (variation viewer)

ClinVar: BENIGN (criteria_provided,_single_submitter)

Variant score: 0.271

Transcripts:: RB1:ENST00000267163.5:c.2212-40_2212-39insT:p.(=); RB1:ENST00000650461.1:c.2212-40_2212-39insT:p.(=)

Pathogenicity Data:: Best Score: 0.2841863; CADD: 0.284 (1.452)

Frequency Data:: ExAC AFR: 0.0943%; ExAC EAS: 0.3030%; ExAC NFE: 0.1154%; ExAC SAS: 0.0200%

INTERGENIC_VARIANT chr13:g.48286124G>GACACACACACAC [0/1] rs71099684 (variation viewer)

Variant score: 0.228

Transcripts:: RB1:ENST00000267163.5::

Pathogenicity Data:: Best Score: 0.22803074; CADD: 0.228 (1.124)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr13:g.48300320A>ATTTTT [0|1]

Variant score: 0.184

Transcripts:: RB1:ENST00000267163.5::; RB1:ENST00000647800.2::

Pathogenicity Data:: Best Score: 0.18360561; CADD: 0.184 (0.881)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr13:g.48300337T>TATATA [0/1] rs1555278754 (variation viewer)

Variant score: 0.165

Transcripts:: RB1:ENST00000267163.5::; RB1:ENST00000647800.2::

Pathogenicity Data:: Best Score: 0.16612685; CADD: 0.166 (0.789)

Frequency Data:: gnomAD_G_NFE: 0.0548%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48471573T>TTAAAAA [-/1] rs71072103 (variation viewer)

Variant score: 0.113

Transcripts:: RB1:ENST00000267163.5:c.2490-1787_2490-1786insTAAAAA:p.(=); RB1:ENST00000650461.1:c.2490-1787_2490-1786insTAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.11325246; CADD: 0.113 (0.522)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48471573T>TTAAAAAA [-/1] rs71072103 (variation viewer)

Variant score: 0.111

Transcripts:: RB1:ENST00000267163.5:c.2490-1787_2490-1786insTAAAAAA:p.(=); RB1:ENST00000650461.1:c.2490-1787_2490-1786insTAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.11100358; CADD: 0.111 (0.511)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48386126C>T [0/1] rs73197547 (variation viewer)

Variant score: 0.018

Transcripts:: RB1:ENST00000267163.5:c.1695+4683C>T:p.(=); RB1:ENST00000650461.1:c.1695+4683C>T:p.(=)

Pathogenicity Data:: Best Score: 0.025234818; CADD: 0.025 (0.111)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0749%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0116%; gnomAD_G_FIN: 1.1091%; gnomAD_G_NFE: 0.0671%; gnomAD_G_OTH: 0.2066%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.48324431A>* [-/1]

Variant score: 0.000

Transcripts:: RB1:ENST00000267163.5:c.264+17025A>*:p.(=); RB1:ENST00000646097.1:c.265-8586A>*:p.(=); RB1:ENST00000650461.1:c.264+17025A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

STIM1

Exomiser Score: 0.677

Phenotype Score: 0.507

Variant Score: 0.954

Phenotype matches:

Phenotypic similarity 0.445 to mouse mutant involving STIM1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0020422, decreased freezing behavior

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:160565 Myopathy, tubular aggregate, 1 - autosomal dominant; OMIM:185070 Stormorken syndrome - autosomal dominant; OMIM:612783 Immunodeficiency 10 - autosomal recessive; ORPHA:2593 Tubular aggregate myopathy; ORPHA:3204 Stormorken-Sjaastad-Langslet syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.677

Phenotype Score: 0.507

Variant Score: 0.954

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3985003G>A [0/1] rs914537945 (variation viewer)

Variant score: 0.954 CONTRIBUTING VARIANT

Transcripts:: STIM1:ENST00000300737.8:c.270+17321G>A:p.(=); STIM1:ENST00000527651.5:c.270+17321G>A:p.(=); STIM1:ENST00000616714.4:c.270+17321G>A:p.(=)

Pathogenicity Data:: Best Score: 0.95397437; CADD: 0.954 (13.370)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.650

Phenotype Score: 0.507

Variant Score: 0.940

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3985003G>A [0/1] rs914537945 (variation viewer)

Variant score: 0.954 CONTRIBUTING VARIANT

Transcripts:: STIM1:ENST00000300737.8:c.270+17321G>A:p.(=); STIM1:ENST00000527651.5:c.270+17321G>A:p.(=); STIM1:ENST00000616714.4:c.270+17321G>A:p.(=)

Pathogenicity Data:: Best Score: 0.95397437; CADD: 0.954 (13.370)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3877549C>T [0/1] rs533307159 (variation viewer)

Variant score: 0.927 CONTRIBUTING VARIANT

Transcripts:: STIM1:ENST00000300737.8:c.139+21140C>T:p.(=); STIM1:ENST00000527651.5:c.139+21140C>T:p.(=); STIM1:ENST00000616714.4:c.139+21140C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9435063; CADD: 0.944 (12.480)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0032%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0133%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3972230G>A [0/1] rs570873135 (variation viewer)

Variant score: 0.642

Transcripts:: STIM1:ENST00000300737.8:c.270+4548G>A:p.(=); STIM1:ENST00000527651.5:c.270+4548G>A:p.(=); STIM1:ENST00000616714.4:c.270+4548G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6532631; CADD: 0.653 (4.600)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0024%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3989002C>G [0/1] rs117692082 (variation viewer)

Variant score: 0.541

Transcripts:: STIM1:ENST00000300737.8:c.270+21320C>G:p.(=); STIM1:ENST00000527651.5:c.270+21320C>G:p.(=); STIM1:ENST00000616714.4:c.270+21320C>G:p.(=)

Pathogenicity Data:: Best Score: 0.77038515; CADD: 0.770 (6.390)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.5479%; UK10K: 1.1637%; gnomAD_G_AFR: 0.1832%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.7446%; gnomAD_G_NFE: 1.0061%; gnomAD_G_OTH: 1.1202%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4015729A>G [0/1] rs558923454 (variation viewer)

Variant score: 0.417

Transcripts:: STIM1:ENST00000300737.8:c.271-8144A>G:p.(=); STIM1:ENST00000527651.5:c.271-8144A>G:p.(=); STIM1:ENST00000616714.4:c.271-8144A>G:p.(=)

Pathogenicity Data:: Best Score: 0.42957312; CADD: 0.430 (2.438)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0940%; gnomAD_G_AFR: 0.1950%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3991950C>CA [0/1] rs1230185435 (variation viewer)

Variant score: 0.354

Transcripts:: STIM1:ENST00000300737.8:c.270+24268_270+24269insA:p.(=); STIM1:ENST00000527651.5:c.270+24268_270+24269insA:p.(=); STIM1:ENST00000616714.4:c.270+24268_270+24269insA:p.(=)

Pathogenicity Data:: Best Score: 0.35434574; CADD: 0.354 (1.900)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3919745G>C [0/1] rs147701602 (variation viewer)

Variant score: 0.342

Transcripts:: STIM1:ENST00000300737.8:c.140-47807G>C:p.(=); STIM1:ENST00000527651.5:c.140-47807G>C:p.(=); STIM1:ENST00000616714.4:c.140-47807G>C:p.(=)

Pathogenicity Data:: Best Score: 0.4948737; CADD: 0.495 (2.966)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.5535%; UK10K: 1.1902%; gnomAD_G_AFR: 0.1835%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.7458%; gnomAD_G_NFE: 1.0263%; gnomAD_G_OTH: 1.1224%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3994598C>T [0/1] rs143601054 (variation viewer)

Variant score: 0.221

Transcripts:: STIM1:ENST00000300737.8:c.270+26916C>T:p.(=); STIM1:ENST00000527651.5:c.270+26916C>T:p.(=); STIM1:ENST00000616714.4:c.270+26916C>T:p.(=)

Pathogenicity Data:: Best Score: 0.23016083; CADD: 0.230 (1.136)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1274%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0347%; gnomAD_G_AMR: 0.1199%; gnomAD_G_FIN: 0.0295%; gnomAD_G_NFE: 0.1694%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4073048G>GTT [1/1] rs56009858 (variation viewer)

Variant score: 0.203

Transcripts:: STIM1:ENST00000300737.8:c.792-1454_792-1453insTT:p.(=); STIM1:ENST00000527651.5:c.792-1454_792-1453insTT:p.(=); STIM1:ENST00000533977.5:c.273-1454_273-1453insTT:p.(=); STIM1:ENST00000616714.4:c.792-1454_792-1453insTT:p.(=)

Pathogenicity Data:: Best Score: 0.20347393; CADD: 0.203 (0.988)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3992081G>GCTT [0/1] rs376329167 (variation viewer)

Variant score: 0.186

Transcripts:: STIM1:ENST00000300737.8:c.270+24399_270+24400insCTT:p.(=); STIM1:ENST00000527651.5:c.270+24399_270+24400insCTT:p.(=); STIM1:ENST00000616714.4:c.270+24399_270+24400insCTT:p.(=)

Pathogenicity Data:: Best Score: 0.18567085; CADD: 0.186 (0.892)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4046059C>CTT [1/1] rs35783768 (variation viewer)

Variant score: 0.175

Transcripts:: STIM1:ENST00000300737.8:c.386-9467_386-9466insTT:p.(=); STIM1:ENST00000527651.5:c.386-9467_386-9466insTT:p.(=); STIM1:ENST00000616714.4:c.386-9467_386-9466insTT:p.(=)

Pathogenicity Data:: Best Score: 0.17491251; CADD: 0.175 (0.835)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3956823C>CAAAAAAAA [0/1] rs78285130 (variation viewer)

Variant score: 0.174

Transcripts:: STIM1:ENST00000300737.8:c.140-10729_140-10728insAAAAAAAA:p.(=); STIM1:ENST00000527651.5:c.140-10729_140-10728insAAAAAAAA:p.(=); STIM1:ENST00000616714.4:c.140-10729_140-10728insAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.17396206; CADD: 0.174 (0.830)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3904196CA>C [1/1] rs57908154 (variation viewer)

Variant score: 0.164

Transcripts:: STIM1:ENST00000300737.8:c.139+47788del:p.(=); STIM1:ENST00000527651.5:c.139+47788del:p.(=); STIM1:ENST00000616714.4:c.139+47788del:p.(=)

Pathogenicity Data:: Best Score: 0.16381955; CADD: 0.164 (0.777)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3941673T>TAG [-/1] rs1554959602 (variation viewer)

Variant score: 0.149

Transcripts:: STIM1:ENST00000300737.8:c.140-25879_140-25878insAG:p.(=); STIM1:ENST00000527651.5:c.140-25879_140-25878insAG:p.(=); STIM1:ENST00000616714.4:c.140-25879_140-25878insAG:p.(=)

Pathogenicity Data:: Best Score: 0.14905792; CADD: 0.149 (0.701)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3948490A>G [0/1]

Variant score: 0.138

Transcripts:: STIM1:ENST00000300737.8:c.140-19062A>G:p.(=); STIM1:ENST00000527651.5:c.140-19062A>G:p.(=); STIM1:ENST00000616714.4:c.140-19062A>G:p.(=)

Pathogenicity Data:: Best Score: 0.13821286; CADD: 0.138 (0.646)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3941673T>TATATAGAGAG [-/1] rs141623520 (variation viewer)

Variant score: 0.128

Transcripts:: STIM1:ENST00000300737.8:c.140-25879_140-25878insATATAGAGAG:p.(=); STIM1:ENST00000527651.5:c.140-25879_140-25878insATATAGAGAG:p.(=); STIM1:ENST00000616714.4:c.140-25879_140-25878insATATAGAGAG:p.(=)

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3980686A>AC [0|1] rs4910589 (variation viewer)

Variant score: 0.042

Transcripts:: STIM1:ENST00000300737.8:c.270+13004_270+13005insC:p.(=); STIM1:ENST00000527651.5:c.270+13004_270+13005insC:p.(=); STIM1:ENST00000616714.4:c.270+13004_270+13005insC:p.(=)

Pathogenicity Data:: Best Score: 0.04676497; CADD: 0.047 (0.208)

Frequency Data:: gnomAD_G_AFR: 0.5496%; gnomAD_G_AMR: 0.2427%; gnomAD_G_EAS: 0.1253%; gnomAD_G_FIN: 0.0585%; gnomAD_G_NFE: 0.4110%; gnomAD_G_OTH: 0.4149%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4054440G>A [0/1] rs184778371 (variation viewer)

Variant score: 0.039

Transcripts:: STIM1:ENST00000300737.8:c.386-1086G>A:p.(=); STIM1:ENST00000527651.5:c.386-1086G>A:p.(=); STIM1:ENST00000616714.4:c.386-1086G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12320107; CADD: 0.123 (0.571)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.9541%; UK10K: 1.6662%; gnomAD_G_AFR: 0.3896%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.6055%; gnomAD_G_NFE: 1.8007%; gnomAD_G_OTH: 1.3265%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4087765A>T [0/1] rs1468487478 (variation viewer)

Variant score: 0.016

Transcripts:: STIM1:ENST00000300737.8:c.1541+1222A>T:p.(=); STIM1:ENST00000527651.5:c.1542-937A>T:p.(=); STIM1:ENST00000533977.5:c.1022+1222A>T:p.(=); STIM1:ENST00000616714.4:c.1859+904A>T:p.(=)

Pathogenicity Data:: Best Score: 0.016441941; CADD: 0.016 (0.072)

Frequency Data:: gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.3858254G>* [-/1]

Variant score: 0.000

Transcripts:: STIM1:ENST00000300737.8:c.139+1845G>*:p.(=); STIM1:ENST00000527651.5:c.139+1845G>*:p.(=); STIM1:ENST00000616714.4:c.139+1845G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NTPCR

Exomiser Score: 0.677

Phenotype Score: 0.503

Variant Score: 0.958

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.677

Phenotype Score: 0.503

Variant Score: 0.958

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr1:g.232978647G>T [0/1] rs1415051437 (variation viewer)

Variant score: 0.958 CONTRIBUTING VARIANT

Transcripts:: NTPCR:ENST00000366628.10:c.*416G>T:p.(=)

Pathogenicity Data:: Best Score: 0.9622428; CADD: 0.962 (14.230)

Frequency Data:: TOPMed: 0.0056%; gnomAD_G_AFR: 0.0344%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.040

Phenotype Score: 0.503

Variant Score: 0.532

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr1:g.232978647G>T [0/1] rs1415051437 (variation viewer)

Variant score: 0.958 CONTRIBUTING VARIANT

Transcripts:: NTPCR:ENST00000366628.10:c.*416G>T:p.(=)

Pathogenicity Data:: Best Score: 0.9622428; CADD: 0.962 (14.230)

Frequency Data:: TOPMed: 0.0056%; gnomAD_G_AFR: 0.0344%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.232965228G>A [0/1] rs181134435 (variation viewer)

Variant score: 0.106 CONTRIBUTING VARIANT

Transcripts:: NTPCR:ENST00000366627.4:c.295-4681G>A:p.(=); NTPCR:ENST00000366628.10:c.295-4681G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11468053; CADD: 0.115 (0.529)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.2110%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.1199%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3066%; gnomAD_G_OTH: 0.2037%

Other passed variants:

SGCE

Exomiser Score: 0.676

Phenotype Score: 0.514

Variant Score: 0.945

Phenotype matches:

Phenotypic similarity 0.514 to Dystonia-11, myoclonic associated with SGCE.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000756, Agoraphobia

Phenotypic similarity 0.436 to mouse mutant involving SGCE.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.500 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:159900 Dystonia-11, myoclonic - autosomal dominant; ORPHA:36899 Myoclonus-dystonia syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.676

Phenotype Score: 0.514

Variant Score: 0.945

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr7:g.94580612C>T [0/1]

Variant score: 0.945 CONTRIBUTING VARIANT

Transcripts:: SGCE:ENST00000647351.1::; SGCE:ENST00000297273.9::

Pathogenicity Data:: Best Score: 0.9454242; CADD: 0.945 (12.630)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.065

Phenotype Score: 0.257

Variant Score: 0.866

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr7:g.94580612C>T [0/1]

Variant score: 0.945 CONTRIBUTING VARIANT

Transcripts:: SGCE:ENST00000647351.1::; SGCE:ENST00000297273.9::

Pathogenicity Data:: Best Score: 0.9454242; CADD: 0.945 (12.630)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.94648376CA>C [0/1] rs71123907 (variation viewer)

Variant score: 0.787 CONTRIBUTING VARIANT

Transcripts:: SGCE:ENST00000415788.3:c.109+7613del:p.(=); SGCE:ENST00000428696.7:c.109+7613del:p.(=); SGCE:ENST00000437425.7:c.109+7613del:p.(=); SGCE:ENST00000445866.7:c.109+7613del:p.(=); SGCE:ENST00000447873.6:c.109+7613del:p.(=); SGCE:ENST00000642394.1:c.109+7613del:p.(=); SGCE:ENST00000642441.1:c.109+7613del:p.(=); SGCE:ENST00000642707.1:c.109+7613del:p.(=); SGCE:ENST00000642933.1:c.109+7613del:p.(=); SGCE:ENST00000643128.1:c.109+7613del:p.(=); SGCE:ENST00000643193.1:c.109+7613del:p.(=); SGCE:ENST00000643272.1:c.109+7613del:p.(=); SGCE:ENST00000643903.1:c.109+7613del:p.(=); SGCE:ENST00000644116.1:c.109+7613del:p.(=); SGCE:ENST00000644122.1:c.109+7613del:p.(=); SGCE:ENST00000644375.1:c.109+7613del:p.(=); SGCE:ENST00000644551.1:c.109+7613del:p.(=); SGCE:ENST00000644609.1:c.109+7613del:p.(=); SGCE:ENST00000644816.1:c.109+7613del:p.(=); SGCE:ENST00000645101.1:c.109+7613del:p.(=); SGCE:ENST00000645109.1:c.109+7613del:p.(=); SGCE:ENST00000645262.1:c.109+7613del:p.(=); SGCE:ENST00000645725.1:c.109+7613del:p.(=); SGCE:ENST00000646098.1:c.109+7613del:p.(=); SGCE:ENST00000646137.1:c.109+7613del:p.(=); SGCE:ENST00000646489.1:c.109+7613del:p.(=); SGCE:ENST00000646879.1:c.109+7613del:p.(=); SGCE:ENST00000646943.1:c.109+7613del:p.(=); SGCE:ENST00000647018.1:c.109+7613del:p.(=); SGCE:ENST00000647096.1:c.109+7613del:p.(=); SGCE:ENST00000647351.1:c.109+7613del:p.(=); SGCE:ENST00000648936.2:c.109+7613del:p.(=); SGCE:ENST00000644681.1:c.-226-3710del:p.(=); SGCE:ENST00000645535.1:c.-165+7977del:p.(=)

Pathogenicity Data:: Best Score: 0.7872841; CADD: 0.787 (6.722)

Frequency Data:: No frequency data

Other passed variants:

UHRF1BP1

Exomiser Score: 0.664

Phenotype Score: 0.504

Variant Score: 0.950

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.664

Phenotype Score: 0.504

Variant Score: 0.950

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.34781624G>A [0/1]

Variant score: 0.950 CONTRIBUTING VARIANT

Transcripts:: UHRF1BP1:ENST00000452449.6::; UHRF1BP1:ENST00000244520.10::

Pathogenicity Data:: Best Score: 0.9502263; CADD: 0.950 (13.030)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.142

Phenotype Score: 0.504

Variant Score: 0.680

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.34781624G>A [0/1]

Variant score: 0.950 CONTRIBUTING VARIANT

Transcripts:: UHRF1BP1:ENST00000452449.6::; UHRF1BP1:ENST00000244520.10::

Pathogenicity Data:: Best Score: 0.9502263; CADD: 0.950 (13.030)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34825626G>A [0/1] rs116001982 (variation viewer)

Variant score: 0.410 CONTRIBUTING VARIANT

Transcripts:: UHRF1BP1:ENST00000192788.6:c.338+2278G>A:p.(=); UHRF1BP1:ENST00000452449.6:c.338+2278G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7381214; CADD: 0.738 (5.819)

Frequency Data:: 1000Genomes: 1.1580%; TOPMed: 0.8577%; UK10K: 0.4099%; gnomAD_G_AFR: 1.4548%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5152%; gnomAD_G_NFE: 0.4801%; gnomAD_G_OTH: 0.6110%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34824514C>T [0/1] rs1307143063 (variation viewer)

Variant score: 0.360

Transcripts:: UHRF1BP1:ENST00000192788.6:c.338+1166C>T:p.(=); UHRF1BP1:ENST00000452449.6:c.338+1166C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3608541; CADD: 0.361 (1.944)

Frequency Data:: gnomAD_G_AFR: 0.0123%; gnomAD_G_NFE: 0.0074%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34808346C>CAAAA [0/1] rs71002503 (variation viewer)

Variant score: 0.291

Transcripts:: UHRF1BP1:ENST00000192788.6:c.45-13307_45-13306insAAAA:p.(=); UHRF1BP1:ENST00000452449.6:c.45-13307_45-13306insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.29140186; CADD: 0.291 (1.496)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34851586A>G [0|1] rs145729935 (variation viewer)

Variant score: 0.270

Transcripts:: UHRF1BP1:ENST00000192788.6:c.1034-4031A>G:p.(=); UHRF1BP1:ENST00000452449.6:c.1034-4031A>G:p.(=)

Pathogenicity Data:: Best Score: 0.3097602; CADD: 0.310 (1.610)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.3170%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0688%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5152%; gnomAD_G_NFE: 0.3203%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34863151C>T [0/1] rs150539644 (variation viewer)

Variant score: 0.249

Transcripts:: UHRF1BP1:ENST00000192788.6:c.3216-851C>T:p.(=); UHRF1BP1:ENST00000452449.6:c.3216-851C>T:p.(=)

Pathogenicity Data:: Best Score: 0.28533912; CADD: 0.285 (1.459)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.3186%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0687%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5158%; gnomAD_G_NFE: 0.3269%; gnomAD_G_OTH: 0.4090%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34829027C>CA [-/1] rs56256446 (variation viewer)

Variant score: 0.236

Transcripts:: UHRF1BP1:ENST00000192788.6:c.339-5190_339-5189insA:p.(=); UHRF1BP1:ENST00000452449.6:c.339-5190_339-5189insA:p.(=)

Pathogenicity Data:: Best Score: 0.23563641; CADD: 0.236 (1.167)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34814769G>A [0/1] rs181703442 (variation viewer)

Variant score: 0.229

Transcripts:: UHRF1BP1:ENST00000192788.6:c.45-6884G>A:p.(=); UHRF1BP1:ENST00000452449.6:c.45-6884G>A:p.(=)

Pathogenicity Data:: Best Score: 0.26209575; CADD: 0.262 (1.320)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.3170%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0688%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5155%; gnomAD_G_NFE: 0.3265%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34795472A>C [0|1] rs371771948 (variation viewer)

Variant score: 0.196

Transcripts:: UHRF1BP1:ENST00000192788.6:c.44+3178A>C:p.(=); UHRF1BP1:ENST00000452449.6:c.44+3178A>C:p.(=)

Pathogenicity Data:: Best Score: 0.22482455; CADD: 0.225 (1.106)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.3010%; gnomAD_G_AFR: 0.0117%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5312%; gnomAD_G_NFE: 0.3219%; gnomAD_G_OTH: 0.4329%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34829027CA>C [-/1] rs56256446 (variation viewer)

Variant score: 0.185

Transcripts:: UHRF1BP1:ENST00000192788.6:c.339-5189del:p.(=); UHRF1BP1:ENST00000452449.6:c.339-5189del:p.(=)

Pathogenicity Data:: Best Score: 0.18548328; CADD: 0.185 (0.891)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34794878G>A [0/1] rs752719490 (variation viewer)

Variant score: 0.113

Transcripts:: UHRF1BP1:ENST00000192788.6:c.44+2584G>A:p.(=); UHRF1BP1:ENST00000452449.6:c.44+2584G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11386478; CADD: 0.114 (0.525)

Frequency Data:: UK10K: 0.0397%; gnomAD_G_NFE: 0.0136%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34808370AG>A [0/1] rs1321140360 (variation viewer)

Variant score: 0.021

Transcripts:: UHRF1BP1:ENST00000192788.6:c.45-13282del:p.(=); UHRF1BP1:ENST00000452449.6:c.45-13282del:p.(=)

Pathogenicity Data:: Best Score: 0.022537708; CADD: 0.023 (0.099)

Frequency Data:: gnomAD_G_AFR: 0.1423%; gnomAD_G_AMR: 0.2632%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.2506%; gnomAD_G_NFE: 0.4025%; gnomAD_G_OTH: 0.1157%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.34811686G>* [-/1]

Variant score: 0.000

Transcripts:: UHRF1BP1:ENST00000192788.6:c.45-9967G>*:p.(=); UHRF1BP1:ENST00000452449.6:c.45-9967G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ATXN3

Exomiser Score: 0.656

Phenotype Score: 0.510

Variant Score: 0.940

Phenotype matches:

Proximity score 0.510 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:109150 Machado-Joseph disease - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.656

Phenotype Score: 0.510

Variant Score: 0.940

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.92067814G>C [0/1] rs768134157 (variation viewer)

Variant score: 0.940 CONTRIBUTING VARIANT

Transcripts:: ATXN3:ENST00000340660.10:c.826+3121C>G:p.(=); ATXN3:ENST00000393287.9:c.838+3121C>G:p.(=); ATXN3:ENST00000429774.6:c.781+3121C>G:p.(=); ATXN3:ENST00000502250.5:c.454+3121C>G:p.(=); ATXN3:ENST00000503767.5:c.946+3121C>G:p.(=); ATXN3:ENST00000545170.5:c.1018+3121C>G:p.(=); ATXN3:ENST00000644486.2:c.991+3121C>G:p.(=)

Pathogenicity Data:: Best Score: 0.94138616; CADD: 0.941 (12.320)

Frequency Data:: TOPMed: 0.0120%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.082

Phenotype Score: 0.255

Variant Score: 0.895

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.92067814G>C [0/1] rs768134157 (variation viewer)

Variant score: 0.940 CONTRIBUTING VARIANT

Transcripts:: ATXN3:ENST00000340660.10:c.826+3121C>G:p.(=); ATXN3:ENST00000393287.9:c.838+3121C>G:p.(=); ATXN3:ENST00000429774.6:c.781+3121C>G:p.(=); ATXN3:ENST00000502250.5:c.454+3121C>G:p.(=); ATXN3:ENST00000503767.5:c.946+3121C>G:p.(=); ATXN3:ENST00000545170.5:c.1018+3121C>G:p.(=); ATXN3:ENST00000644486.2:c.991+3121C>G:p.(=)

Pathogenicity Data:: Best Score: 0.94138616; CADD: 0.941 (12.320)

Frequency Data:: TOPMed: 0.0120%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

INFRAME_INSERTION chr14:g.92071010C>CCTGCTGCTGCTGCTGCTGCTGCTGCTG [-/1] rs193922928 (variation viewer)

Variant score: 0.850 CONTRIBUTING VARIANT

Transcripts:: ATXN3:ENST00000340660.10:c.750_751insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln242_Gln250dup); ATXN3:ENST00000393287.9:c.762_763insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln246_Gln254dup); ATXN3:ENST00000429774.6:c.705_706insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln227_Gln235dup); ATXN3:ENST00000502250.5:c.378_379insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln118_Gln126dup); ATXN3:ENST00000503767.5:c.870_871insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln282_Gln290dup); ATXN3:ENST00000532032.5:c.915_916insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln297_Gln305dup); ATXN3:ENST00000545170.5:c.942_943insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln306_Gln314dup); ATXN3:ENST00000620536.4:c.942_943insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln306_Gln314dup); ATXN3:ENST00000644486.2:c.915_916insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln297_Gln305dup); ATXN3:ENST00000617719.4:c.*73_*74insCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(=)

Pathogenicity Data:: Best Score: 0.34807146; CADD: 0.348 (1.858)

Frequency Data:: No frequency data

Other passed variants:

INFRAME_INSERTION chr14:g.92071010C>CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG [-/1] rs193922928 (variation viewer)

ClinVar: BENIGN (criteria_provided,_single_submitter)

Variant score: 0.850

Transcripts:: ATXN3:ENST00000340660.10:c.750_751insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln241_Gln250dup); ATXN3:ENST00000393287.9:c.762_763insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln245_Gln254dup); ATXN3:ENST00000429774.6:c.705_706insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln226_Gln235dup); ATXN3:ENST00000502250.5:c.378_379insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln117_Gln126dup); ATXN3:ENST00000503767.5:c.870_871insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln281_Gln290dup); ATXN3:ENST00000532032.5:c.915_916insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln296_Gln305dup); ATXN3:ENST00000545170.5:c.942_943insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln305_Gln314dup); ATXN3:ENST00000620536.4:c.942_943insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln305_Gln314dup); ATXN3:ENST00000644486.2:c.915_916insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(Gln296_Gln305dup); ATXN3:ENST00000617719.4:c.*73_*74insCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG:p.(=)

Pathogenicity Data:: Best Score: 0.33257878; CADD: 0.333 (1.756)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.92094347C>T [0/1] rs184511990 (variation viewer)

Variant score: 0.718

Transcripts:: ATXN3:ENST00000340660.10:c.70-516G>A:p.(=); ATXN3:ENST00000393287.9:c.234+1746G>A:p.(=); ATXN3:ENST00000429774.6:c.25-516G>A:p.(=); ATXN3:ENST00000503767.5:c.190-516G>A:p.(=); ATXN3:ENST00000532032.5:c.235-516G>A:p.(=); ATXN3:ENST00000545170.5:c.235-516G>A:p.(=); ATXN3:ENST00000617719.4:c.235-516G>A:p.(=); ATXN3:ENST00000620536.4:c.235-516G>A:p.(=); ATXN3:ENST00000621269.4:c.235-516G>A:p.(=); ATXN3:ENST00000644486.2:c.235-516G>A:p.(=); ATXN3:ENST00000502250.5:c.-217-1029G>A:p.(=)

Pathogenicity Data:: Best Score: 0.74525833; CADD: 0.745 (5.939)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1258%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0344%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.1868%

DOWNSTREAM_GENE_VARIANT chr14:g.92054972C>T [0/1] rs190625806 (variation viewer)

Variant score: 0.148

Transcripts:: ATXN3:ENST00000644486.2::; ATXN3:ENST00000267622.8::

Pathogenicity Data:: Best Score: 0.16015333; CADD: 0.160 (0.758)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2548%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0458%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.3723%; gnomAD_G_NFE: 0.4399%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.92094264G>A [0/1] rs956102237 (variation viewer)

Variant score: 0.031

Transcripts:: ATXN3:ENST00000340660.10:c.70-433C>T:p.(=); ATXN3:ENST00000393287.9:c.234+1829C>T:p.(=); ATXN3:ENST00000429774.6:c.25-433C>T:p.(=); ATXN3:ENST00000503767.5:c.190-433C>T:p.(=); ATXN3:ENST00000532032.5:c.235-433C>T:p.(=); ATXN3:ENST00000545170.5:c.235-433C>T:p.(=); ATXN3:ENST00000617719.4:c.235-433C>T:p.(=); ATXN3:ENST00000620536.4:c.235-433C>T:p.(=); ATXN3:ENST00000621269.4:c.235-433C>T:p.(=); ATXN3:ENST00000644486.2:c.235-433C>T:p.(=); ATXN3:ENST00000502250.5:c.-217-946C>T:p.(=)

Pathogenicity Data:: Best Score: 0.031053066; CADD: 0.031 (0.137)

Frequency Data:: TOPMed: 0.0120%; gnomAD_G_NFE: 0.0067%

CHRNA7

Exomiser Score: 0.651

Phenotype Score: 1.000

Variant Score: 0.383

Phenotype matches:

Phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Phenotypic similarity 0.436 to mouse mutant involving CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.500 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:199318 15q13.3 microdeletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.651

Phenotype Score: 1.000

Variant Score: 0.383

Variants contributing to score:

INTERGENIC_VARIANT chr15:g.32189061G>T [0/1] rs79532403 (variation viewer)

Variant score: 0.383 CONTRIBUTING VARIANT

Transcripts:: CHRNA7:ENST00000306901.9::; CHRNA7:ENST00000605648.1::

Pathogenicity Data:: Best Score: 0.383121; CADD: 0.383 (2.098)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.037

Phenotype Score: 0.500

Variant Score: 0.525

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr15:g.32173331C>T [1/1] rs1416828530 (variation viewer)

Variant score: 0.525 CONTRIBUTING VARIANT

Transcripts:: CHRNA7:ENST00000306901.9::; CHRNA7:ENST00000605648.1::

Pathogenicity Data:: Best Score: 0.5459538; CADD: 0.546 (3.429)

Frequency Data:: gnomAD_G_NFE: 0.2500%

Other passed variants:

INTERGENIC_VARIANT chr15:g.32182971C>T [1/1] rs450120 (variation viewer)

Variant score: 0.439

Transcripts:: CHRNA7:ENST00000306901.9::; CHRNA7:ENST00000605648.1::

Pathogenicity Data:: Best Score: 0.53548473; CADD: 0.535 (3.330)

Frequency Data:: gnomAD_G_AFR: 0.8439%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32046020A>G [0/1] rs765164387 (variation viewer)

Variant score: 0.384

Transcripts:: CHRNA7:ENST00000306901.9:c.195+14983A>G:p.(=); CHRNA7:ENST00000454250.7:c.282+14983A>G:p.(=); CHRNA7:ENST00000635884.1:c.9+14983A>G:p.(=); CHRNA7:ENST00000636603.1:c.9+14983A>G:p.(=); CHRNA7:ENST00000637033.1:c.9+14983A>G:p.(=); CHRNA7:ENST00000637183.1:c.-42-55283A>G:p.(=)

Pathogenicity Data:: Best Score: 0.39674628; CADD: 0.397 (2.195)

Frequency Data:: TOPMed: 0.1346%; gnomAD_G_AFR: 0.0232%; gnomAD_G_AMR: 0.1238%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.2191%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32167436G>C [0/1] rs286097 (variation viewer)

Variant score: 0.331

Transcripts:: CHRNA7:ENST00000306901.9:c.991-504G>C:p.(=); CHRNA7:ENST00000454250.7:c.1078-504G>C:p.(=); CHRNA7:ENST00000635884.1:c.695-504G>C:p.(=); CHRNA7:ENST00000636603.1:c.805-504G>C:p.(=); CHRNA7:ENST00000637033.1:c.805-504G>C:p.(=); CHRNA7:ENST00000637183.1:c.754-504G>C:p.(=)

Pathogenicity Data:: Best Score: 0.3307321; CADD: 0.331 (1.744)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32047480A>G [0|1] rs547476096 (variation viewer)

Variant score: 0.289

Transcripts:: CHRNA7:ENST00000306901.9:c.195+16443A>G:p.(=); CHRNA7:ENST00000454250.7:c.282+16443A>G:p.(=); CHRNA7:ENST00000635884.1:c.9+16443A>G:p.(=); CHRNA7:ENST00000636603.1:c.9+16443A>G:p.(=); CHRNA7:ENST00000637033.1:c.9+16443A>G:p.(=); CHRNA7:ENST00000637183.1:c.-42-53823A>G:p.(=)

Pathogenicity Data:: Best Score: 0.30673385; CADD: 0.307 (1.591)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1617%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.3497%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.2372%

INTERGENIC_VARIANT chr15:g.31957912C>A [0/1] rs143028325 (variation viewer)

Variant score: 0.235

Transcripts:: CHRNA7:ENST00000636603.1::; CHRNA7:ENST00000613847.1::

Pathogenicity Data:: Best Score: 0.31797546; CADD: 0.318 (1.662)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.5153%; UK10K: 0.9125%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.5664%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32059944CA>C [1/1] rs34200550 (variation viewer)

Variant score: 0.144

Transcripts:: CHRNA7:ENST00000306901.9:c.195+28908del:p.(=); CHRNA7:ENST00000454250.7:c.282+28908del:p.(=); CHRNA7:ENST00000635884.1:c.9+28908del:p.(=); CHRNA7:ENST00000636603.1:c.9+28908del:p.(=); CHRNA7:ENST00000637033.1:c.9+28908del:p.(=); CHRNA7:ENST00000637183.1:c.-42-41358del:p.(=)

Pathogenicity Data:: Best Score: 0.14375114; CADD: 0.144 (0.674)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32047484G>C [0|1] rs560903804 (variation viewer)

Variant score: 0.113

Transcripts:: CHRNA7:ENST00000306901.9:c.195+16447G>C:p.(=); CHRNA7:ENST00000454250.7:c.282+16447G>C:p.(=); CHRNA7:ENST00000635884.1:c.9+16447G>C:p.(=); CHRNA7:ENST00000636603.1:c.9+16447G>C:p.(=); CHRNA7:ENST00000637033.1:c.9+16447G>C:p.(=); CHRNA7:ENST00000637183.1:c.-42-53819G>C:p.(=)

Pathogenicity Data:: Best Score: 0.11955953; CADD: 0.120 (0.553)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1617%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3521%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.2366%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32114061C>CAT [-/1] rs35944403 (variation viewer)

Variant score: 0.103

Transcripts:: CHRNA7:ENST00000306901.9:c.350+2162_350+2163insAT:p.(=); CHRNA7:ENST00000454250.7:c.437+2162_437+2163insAT:p.(=); CHRNA7:ENST00000635884.1:c.164+2162_164+2163insAT:p.(=); CHRNA7:ENST00000636603.1:c.164+2162_164+2163insAT:p.(=); CHRNA7:ENST00000637033.1:c.164+2162_164+2163insAT:p.(=); CHRNA7:ENST00000637183.1:c.113+2162_113+2163insAT:p.(=)

Pathogenicity Data:: Best Score: 0.10339737; CADD: 0.103 (0.474)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32114061C>CACATAT [-/1] rs1555383701 (variation viewer)

Variant score: 0.095

Transcripts:: CHRNA7:ENST00000306901.9:c.350+2162_350+2163insACATAT:p.(=); CHRNA7:ENST00000454250.7:c.437+2162_437+2163insACATAT:p.(=); CHRNA7:ENST00000635884.1:c.164+2162_164+2163insACATAT:p.(=); CHRNA7:ENST00000636603.1:c.164+2162_164+2163insACATAT:p.(=); CHRNA7:ENST00000637033.1:c.164+2162_164+2163insACATAT:p.(=); CHRNA7:ENST00000637183.1:c.113+2162_113+2163insACATAT:p.(=)

Pathogenicity Data:: Best Score: 0.095309556; CADD: 0.095 (0.435)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.32031617G>A [0/1] rs529122749 (variation viewer)

Variant score: 0.072

Transcripts:: CHRNA7:ENST00000306901.9:c.195+580G>A:p.(=); CHRNA7:ENST00000454250.7:c.282+580G>A:p.(=); CHRNA7:ENST00000635884.1:c.9+580G>A:p.(=); CHRNA7:ENST00000636603.1:c.9+580G>A:p.(=); CHRNA7:ENST00000637033.1:c.9+580G>A:p.(=); CHRNA7:ENST00000637183.1:c.-43+53423G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0761531; CADD: 0.076 (0.344)

Frequency Data:: TOPMed: 0.1346%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.2267%

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.31986658G>* [-/1]

Variant score: 0.000

Transcripts:: CHRNA7:ENST00000636603.1:c.-132+20092G>*:p.(=); CHRNA7:ENST00000637183.1:c.-43+8464G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.31986659T>* [-/1]

Variant score: 0.000

Transcripts:: CHRNA7:ENST00000636603.1:c.-132+20093T>*:p.(=); CHRNA7:ENST00000637183.1:c.-43+8465T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PIK3R3

Exomiser Score: 0.648

Phenotype Score: 0.507

Variant Score: 0.939

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.648

Phenotype Score: 0.507

Variant Score: 0.939

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.46113934T>C [0|1] rs534952598 (variation viewer)

Variant score: 0.939 CONTRIBUTING VARIANT

Transcripts:: PIK3R3:ENST00000262741.10:c.106+17913A>G:p.(=); PIK3R3:ENST00000372006.5:c.106+17913A>G:p.(=); PIK3R3:ENST00000420542.5:c.106+17913A>G:p.(=); PIK3R3:ENST00000423209.5:c.106+17913A>G:p.(=); PIK3R3:ENST00000540385.2:c.245-33184A>G:p.(=)

Pathogenicity Data:: Best Score: 0.94466496; CADD: 0.945 (12.570)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0056%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.124

Phenotype Score: 0.507

Variant Score: 0.661

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.46113934T>C [0|1] rs534952598 (variation viewer)

Variant score: 0.939 CONTRIBUTING VARIANT

Transcripts:: PIK3R3:ENST00000262741.10:c.106+17913A>G:p.(=); PIK3R3:ENST00000372006.5:c.106+17913A>G:p.(=); PIK3R3:ENST00000420542.5:c.106+17913A>G:p.(=); PIK3R3:ENST00000423209.5:c.106+17913A>G:p.(=); PIK3R3:ENST00000540385.2:c.245-33184A>G:p.(=)

Pathogenicity Data:: Best Score: 0.94466496; CADD: 0.945 (12.570)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0056%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.46101718TG>T [0/1] rs537973990 (variation viewer)

Variant score: 0.382 CONTRIBUTING VARIANT

Transcripts:: PIK3R3:ENST00000262741.10:c.107-20969del:p.(=); PIK3R3:ENST00000372006.5:c.107-20969del:p.(=); PIK3R3:ENST00000420542.5:c.107-20969del:p.(=); PIK3R3:ENST00000423209.5:c.107-20969del:p.(=); PIK3R3:ENST00000540385.2:c.245-20969del:p.(=)

Pathogenicity Data:: Best Score: 0.3818413; CADD: 0.382 (2.089)

Frequency Data:: TOPMed: 0.0024%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.46071759A>C [1/1] rs190230436 (variation viewer)

Variant score: 0.634

Transcripts:: PIK3R3:ENST00000262741.10:c.315-4668T>G:p.(=); PIK3R3:ENST00000372006.5:c.315-4668T>G:p.(=); PIK3R3:ENST00000420542.5:c.315-4668T>G:p.(=); PIK3R3:ENST00000423209.5:c.315-4668T>G:p.(=); PIK3R3:ENST00000540385.2:c.453-4668T>G:p.(=)

Pathogenicity Data:: Best Score: 0.6338154; CADD: 0.634 (4.363)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.46087314T>TA [0/1] rs112363497 (variation viewer)

Variant score: 0.183

Transcripts:: PIK3R3:ENST00000262741.10:c.107-6565_107-6564insT:p.(=); PIK3R3:ENST00000372006.5:c.107-6565_107-6564insT:p.(=); PIK3R3:ENST00000420542.5:c.107-6565_107-6564insT:p.(=); PIK3R3:ENST00000423209.5:c.107-6565_107-6564insT:p.(=); PIK3R3:ENST00000540385.2:c.245-6565_245-6564insT:p.(=)

Pathogenicity Data:: Best Score: 0.20402396; CADD: 0.204 (0.991)

Frequency Data:: gnomAD_G_AFR: 0.2455%; gnomAD_G_AMR: 0.1901%; gnomAD_G_EAS: 0.1302%; gnomAD_G_FIN: 0.5591%; gnomAD_G_NFE: 0.3826%; gnomAD_G_OTH: 0.4274%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.46101980C>CTT [1/1] rs538688681 (variation viewer)

Variant score: 0.143

Transcripts:: PIK3R3:ENST00000262741.10:c.107-21231_107-21230insAA:p.(=); PIK3R3:ENST00000372006.5:c.107-21231_107-21230insAA:p.(=); PIK3R3:ENST00000420542.5:c.107-21231_107-21230insAA:p.(=); PIK3R3:ENST00000423209.5:c.107-21231_107-21230insAA:p.(=); PIK3R3:ENST00000540385.2:c.245-21231_245-21230insAA:p.(=)

Pathogenicity Data:: Best Score: 0.14296216; CADD: 0.143 (0.670)

Frequency Data:: No frequency data

AMD1

Exomiser Score: 0.638

Phenotype Score: 0.504

Variant Score: 0.938

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.638

Phenotype Score: 0.504

Variant Score: 0.938

Variants contributing to score:

REGULATORY_REGION_VARIANT chr6:g.110934109T>C [0/1] rs996355123 (variation viewer)

Variant score: 0.938 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.9412511; CADD: 0.941 (12.310)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_NFE: 0.0267%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.617

Phenotype Score: 0.504

Variant Score: 0.928

Variants contributing to score:

REGULATORY_REGION_VARIANT chr6:g.110934109T>C [0/1] rs996355123 (variation viewer)

Variant score: 0.938 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.9412511; CADD: 0.941 (12.310)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.110886935C>T [0/1] rs1048766008 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: AMD1:ENST00000368882.8:c.111-570C>T:p.(=); AMD1:ENST00000368885.8:c.111-570C>T:p.(=); AMD1:ENST00000672937.2:c.111-570C>T:p.(=); AMD1:ENST00000368876.2:c.-97-570C>T:p.(=); AMD1:ENST00000368877.9:c.-10-1922C>T:p.(=)

Pathogenicity Data:: Best Score: 0.922017; CADD: 0.922 (11.080)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_NFE: 0.0266%

Other passed variants:

INTERGENIC_VARIANT chr6:g.110917099C>T [0/1] rs182201838 (variation viewer)

Variant score: 0.672

Transcripts:: AMD1:ENST00000672937.2::; AMD1:ENST00000402967.1::

Pathogenicity Data:: Best Score: 0.6742383; CADD: 0.674 (4.871)

Frequency Data:: TOPMed: 0.0151%; gnomAD_G_NFE: 0.0267%

THREE_PRIME_UTR_EXON_VARIANT chr6:g.110897563C>T [0/1] rs1038137988 (variation viewer)

Variant score: 0.412

Transcripts:: AMD1:ENST00000672937.2:c.*3563C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4130515; CADD: 0.413 (2.314)

Frequency Data:: TOPMed: 0.0167%; gnomAD_G_NFE: 0.0267%

INTERGENIC_VARIANT chr6:g.110914812C>T [0/1] rs897677029 (variation viewer)

Variant score: 0.236

Transcripts:: AMD1:ENST00000672937.2::; AMD1:ENST00000402967.1::

Pathogenicity Data:: Best Score: 0.23563641; CADD: 0.236 (1.167)

Frequency Data:: TOPMed: 0.0040%

INTERGENIC_VARIANT chr6:g.110911832T>TAA [-/1] rs200819688 (variation viewer)

Variant score: 0.232

Transcripts:: AMD1:ENST00000672937.2::; AMD1:ENST00000402967.1::

Pathogenicity Data:: Best Score: 0.23669165; CADD: 0.237 (1.173)

Frequency Data:: gnomAD_G_AFR: 0.0262%; gnomAD_G_EAS: 0.1309%; gnomAD_G_NFE: 0.0243%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.110888457G>C [0/1] rs957507660 (variation viewer)

Variant score: 0.226

Transcripts:: AMD1:ENST00000368882.8:c.198-400G>C:p.(=); AMD1:ENST00000368885.8:c.198-400G>C:p.(=); AMD1:ENST00000672937.2:c.198-400G>C:p.(=); AMD1:ENST00000368876.2:c.-10-400G>C:p.(=); AMD1:ENST00000368877.9:c.-10-400G>C:p.(=)

Pathogenicity Data:: Best Score: 0.22714144; CADD: 0.227 (1.119)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_NFE: 0.0268%

JAK2

Exomiser Score: 0.632

Phenotype Score: 0.519

Variant Score: 0.919

Phenotype matches:

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:133100 Erythrocytosis, somatic - autosomal dominant; OMIM:254450 Myelofibrosis, somatic - somatic; OMIM:263300 Polycythemia vera, somatic - autosomal dominant; OMIM:600880 Budd-Chiari syndrome, somatic (susceptibility); OMIM:601626 Leukemia, acute myeloid, somatic - autosomal dominant; OMIM:614521 Thrombocythemia 3 - autosomal dominant; ORPHA:131 Budd-Chiari syndrome; ORPHA:3318 Essential thrombocythemia; ORPHA:71493 Familial thrombocytosis; ORPHA:729 Polycythemia vera; ORPHA:824 Primary myelofibrosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.632

Phenotype Score: 0.519

Variant Score: 0.919

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.5003551T>G [0/1]

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: JAK2:ENST00000381652.3:c.-26+17529T>G:p.(=)

Pathogenicity Data:: Best Score: 0.9187169; CADD: 0.919 (10.900)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.148

Phenotype Score: 0.519

Variant Score: 0.669

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.5003551T>G [0/1]

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: JAK2:ENST00000381652.3:c.-26+17529T>G:p.(=)

Pathogenicity Data:: Best Score: 0.9187169; CADD: 0.919 (10.900)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.5089537C>CA [0/1] rs58042774 (variation viewer)

Variant score: 0.419 CONTRIBUTING VARIANT

Transcripts:: JAK2:ENST00000381652.3:c.2572-137_2572-136insA:p.(=)

Pathogenicity Data:: Best Score: 0.4192356; CADD: 0.419 (2.360)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.5059593T>C [0/1] rs528690953 (variation viewer)

Variant score: 0.355

Transcripts:: JAK2:ENST00000381652.3:c.1056+3805T>C:p.(=)

Pathogenicity Data:: Best Score: 0.37683934; CADD: 0.377 (2.054)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1633%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.2069%

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.5018541G>T [0/1] rs1030062108 (variation viewer)

Variant score: 0.263

Transcripts:: JAK2:ENST00000381652.3:c.-25-3422G>T:p.(=)

Pathogenicity Data:: Best Score: 0.26328415; CADD: 0.263 (1.327)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.5062500T>TA [1/1] rs58424625 (variation viewer)

Variant score: 0.177

Transcripts:: JAK2:ENST00000381652.3:c.1057-2383_1057-2382insA:p.(=)

Pathogenicity Data:: Best Score: 0.17699969; CADD: 0.177 (0.846)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.5125534TAAGTAA>T [0/1] rs202087693 (variation viewer)

Variant score: 0.156

Transcripts:: JAK2:ENST00000381652.3:c.3178-798_3178-793del:p.(=); JAK2:ENST00000649639.1:c.*11-1029_*11-1024del:p.(=)

Pathogenicity Data:: Best Score: 0.26616234; CADD: 0.266 (1.344)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.9716%; UK10K: 1.0182%; gnomAD_G_AFR: 0.8712%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.1238%; gnomAD_G_FIN: 0.4394%; gnomAD_G_NFE: 1.4014%; gnomAD_G_OTH: 1.2295%

THREE_PRIME_UTR_EXON_VARIANT chr9:g.5128083TG>T [0|1]

Variant score: 0.155

Transcripts:: JAK2:ENST00000381652.3:c.*1293del:p.(=); JAK2:ENST00000649639.1:c.*11-3573del:p.(=)

Pathogenicity Data:: Best Score: 0.15957296; CADD: 0.160 (0.755)

Frequency Data:: gnomAD_G_NFE: 0.0340%; gnomAD_G_OTH: 0.1736%

THREE_PRIME_UTR_EXON_VARIANT chr9:g.5128081TG>T [-/1] rs1312009021 (variation viewer)

Variant score: 0.117

Transcripts:: JAK2:ENST00000381652.3:c.*1291del:p.(=); JAK2:ENST00000649639.1:c.*11-3571del:p.(=)

Pathogenicity Data:: Best Score: 0.1743424; CADD: 0.174 (0.832)

Frequency Data:: gnomAD_G_EAS: 1.2367%; gnomAD_G_NFE: 0.0266%; gnomAD_G_OTH: 0.1449%

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.5021421G>A [0/1] rs184211496 (variation viewer)

Variant score: 0.034

Transcripts:: JAK2:ENST00000381652.3:c.-25-542G>A:p.(=)

Pathogenicity Data:: Best Score: 0.034616232; CADD: 0.035 (0.153)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1195%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.1200%; gnomAD_G_OTH: 0.2037%

THREE_PRIME_UTR_EXON_VARIANT chr9:g.5128081TG>* [-/1]

Variant score: 0.000

Transcripts:: JAK2:ENST00000381652.3:c.*1290_*1291delTGins*:p.(=); JAK2:ENST00000649639.1:c.*11-3571_*11-3570delCAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AKAP7

Exomiser Score: 0.616

Phenotype Score: 0.506

Variant Score: 0.925

Phenotype matches:

Proximity score 0.506 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.616

Phenotype Score: 0.506

Variant Score: 0.925

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.131137869A>G [0/1] rs775317548 (variation viewer)

Variant score: 0.925 CONTRIBUTING VARIANT

Transcripts:: AKAP7:ENST00000431975.7:c.19+2087A>G:p.(=); AKAP7:ENST00000541650.5:c.19+2087A>G:p.(=)

Pathogenicity Data:: Best Score: 0.92969275; CADD: 0.930 (11.530)

Frequency Data:: TOPMed: 0.0167%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0333%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.279

Phenotype Score: 0.506

Variant Score: 0.771

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.131137869A>G [0/1] rs775317548 (variation viewer)

Variant score: 0.925 CONTRIBUTING VARIANT

Transcripts:: AKAP7:ENST00000431975.7:c.19+2087A>G:p.(=); AKAP7:ENST00000541650.5:c.19+2087A>G:p.(=)

Pathogenicity Data:: Best Score: 0.92969275; CADD: 0.930 (11.530)

Frequency Data:: TOPMed: 0.0167%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0333%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.131223236G>A [0/1]

Variant score: 0.616 CONTRIBUTING VARIANT

Transcripts:: AKAP7:ENST00000263050.3:c.58+3428G>A:p.(=); AKAP7:ENST00000431975.7:c.850+3428G>A:p.(=); AKAP7:ENST00000537868.5:c.58+3428G>A:p.(=); AKAP7:ENST00000541650.5:c.847+3428G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6160276; CADD: 0.616 (4.157)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr6:g.131299166G>A [0/1] rs145023873 (variation viewer)

Variant score: 0.102

Transcripts:: AKAP7:ENST00000263050.3::; AKAP7:ENST00000402896.2::

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: TOPMed: 0.3249%; gnomAD_G_AFR: 0.0689%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_FIN: 0.2294%; gnomAD_G_NFE: 0.3617%; gnomAD_G_OTH: 0.5123%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.131247269G>GTATATA [0/1] rs60033504 (variation viewer)

Variant score: 0.095

Transcripts:: AKAP7:ENST00000263050.3:c.58+27461_58+27462insTATATA:p.(=); AKAP7:ENST00000431975.7:c.850+27461_850+27462insTATATA:p.(=); AKAP7:ENST00000537868.5:c.58+27461_58+27462insTATATA:p.(=); AKAP7:ENST00000541650.5:c.847+27461_847+27462insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.09468442; CADD: 0.095 (0.432)

Frequency Data:: No frequency data

PRKAR2A

Exomiser Score: 0.613

Phenotype Score: 0.507

Variant Score: 0.923

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.613

Phenotype Score: 0.507

Variant Score: 0.923

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48778105T>G [0/1]

Variant score: 0.923 CONTRIBUTING VARIANT

Transcripts:: PRKAR2A:ENST00000265563.13:c.542+4881A>C:p.(=); PRKAR2A:ENST00000296446.12:c.542+4881A>C:p.(=); PRKAR2A:ENST00000454963.5:c.542+4881A>C:p.(=)

Pathogenicity Data:: Best Score: 0.92326385; CADD: 0.923 (11.150)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.568

Phenotype Score: 0.507

Variant Score: 0.903

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48778105T>G [0/1]

Variant score: 0.923 CONTRIBUTING VARIANT

Transcripts:: PRKAR2A:ENST00000265563.13:c.542+4881A>C:p.(=); PRKAR2A:ENST00000296446.12:c.542+4881A>C:p.(=); PRKAR2A:ENST00000454963.5:c.542+4881A>C:p.(=)

Pathogenicity Data:: Best Score: 0.92326385; CADD: 0.923 (11.150)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr3:g.48748586G>C [0/1] rs1425454960 (variation viewer)

Variant score: 0.883 CONTRIBUTING VARIANT

Transcripts:: PRKAR2A:ENST00000265563.13:c.*2999C>G:p.(=); PRKAR2A:ENST00000454963.5:c.*1-646C>G:p.(=)

Pathogenicity Data:: Best Score: 0.8841756; CADD: 0.884 (9.362)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48809430A>C [0/1] rs1292017099 (variation viewer)

Variant score: 0.784

Transcripts:: PRKAR2A:ENST00000265563.13:c.263-1746T>G:p.(=); PRKAR2A:ENST00000296446.12:c.263-1746T>G:p.(=); PRKAR2A:ENST00000454963.5:c.263-1746T>G:p.(=)

Pathogenicity Data:: Best Score: 0.78447384; CADD: 0.784 (6.665)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48776837T>C [0/1] rs575890762 (variation viewer)

Variant score: 0.524

Transcripts:: PRKAR2A:ENST00000265563.13:c.543-3729A>G:p.(=); PRKAR2A:ENST00000296446.12:c.543-3729A>G:p.(=); PRKAR2A:ENST00000454963.5:c.543-3729A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6802578; CADD: 0.680 (4.952)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.2509%; UK10K: 0.3703%; gnomAD_G_AFR: 0.0688%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.2334%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48841543CA>C [1/1] rs397874491 (variation viewer)

Variant score: 0.515

Transcripts:: PRKAR2A:ENST00000265563.13:c.262+5791del:p.(=); PRKAR2A:ENST00000296446.12:c.262+5791del:p.(=); PRKAR2A:ENST00000454963.5:c.262+5791del:p.(=)

Pathogenicity Data:: Best Score: 0.5149349; CADD: 0.515 (3.142)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr3:g.48750595G>A [0/1] rs186656212 (variation viewer)

Variant score: 0.485

Transcripts:: PRKAR2A:ENST00000265563.13:c.*990C>T:p.(=); PRKAR2A:ENST00000296446.12:c.*990C>T:p.(=); PRKAR2A:ENST00000454963.5:c.1215+990C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6293193; CADD: 0.629 (4.310)

Frequency Data:: TOPMed: 0.2493%; UK10K: 0.3835%; gnomAD_G_AFR: 0.0687%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.2265%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48835235T>C [0/1] rs1009592845 (variation viewer)

Variant score: 0.409

Transcripts:: PRKAR2A:ENST00000265563.13:c.262+12100A>G:p.(=); PRKAR2A:ENST00000296446.12:c.262+12100A>G:p.(=); PRKAR2A:ENST00000454963.5:c.262+12100A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4092551; CADD: 0.409 (2.286)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48821674T>G [0/1] rs764538994 (variation viewer)

Variant score: 0.216

Transcripts:: PRKAR2A:ENST00000265563.13:c.263-13990A>C:p.(=); PRKAR2A:ENST00000296446.12:c.263-13990A>C:p.(=); PRKAR2A:ENST00000454963.5:c.263-13990A>C:p.(=)

Pathogenicity Data:: Best Score: 0.28038538; CADD: 0.280 (1.429)

Frequency Data:: TOPMed: 0.1824%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0459%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1869%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48763739C>A [0/1] rs78088158 (variation viewer)

Variant score: 0.171

Transcripts:: PRKAR2A:ENST00000265563.13:c.873+1265G>T:p.(=); PRKAR2A:ENST00000296446.12:c.873+1265G>T:p.(=); PRKAR2A:ENST00000454963.5:c.873+1265G>T:p.(=)

Pathogenicity Data:: Best Score: 0.27272278; CADD: 0.273 (1.383)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.5559%; UK10K: 0.7273%; gnomAD_G_AFR: 0.1488%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.2879%; gnomAD_G_NFE: 0.7468%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.48829847G>GTGTATATATATA [0/1] rs777532795 (variation viewer)

Variant score: 0.109

Transcripts:: PRKAR2A:ENST00000265563.13:c.262+17487_262+17488insTATATATATACA:p.(=); PRKAR2A:ENST00000296446.12:c.262+17487_262+17488insTATATATATACA:p.(=); PRKAR2A:ENST00000454963.5:c.262+17487_262+17488insTATATATATACA:p.(=)

Pathogenicity Data:: Best Score: 0.10895425; CADD: 0.109 (0.501)

Frequency Data:: No frequency data

CCND3

Exomiser Score: 0.610

Phenotype Score: 0.510

Variant Score: 0.919

Phenotype matches:

Proximity score 0.510 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.610

Phenotype Score: 0.510

Variant Score: 0.919

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41992238T>C [0|1] rs1446421736 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: CCND3:ENST00000372988.8:c.-45-51653A>G:p.(=); CCND3:ENST00000415497.6:c.-174-54844A>G:p.(=); CCND3:ENST00000510503.5:c.-45-51653A>G:p.(=); CCND3:ENST00000511642.5:c.-45-51653A>G:p.(=); CCND3:ENST00000616010.4:c.-175+37771A>G:p.(=)

Pathogenicity Data:: Best Score: 0.91852957; CADD: 0.919 (10.890)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.491

Phenotype Score: 0.510

Variant Score: 0.866

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41992238T>C [0|1] rs1446421736 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: CCND3:ENST00000372988.8:c.-45-51653A>G:p.(=); CCND3:ENST00000415497.6:c.-174-54844A>G:p.(=); CCND3:ENST00000510503.5:c.-45-51653A>G:p.(=); CCND3:ENST00000511642.5:c.-45-51653A>G:p.(=); CCND3:ENST00000616010.4:c.-175+37771A>G:p.(=)

Pathogenicity Data:: Best Score: 0.91852957; CADD: 0.919 (10.890)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41942687C>T [0/1] rs190266656 (variation viewer)

Variant score: 0.813 CONTRIBUTING VARIANT

Transcripts:: CCND3:ENST00000372988.8:c.-45-2102G>A:p.(=); CCND3:ENST00000415497.6:c.-174-5293G>A:p.(=); CCND3:ENST00000510503.5:c.-45-2102G>A:p.(=); CCND3:ENST00000511642.5:c.-45-2102G>A:p.(=); CCND3:ENST00000616010.4:c.-174-5293G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9140986; CADD: 0.914 (10.660)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.1871%; UK10K: 0.2116%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.5981%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.1601%; gnomAD_G_OTH: 0.4073%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41965058CTTTTTTTT>C [-/1] rs56138276 (variation viewer)

Variant score: 0.801

Transcripts:: CCND3:ENST00000372988.8:c.-45-24481_-45-24474del:p.(=); CCND3:ENST00000415497.6:c.-174-27672_-174-27665del:p.(=); CCND3:ENST00000510503.5:c.-45-24481_-45-24474del:p.(=); CCND3:ENST00000511642.5:c.-45-24481_-45-24474del:p.(=); CCND3:ENST00000616010.4:c.-174-27672_-174-27665del:p.(=)

Pathogenicity Data:: Best Score: 0.80074924; CADD: 0.801 (7.006)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.42036866T>C [0/1] rs572582922 (variation viewer)

Variant score: 0.740

Transcripts:: CCND3:ENST00000372988.8:c.-46+11635A>G:p.(=); CCND3:ENST00000415497.6:c.-175+11635A>G:p.(=); CCND3:ENST00000510503.5:c.-46+11635A>G:p.(=); CCND3:ENST00000511642.5:c.-46+12785A>G:p.(=); CCND3:ENST00000616010.4:c.-356-6676A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7853159; CADD: 0.785 (6.682)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1609%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.3580%; gnomAD_G_NFE: 0.1466%; gnomAD_G_OTH: 0.1018%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41985864C>G [1|1] rs55831029 (variation viewer)

Variant score: 0.414

Transcripts:: CCND3:ENST00000372988.8:c.-45-45279G>C:p.(=); CCND3:ENST00000415497.6:c.-174-48470G>C:p.(=); CCND3:ENST00000510503.5:c.-45-45279G>C:p.(=); CCND3:ENST00000511642.5:c.-45-45279G>C:p.(=); CCND3:ENST00000616010.4:c.-175+44145G>C:p.(=)

Pathogenicity Data:: Best Score: 0.4141317; CADD: 0.414 (2.322)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.41934729A>C [0/1] rs3218111 (variation viewer)

Variant score: 0.351

Transcripts:: CCND3:ENST00000372991.8::; CCND3:ENST00000230340.9::

Pathogenicity Data:: Best Score: 0.35716426; CADD: 0.357 (1.919)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0653%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0667%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41977923C>G [0/1] rs182913055 (variation viewer)

Variant score: 0.235

Transcripts:: CCND3:ENST00000372988.8:c.-45-37338G>C:p.(=); CCND3:ENST00000415497.6:c.-174-40529G>C:p.(=); CCND3:ENST00000510503.5:c.-45-37338G>C:p.(=); CCND3:ENST00000511642.5:c.-45-37338G>C:p.(=); CCND3:ENST00000616010.4:c.-174-40529G>C:p.(=)

Pathogenicity Data:: Best Score: 0.237921; CADD: 0.238 (1.180)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0645%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0533%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41951575C>A [1/1] rs71544447 (variation viewer)

Variant score: 0.232

Transcripts:: CCND3:ENST00000372988.8:c.-45-10990G>T:p.(=); CCND3:ENST00000415497.6:c.-174-14181G>T:p.(=); CCND3:ENST00000510503.5:c.-45-10990G>T:p.(=); CCND3:ENST00000511642.5:c.-45-10990G>T:p.(=); CCND3:ENST00000616010.4:c.-174-14181G>T:p.(=)

Pathogenicity Data:: Best Score: 0.23228502; CADD: 0.232 (1.148)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41980010T>TCACACACACACACACACA [1/1] rs58375638 (variation viewer)

Variant score: 0.219

Transcripts:: CCND3:ENST00000372988.8:c.-45-39426_-45-39425insTGTGTGTGTGTGTGTGTG:p.(=); CCND3:ENST00000415497.6:c.-174-42617_-174-42616insTGTGTGTGTGTGTGTGTG:p.(=); CCND3:ENST00000510503.5:c.-45-39426_-45-39425insTGTGTGTGTGTGTGTGTG:p.(=); CCND3:ENST00000511642.5:c.-45-39426_-45-39425insTGTGTGTGTGTGTGTGTG:p.(=); CCND3:ENST00000616010.4:c.-174-42617_-174-42616insTGTGTGTGTGTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.21909177; CADD: 0.219 (1.074)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41985867G>A [1|1] rs183058422 (variation viewer)

Variant score: 0.218

Transcripts:: CCND3:ENST00000372988.8:c.-45-45282C>T:p.(=); CCND3:ENST00000415497.6:c.-174-48473C>T:p.(=); CCND3:ENST00000510503.5:c.-45-45282C>T:p.(=); CCND3:ENST00000511642.5:c.-45-45282C>T:p.(=); CCND3:ENST00000616010.4:c.-175+44142C>T:p.(=)

Pathogenicity Data:: Best Score: 0.21765196; CADD: 0.218 (1.066)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.42000234C>CTTTT [-/1] rs70987562 (variation viewer)

Variant score: 0.173

Transcripts:: CCND3:ENST00000372988.8:c.-46+48266_-46+48267insAAAA:p.(=); CCND3:ENST00000415497.6:c.-175+48266_-175+48267insAAAA:p.(=); CCND3:ENST00000510503.5:c.-46+48266_-46+48267insAAAA:p.(=); CCND3:ENST00000511642.5:c.-46+49416_-46+49417insAAAA:p.(=); CCND3:ENST00000616010.4:c.-175+29774_-175+29775insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.1732009; CADD: 0.173 (0.826)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.42000234C>CTTTTTTTT [-/1] rs70987562 (variation viewer)

Variant score: 0.161

Transcripts:: CCND3:ENST00000372988.8:c.-46+48266_-46+48267insAAAAAAAA:p.(=); CCND3:ENST00000415497.6:c.-175+48266_-175+48267insAAAAAAAA:p.(=); CCND3:ENST00000510503.5:c.-46+48266_-46+48267insAAAAAAAA:p.(=); CCND3:ENST00000511642.5:c.-46+49416_-46+49417insAAAAAAAA:p.(=); CCND3:ENST00000616010.4:c.-175+29774_-175+29775insAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.16073328; CADD: 0.161 (0.761)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.41934788A>G [0/1] rs144960851 (variation viewer)

Variant score: 0.135

Transcripts:: CCND3:ENST00000372991.8::; CCND3:ENST00000230340.9::

Pathogenicity Data:: Best Score: 0.57713664; CADD: 0.577 (3.738)

Frequency Data:: 1000Genomes: 1.8970%; TOPMed: 0.8529%; UK10K: 0.2645%; gnomAD_G_AFR: 1.7518%; gnomAD_G_AMR: 0.7160%; gnomAD_G_EAS: 0.1233%; gnomAD_G_NFE: 0.1799%; gnomAD_G_OTH: 1.0183%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41954250TAAAAAA>T [1/1] rs34556754 (variation viewer)

Variant score: 0.117

Transcripts:: CCND3:ENST00000372988.8:c.-45-13671_-45-13666del:p.(=); CCND3:ENST00000415497.6:c.-174-16862_-174-16857del:p.(=); CCND3:ENST00000510503.5:c.-45-13671_-45-13666del:p.(=); CCND3:ENST00000511642.5:c.-45-13671_-45-13666del:p.(=); CCND3:ENST00000616010.4:c.-174-16862_-174-16857del:p.(=)

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41990660ATTTTTTTTTT>A [1/1] rs67939325 (variation viewer)

Variant score: 0.106

Transcripts:: CCND3:ENST00000372988.8:c.-45-50085_-45-50076del:p.(=); CCND3:ENST00000415497.6:c.-174-53276_-174-53267del:p.(=); CCND3:ENST00000510503.5:c.-45-50085_-45-50076del:p.(=); CCND3:ENST00000511642.5:c.-45-50085_-45-50076del:p.(=); CCND3:ENST00000616010.4:c.-175+39339_-175+39348del:p.(=)

Pathogenicity Data:: Best Score: 0.10587138; CADD: 0.106 (0.486)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41957981T>C [0/1] rs180673743 (variation viewer)

Variant score: 0.064

Transcripts:: CCND3:ENST00000372988.8:c.-45-17396A>G:p.(=); CCND3:ENST00000415497.6:c.-174-20587A>G:p.(=); CCND3:ENST00000510503.5:c.-45-17396A>G:p.(=); CCND3:ENST00000511642.5:c.-45-17396A>G:p.(=); CCND3:ENST00000616010.4:c.-174-20587A>G:p.(=)

Pathogenicity Data:: Best Score: 0.07252973; CADD: 0.073 (0.327)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.1887%; gnomAD_G_AFR: 0.0818%; gnomAD_G_AMR: 0.6266%; gnomAD_G_EAS: 0.0627%; gnomAD_G_NFE: 0.1632%; gnomAD_G_OTH: 0.4283%

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41972240AAAAAG>* [-/1]

Variant score: 0.000

Transcripts:: CCND3:ENST00000372988.8:c.-45-31660_-45-31655delCTTTTTins:p.(=); CCND3:ENST00000415497.6:c.-174-34851_-174-34846delCTTTTTins:p.(=); CCND3:ENST00000510503.5:c.-45-31660_-45-31655delCTTTTTins:p.(=); CCND3:ENST00000511642.5:c.-45-31660_-45-31655delCTTTTTins:p.(=); CCND3:ENST00000616010.4:c.-174-34851_-174-34846delCTTTTTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41987505CTCTCTCTCTCTCTGTGTGTGTGTGTGTGTG>* [-/1]

Variant score: 0.000

Transcripts:: CCND3:ENST00000372988.8:c.-45-46950_-45-46920delCACACACACACACACACAGAGAGAGAGAGAGins:p.(=); CCND3:ENST00000415497.6:c.-174-50141_-174-50111delCACACACACACACACACAGAGAGAGAGAGAGins:p.(=); CCND3:ENST00000510503.5:c.-45-46950_-45-46920delCACACACACACACACACAGAGAGAGAGAGAGins:p.(=); CCND3:ENST00000511642.5:c.-45-46950_-45-46920delCACACACACACACACACAGAGAGAGAGAGAGins:p.(=); CCND3:ENST00000616010.4:c.-175+42474_-175+42504delCACACACACACACACACAGAGAGAGAGAGAGins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.41996146TG>* [-/1]

Variant score: 0.000

Transcripts:: CCND3:ENST00000372988.8:c.-46+52354_-46+52355delCAins:p.(=); CCND3:ENST00000415497.6:c.-175+52354_-175+52355delCAins:p.(=); CCND3:ENST00000510503.5:c.-46+52354_-46+52355delCAins:p.(=); CCND3:ENST00000511642.5:c.-46+53504_-46+53505delCAins:p.(=); CCND3:ENST00000616010.4:c.-175+33862_-175+33863delCAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.42024415T>* [-/1]

Variant score: 0.000

Transcripts:: CCND3:ENST00000372988.8:c.-46+24086A>:p.(=); CCND3:ENST00000415497.6:c.-175+24086A>:p.(=); CCND3:ENST00000510503.5:c.-46+24086A>:p.(=); CCND3:ENST00000511642.5:c.-46+25236A>:p.(=); CCND3:ENST00000616010.4:c.-175+5594A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MMP2

Exomiser Score: 0.605

Phenotype Score: 0.502

Variant Score: 0.925

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:259600 Multicentric osteolysis, nodulosis, and arthropathy - autosomal recessive; ORPHA:371428 Multicentric osteolysis-nodulosis-arthropathy spectrum

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.086

Phenotype Score: 0.251

Variant Score: 0.905

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55434040C>T [0/1] rs540190828 (variation viewer)

Variant score: 0.905 CONTRIBUTING VARIANT

Transcripts:: MMP2:ENST00000570308.5:c.-349-30512C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9108749; CADD: 0.911 (10.500)

Frequency Data:: TOPMed: 0.0311%; UK10K: 0.0264%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0466%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.605

Phenotype Score: 0.502

Variant Score: 0.925

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55429293G>T [0/1] rs181311021 (variation viewer)

Variant score: 0.946 CONTRIBUTING VARIANT

Transcripts:: MMP2:ENST00000570308.5:c.-349-35259G>T:p.(=)

Pathogenicity Data:: Best Score: 0.9939744; CADD: 0.994 (22.200)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1744%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0917%; gnomAD_G_FIN: 0.2582%; gnomAD_G_NFE: 0.2266%; gnomAD_G_OTH: 0.3061%

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55434040C>T [0/1] rs540190828 (variation viewer)

Variant score: 0.905 CONTRIBUTING VARIANT

Transcripts:: MMP2:ENST00000570308.5:c.-349-30512C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9108749; CADD: 0.911 (10.500)

Frequency Data:: TOPMed: 0.0311%; UK10K: 0.0264%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0466%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55417641C>G [0/1] rs777791339 (variation viewer)

Variant score: 0.344

Transcripts:: MMP2:ENST00000570308.5:c.-350+27606C>G:p.(=)

Pathogenicity Data:: Best Score: 0.35479164; CADD: 0.355 (1.903)

Frequency Data:: TOPMed: 0.1043%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0688%; gnomAD_G_FIN: 0.1147%; gnomAD_G_NFE: 0.1603%; gnomAD_G_OTH: 0.2037%

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55469264G>A [0/1]

Variant score: 0.292

Transcripts:: MMP2:ENST00000570308.5:c.-76+4439G>A:p.(=)

Pathogenicity Data:: Best Score: 0.29189116; CADD: 0.292 (1.499)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55427624G>GGGGAGAGAGAGAGA [0/1] rs376397721 (variation viewer)

Variant score: 0.274

Transcripts:: MMP2:ENST00000570308.5:c.-349-36928_-349-36927insGGGAGAGAGAGAGA:p.(=)

Pathogenicity Data:: Best Score: 0.2740612; CADD: 0.274 (1.391)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.55500494T>TACACACACAC [-/1] rs55996787 (variation viewer)

Variant score: 0.211

Transcripts:: MMP2:ENST00000219070.9:c.1769+2046_1769+2047insACACACACAC:p.(=); MMP2:ENST00000437642.6:c.1619+2046_1619+2047insACACACACAC:p.(=); MMP2:ENST00000543485.5:c.1541+2046_1541+2047insACACACACAC:p.(=); MMP2:ENST00000570308.5:c.1541+2046_1541+2047insACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.21077651; CADD: 0.211 (1.028)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55461810GTTTCTTTC>G [-/1] rs3040194 (variation viewer)

Variant score: 0.200

Transcripts:: MMP2:ENST00000570308.5:c.-349-2741_-349-2734del:p.(=)

Pathogenicity Data:: Best Score: 0.19998157; CADD: 0.200 (0.969)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55468675C>A [-/1] rs837544 (variation viewer)

Variant score: 0.074

Transcripts:: MMP2:ENST00000570308.5:c.-76+3850C>A:p.(=)

Pathogenicity Data:: Best Score: 0.07679105; CADD: 0.077 (0.347)

Frequency Data:: UK10K: 0.2380%; gnomAD_G_AFR: 0.0805%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.1670%; gnomAD_G_OTH: 0.2041%

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55461810G>GTTTCTTTCTTTCTTTC [-/1] rs3040194 (variation viewer)

Variant score: 0.055

Transcripts:: MMP2:ENST00000570308.5:c.-349-2742_-349-2741insTTTCTTTCTTTCTTTC:p.(=)

Pathogenicity Data:: Best Score: 0.055286765; CADD: 0.055 (0.247)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.55435765C>T [0/1] rs189544421 (variation viewer)

Variant score: 0.022

Transcripts:: MMP2:ENST00000570308.5:c.-349-28787C>T:p.(=)

Pathogenicity Data:: Best Score: 0.022762775; CADD: 0.023 (0.100)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1800%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0801%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 0.2197%; gnomAD_G_OTH: 0.3055%

MARK1

Exomiser Score: 0.601

Phenotype Score: 0.501

Variant Score: 0.924

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.601

Phenotype Score: 0.501

Variant Score: 0.924

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr1:g.220525070A>G [0/1] rs926961177 (variation viewer)

Variant score: 0.924 CONTRIBUTING VARIANT

Transcripts:: MARK1:ENST00000402574.5::; MARK1:ENST00000457142.1::

Pathogenicity Data:: Best Score: 0.9275564; CADD: 0.928 (11.400)

Frequency Data:: TOPMed: 0.0239%; gnomAD_G_NFE: 0.0267%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.051

Phenotype Score: 0.501

Variant Score: 0.561

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr1:g.220525070A>G [0/1] rs926961177 (variation viewer)

Variant score: 0.924 CONTRIBUTING VARIANT

Transcripts:: MARK1:ENST00000402574.5::; MARK1:ENST00000457142.1::

Pathogenicity Data:: Best Score: 0.9275564; CADD: 0.928 (11.400)

Frequency Data:: TOPMed: 0.0239%; gnomAD_G_NFE: 0.0267%

INTERGENIC_VARIANT chr1:g.220520723G>A [0/1] rs1018247476 (variation viewer)

Variant score: 0.198 CONTRIBUTING VARIANT

Transcripts:: MARK1:ENST00000402574.5::; MARK1:ENST00000457142.1::

Pathogenicity Data:: Best Score: 0.19887555; CADD: 0.199 (0.963)

Frequency Data:: TOPMed: 0.0207%; gnomAD_G_NFE: 0.0200%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.220556485C>CA [1/1] rs55808704 (variation viewer)

Variant score: 0.145

Transcripts:: MARK1:ENST00000366917.5:c.52-22869_52-22868insA:p.(=); MARK1:ENST00000366918.8:c.52-22869_52-22868insA:p.(=); MARK1:ENST00000402574.5:c.52-22869_52-22868insA:p.(=); MARK1:ENST00000611084.4:c.52-22869_52-22868insA:p.(=)

Pathogenicity Data:: Best Score: 0.14473641; CADD: 0.145 (0.679)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.220622152GT>G [0/1] rs559820463 (variation viewer)

Variant score: 0.067

Transcripts:: MARK1:ENST00000366917.5:c.909+3398del:p.(=); MARK1:ENST00000366918.8:c.843+3398del:p.(=); MARK1:ENST00000402574.5:c.909+3398del:p.(=); MARK1:ENST00000611084.4:c.909+3398del:p.(=)

Pathogenicity Data:: Best Score: 0.08735895; CADD: 0.087 (0.397)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.7876%; UK10K: 0.8728%; gnomAD_G_AFR: 0.2757%; gnomAD_G_AMR: 0.7212%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.1739%; gnomAD_G_NFE: 1.0165%; gnomAD_G_OTH: 0.3093%

ATM

Exomiser Score: 0.595

Phenotype Score: 0.503

Variant Score: 0.919

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:114480 Breast cancer, susceptibility to (susceptibility); OMIM:208900 Ataxia-telangiectasia - autosomal recessive; ORPHA:100 Ataxia-telangiectasia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.595

Phenotype Score: 0.503

Variant Score: 0.919

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108277851T>C [0/1] rs1004214237 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: ATM:ENST00000278616.8:c.3285-1640T>C:p.(=); ATM:ENST00000452508.6:c.3285-1640T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9218372; CADD: 0.922 (11.070)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.409

Phenotype Score: 0.503

Variant Score: 0.837

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108277851T>C [0/1] rs1004214237 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: ATM:ENST00000278616.8:c.3285-1640T>C:p.(=); ATM:ENST00000452508.6:c.3285-1640T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9218372; CADD: 0.922 (11.070)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108317615T>TTA [-/1] rs376158749 (variation viewer)

Variant score: 0.755 CONTRIBUTING VARIANT

Transcripts:: ATM:ENST00000278616.8:c.6347+94_6347+95insTA:p.(=); ATM:ENST00000452508.6:c.6347+94_6347+95insTA:p.(=); ATM:ENST00000525729.5:c.641-8545_641-8544insTA:p.(=)

Pathogenicity Data:: Best Score: 0.7550373; CADD: 0.755 (6.109)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108231696C>CA [0/1] rs144747278 (variation viewer)

Variant score: 0.423

Transcripts:: ATM:ENST00000278616.8:c.331+2373_331+2374insA:p.(=); ATM:ENST00000452508.6:c.331+2373_331+2374insA:p.(=); ATM:ENST00000530958.5:c.331+2373_331+2374insA:p.(=)

Pathogenicity Data:: Best Score: 0.42270207; CADD: 0.423 (2.386)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108234782T>G [0/1] rs993379156 (variation viewer)

Variant score: 0.373

Transcripts:: ATM:ENST00000278616.8:c.332-888T>G:p.(=); ATM:ENST00000452508.6:c.332-888T>G:p.(=); ATM:ENST00000530958.5:c.332-888T>G:p.(=)

Pathogenicity Data:: Best Score: 0.3735304; CADD: 0.374 (2.031)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108232527CTTTT>C [-/1] rs71047685 (variation viewer)

Variant score: 0.256

Transcripts:: ATM:ENST00000278616.8:c.332-3142_332-3139del:p.(=); ATM:ENST00000452508.6:c.332-3142_332-3139del:p.(=); ATM:ENST00000530958.5:c.332-3142_332-3139del:p.(=)

Pathogenicity Data:: Best Score: 0.2557823; CADD: 0.256 (1.283)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108317652T>C [0/1] rs3017871 (variation viewer)

Variant score: 0.187

Transcripts:: ATM:ENST00000278616.8:c.6347+131T>C:p.(=); ATM:ENST00000452508.6:c.6347+131T>C:p.(=); ATM:ENST00000525729.5:c.641-8581A>G:p.(=)

Pathogenicity Data:: Best Score: 0.18698233; CADD: 0.187 (0.899)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108260030CT>C [0/1] rs754362678 (variation viewer)

Variant score: 0.173

Transcripts:: ATM:ENST00000278616.8:c.2466+956del:p.(=); ATM:ENST00000452508.6:c.2466+956del:p.(=)

Pathogenicity Data:: Best Score: 0.17339122; CADD: 0.173 (0.827)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108232527C>CT [-/1] rs71047685 (variation viewer)

Variant score: 0.125

Transcripts:: ATM:ENST00000278616.8:c.332-3143_332-3142insT:p.(=); ATM:ENST00000452508.6:c.332-3143_332-3142insT:p.(=); ATM:ENST00000530958.5:c.332-3143_332-3142insT:p.(=)

Pathogenicity Data:: Best Score: 0.12541908; CADD: 0.125 (0.582)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.108293894A>T [0/1] rs11212581 (variation viewer)

Variant score: 0.097

Transcripts:: ATM:ENST00000278616.8:c.4776+417A>T:p.(=); ATM:ENST00000452508.6:c.4776+417A>T:p.(=)

Pathogenicity Data:: Best Score: 0.09655857; CADD: 0.097 (0.441)

Frequency Data:: No frequency data

ATXN7

Exomiser Score: 0.594

Phenotype Score: 0.511

Variant Score: 0.910

Phenotype matches:

Proximity score 0.511 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:164500 Spinocerebellar ataxia 7 - autosomal dominant; ORPHA:94147 Spinocerebellar ataxia type 7

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.594

Phenotype Score: 0.511

Variant Score: 0.910

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr3:g.64007132C>T [0/1]

Variant score: 0.910 CONTRIBUTING VARIANT

Transcripts:: ATXN7:ENST00000295900.10::

Pathogenicity Data:: Best Score: 0.9100503; CADD: 0.910 (10.460)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.051

Phenotype Score: 0.255

Variant Score: 0.840

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr3:g.64007132C>T [0/1]

Variant score: 0.910 CONTRIBUTING VARIANT

Transcripts:: ATXN7:ENST00000295900.10::

Pathogenicity Data:: Best Score: 0.9100503; CADD: 0.910 (10.460)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr3:g.64003205CT>C [0/1] rs754267860 (variation viewer)

Variant score: 0.769 CONTRIBUTING VARIANT

Transcripts:: ATXN7:ENST00000538065.5:c.*3670del:p.(=); ATXN7:ENST00000295900.10:c.*3762del:p.(=)

Pathogenicity Data:: Best Score: 0.7694315; CADD: 0.769 (6.372)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.63903386C>CA [0/1] rs775558434 (variation viewer)

Variant score: 0.373

Transcripts:: ATXN7:ENST00000538065.5:c.-12+4889_-12+4890insA:p.(=); ATXN7:ENST00000295900.10:c.-12+4889_-12+4890insA:p.(=); ATXN7:ENST00000474112.5:c.-12+4889_-12+4890insA:p.(=)

Pathogenicity Data:: Best Score: 0.37280875; CADD: 0.373 (2.026)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.63929269CT>C [0/1] rs1029963204 (variation viewer)

Variant score: 0.164

Transcripts:: ATXN7:ENST00000487717.5:c.394+16045del:p.(=); ATXN7:ENST00000522345.2:c.394+16045del:p.(=); ATXN7:ENST00000538065.5:c.394+16045del:p.(=); ATXN7:ENST00000295900.10:c.394+16045del:p.(=); ATXN7:ENST00000474112.5:c.394+16045del:p.(=)

Pathogenicity Data:: Best Score: 0.16420454; CADD: 0.164 (0.779)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.63962908C>CTAT [0|1] rs1553691654 (variation viewer)

Variant score: 0.114

Transcripts:: ATXN7:ENST00000487717.5:c.499+10425_499+10426insTAT:p.(=); ATXN7:ENST00000522345.2:c.499+10425_499+10426insTAT:p.(=); ATXN7:ENST00000538065.5:c.499+10425_499+10426insTAT:p.(=); ATXN7:ENST00000295900.10:c.499+10425_499+10426insTAT:p.(=); ATXN7:ENST00000474112.5:c.499+10425_499+10426insTAT:p.(=)

Pathogenicity Data:: Best Score: 0.11427277; CADD: 0.114 (0.527)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.63903269C>G [0|1] rs146901788 (variation viewer)

Variant score: 0.076

Transcripts:: ATXN7:ENST00000538065.5:c.-12+4772C>G:p.(=); ATXN7:ENST00000295900.10:c.-12+4772C>G:p.(=); ATXN7:ENST00000474112.5:c.-12+4772C>G:p.(=)

Pathogenicity Data:: Best Score: 0.27889252; CADD: 0.279 (1.420)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 1.2620%; UK10K: 1.8514%; gnomAD_G_AFR: 0.2992%; gnomAD_G_AMR: 0.7212%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.0989%; gnomAD_G_NFE: 1.6593%; gnomAD_G_OTH: 1.0309%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.63954712T>* [-/1]

Variant score: 0.000

Transcripts:: ATXN7:ENST00000487717.5:c.499+2229T>*:p.(=); ATXN7:ENST00000522345.2:c.499+2229T>*:p.(=); ATXN7:ENST00000538065.5:c.499+2229T>*:p.(=); ATXN7:ENST00000295900.10:c.499+2229T>*:p.(=); ATXN7:ENST00000474112.5:c.499+2229T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TBCK

Exomiser Score: 0.586

Phenotype Score: 1.000

Variant Score: 0.353

Phenotype matches:

Phenotypic similarity 1.000 to TBCK-related intellectual disability syndrome associated with TBCK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616900 Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 - autosomal recessive; ORPHA:488632 TBCK-related intellectual disability syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.015

Phenotype Score: 0.500

Variant Score: 0.426

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106204751A>AT [0/1] rs34775295 (variation viewer)

Variant score: 0.426 CONTRIBUTING VARIANT

Transcripts:: TBCK:ENST00000273980.10:c.1860+7998_1860+7999insA:p.(=); TBCK:ENST00000361687.8:c.1671+7998_1671+7999insA:p.(=); TBCK:ENST00000394706.7:c.1743+7998_1743+7999insA:p.(=); TBCK:ENST00000394708.7:c.1860+7998_1860+7999insA:p.(=)

Pathogenicity Data:: Best Score: 0.42561907; CADD: 0.426 (2.408)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.586

Phenotype Score: 1.000

Variant Score: 0.353

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106204751A>AT [0/1] rs34775295 (variation viewer)

Variant score: 0.426 CONTRIBUTING VARIANT

Transcripts:: TBCK:ENST00000273980.10:c.1860+7998_1860+7999insA:p.(=); TBCK:ENST00000361687.8:c.1671+7998_1671+7999insA:p.(=); TBCK:ENST00000394706.7:c.1743+7998_1743+7999insA:p.(=); TBCK:ENST00000394708.7:c.1860+7998_1860+7999insA:p.(=)

Pathogenicity Data:: Best Score: 0.42561907; CADD: 0.426 (2.408)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106124000C>T [0/1] rs1450451138 (variation viewer)

Variant score: 0.280 CONTRIBUTING VARIANT

Transcripts:: TBCK:ENST00000273980.10:c.2236-7622G>A:p.(=); TBCK:ENST00000361687.8:c.2047-7622G>A:p.(=); TBCK:ENST00000394706.7:c.2119-7622G>A:p.(=); TBCK:ENST00000394708.7:c.2236-7622G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3092832; CADD: 0.309 (1.607)

Frequency Data:: gnomAD_G_AFR: 0.2969%; gnomAD_G_AMR: 0.5249%; gnomAD_G_EAS: 0.1263%; gnomAD_G_FIN: 0.3509%; gnomAD_G_NFE: 0.3646%; gnomAD_G_OTH: 0.4587%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106118008C>CA [0|1] rs1006398569 (variation viewer)

Variant score: 0.274

Transcripts:: TBCK:ENST00000273980.10:c.2236-1631_2236-1630insT:p.(=); TBCK:ENST00000361687.8:c.2047-1631_2047-1630insT:p.(=); TBCK:ENST00000394706.7:c.2119-1631_2119-1630insT:p.(=); TBCK:ENST00000394708.7:c.2236-1631_2236-1630insT:p.(=)

Pathogenicity Data:: Best Score: 0.2740612; CADD: 0.274 (1.391)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106084350C>T [0|1] rs143850995 (variation viewer)

Variant score: 0.215

Transcripts:: TBCK:ENST00000273980.10:c.2571+11132G>A:p.(=); TBCK:ENST00000361687.8:c.2382+11132G>A:p.(=); TBCK:ENST00000394706.7:c.2454+11132G>A:p.(=); TBCK:ENST00000394708.7:c.2571+11132G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2421208; CADD: 0.242 (1.204)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3018%; UK10K: 0.4628%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.4298%; gnomAD_G_NFE: 0.3599%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106195492T>TGTGTGTGTG [-/1] rs371211369 (variation viewer)

Variant score: 0.137

Transcripts:: TBCK:ENST00000273980.10:c.1861-739_1861-738insCACACACAC:p.(=); TBCK:ENST00000361687.8:c.1672-739_1672-738insCACACACAC:p.(=); TBCK:ENST00000394706.7:c.1744-739_1744-738insCACACACAC:p.(=); TBCK:ENST00000394708.7:c.1861-739_1861-738insCACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.13741875; CADD: 0.137 (0.642)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106195492T>TGTGTGTGTGTGTG [-/1] rs371211369 (variation viewer)

Variant score: 0.127

Transcripts:: TBCK:ENST00000273980.10:c.1861-739_1861-738insCACACACACACAC:p.(=); TBCK:ENST00000361687.8:c.1672-739_1672-738insCACACACACACAC:p.(=); TBCK:ENST00000394706.7:c.1744-739_1744-738insCACACACACACAC:p.(=); TBCK:ENST00000394708.7:c.1861-739_1861-738insCACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.12722963; CADD: 0.127 (0.591)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106125274C>A [0/1]

Variant score: 0.082

Transcripts:: TBCK:ENST00000273980.10:c.2236-8896G>T:p.(=); TBCK:ENST00000361687.8:c.2047-8896G>T:p.(=); TBCK:ENST00000394706.7:c.2119-8896G>T:p.(=); TBCK:ENST00000394708.7:c.2236-8896G>T:p.(=)

Pathogenicity Data:: Best Score: 0.08230156; CADD: 0.082 (0.373)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106050006C>T [0/1] rs529044016 (variation viewer)

Variant score: 0.080

Transcripts:: TBCK:ENST00000273980.10:c.2572-3326G>A:p.(=); TBCK:ENST00000361687.8:c.2383-3326G>A:p.(=); TBCK:ENST00000394706.7:c.2455-3326G>A:p.(=); TBCK:ENST00000394708.7:c.2572-3326G>A:p.(=)

Pathogenicity Data:: Best Score: 0.08018601; CADD: 0.080 (0.363)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0334%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0114%; gnomAD_G_NFE: 0.0534%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106197411G>GTATATA [0/1] rs1553957897 (variation viewer)

Variant score: 0.078

Transcripts:: TBCK:ENST00000273980.10:c.1861-2658_1861-2657insTATATA:p.(=); TBCK:ENST00000361687.8:c.1672-2658_1672-2657insTATATA:p.(=); TBCK:ENST00000394706.7:c.1744-2658_1744-2657insTATATA:p.(=); TBCK:ENST00000394708.7:c.1861-2658_1861-2657insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.07785332; CADD: 0.078 (0.352)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106266865G>A [0/1] rs560194196 (variation viewer)

Variant score: 0.075

Transcripts:: TBCK:ENST00000273980.10:c.267-4653C>T:p.(=); TBCK:ENST00000361687.8:c.267-14858C>T:p.(=); TBCK:ENST00000394706.7:c.267-4653C>T:p.(=); TBCK:ENST00000394708.7:c.267-4653C>T:p.(=)

Pathogenicity Data:: Best Score: 0.07508886; CADD: 0.075 (0.339)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0350%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0535%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106125726G>A [0/1] rs148720922 (variation viewer)

Variant score: 0.045

Transcripts:: TBCK:ENST00000273980.10:c.2236-9348C>T:p.(=); TBCK:ENST00000361687.8:c.2047-9348C>T:p.(=); TBCK:ENST00000394706.7:c.2119-9348C>T:p.(=); TBCK:ENST00000394708.7:c.2236-9348C>T:p.(=)

Pathogenicity Data:: Best Score: 0.04522729; CADD: 0.045 (0.201)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0120%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106236362T>C [0/1] rs1318802646 (variation viewer)

Variant score: 0.045

Transcripts:: TBCK:ENST00000273980.10:c.1350+28A>G:p.(=); TBCK:ENST00000361687.8:c.1161+28A>G:p.(=); TBCK:ENST00000394706.7:c.1233+28A>G:p.(=); TBCK:ENST00000394708.7:c.1350+28A>G:p.(=)

Pathogenicity Data:: Best Score: 0.045007408; CADD: 0.045 (0.200)

Frequency Data:: TOPMed: 0.0016%; gnomAD_E_SAS: 0.0054%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106068141TTTTTA>T [0/1] rs200052457 (variation viewer)

Variant score: 0.016

Transcripts:: TBCK:ENST00000273980.10:c.2572-21466_2572-21462del:p.(=); TBCK:ENST00000361687.8:c.2383-21466_2383-21462del:p.(=); TBCK:ENST00000394706.7:c.2455-21466_2455-21462del:p.(=); TBCK:ENST00000394708.7:c.2572-21466_2572-21462del:p.(=)

Pathogenicity Data:: Best Score: 0.1199649; CADD: 0.120 (0.555)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.1797%; UK10K: 1.0315%; gnomAD_G_AFR: 0.2176%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 2.0000%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 0.6069%; gnomAD_G_NFE: 0.8863%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.106227673C>T [0/1] rs922746905 (variation viewer)

Variant score: 0.014

Transcripts:: TBCK:ENST00000273980.10:c.1774+2690G>A:p.(=); TBCK:ENST00000361687.8:c.1585+2690G>A:p.(=); TBCK:ENST00000394706.7:c.1657+2690G>A:p.(=); TBCK:ENST00000394708.7:c.1774+2690G>A:p.(=)

Pathogenicity Data:: Best Score: 0.013720512; CADD: 0.014 (0.060)

Frequency Data:: No frequency data

YOD1

Exomiser Score: 0.583

Phenotype Score: 0.506

Variant Score: 0.911

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.583

Phenotype Score: 0.506

Variant Score: 0.911

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr1:g.207042549CAAAAAAAAAAA>C [-/1] rs57077682 (variation viewer)

Variant score: 0.911 CONTRIBUTING VARIANT

Transcripts:: YOD1:ENST00000315927.8::; YOD1:ENST00000461135.2::

Pathogenicity Data:: Best Score: 0.9112844; CADD: 0.911 (10.520)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.485

Phenotype Score: 0.506

Variant Score: 0.868

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr1:g.207042549CAAAAAAAAAAA>C [-/1] rs57077682 (variation viewer)

Variant score: 0.911 CONTRIBUTING VARIANT

Transcripts:: YOD1:ENST00000315927.8::; YOD1:ENST00000461135.2::

Pathogenicity Data:: Best Score: 0.9112844; CADD: 0.911 (10.520)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr1:g.207042549C>CA [-/1] rs57077682 (variation viewer)

Variant score: 0.824 CONTRIBUTING VARIANT

Transcripts:: YOD1:ENST00000315927.8::; YOD1:ENST00000461135.2::

Pathogenicity Data:: Best Score: 0.8244504; CADD: 0.824 (7.556)

Frequency Data:: No frequency data

Other passed variants:

HLA-DRB1

Exomiser Score: 0.580

Phenotype Score: 0.504

Variant Score: 0.911

Phenotype matches:

Phenotypic similarity 0.479 to Multiple sclerosis, susceptibility to, 1 associated with HLA-DRB1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:126200 Multiple sclerosis, susceptibility to, 1 (susceptibility); OMIM:181000 Sarcoidosis, susceptibility to, 1 (susceptibility); ORPHA:2073 Narcolepsy type 1; ORPHA:545 Follicular lymphoma; ORPHA:797 Sarcoidosis; ORPHA:85414 Systemic-onset juvenile idiopathic arthritis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.580

Phenotype Score: 0.504

Variant Score: 0.911

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588848A>G [0/1] rs9270219 (variation viewer)

Variant score: 0.911 CONTRIBUTING VARIANT

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+795T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9112844; CADD: 0.911 (10.520)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.083

Phenotype Score: 0.252

Variant Score: 0.899

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588848A>G [0/1] rs9270219 (variation viewer)

Variant score: 0.911 CONTRIBUTING VARIANT

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+795T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9112844; CADD: 0.911 (10.520)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589537A>T [0|1] rs796855909 (variation viewer)

Variant score: 0.888 CONTRIBUTING VARIANT

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+106T>A:p.(=)

Pathogenicity Data:: Best Score: 0.8875395; CADD: 0.888 (9.490)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589538A>T [0|1] rs796182409 (variation viewer)

Variant score: 0.880

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+105T>A:p.(=)

Pathogenicity Data:: Best Score: 0.87963504; CADD: 0.880 (9.195)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574252C>T [0/1] rs41293334 (variation viewer)

Variant score: 0.870

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.8696833; CADD: 0.870 (8.850)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589234C>T [0/1] rs9270253 (variation viewer)

Variant score: 0.868

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+409G>A:p.(=)

Pathogenicity Data:: Best Score: 0.86844724; CADD: 0.868 (8.809)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589501A>T [0|1] rs9270284 (variation viewer)

Variant score: 0.867

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+142T>A:p.(=)

Pathogenicity Data:: Best Score: 0.866525; CADD: 0.867 (8.746)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587971C>A [0|1] rs4713547 (variation viewer)

Variant score: 0.863

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1672G>T:p.(=)

Pathogenicity Data:: Best Score: 0.86316407; CADD: 0.863 (8.638)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588630T>C [0|1] rs41288868 (variation viewer)

Variant score: 0.861

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1013A>G:p.(=)

Pathogenicity Data:: Best Score: 0.86068434; CADD: 0.861 (8.560)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32589980A>C [0|1] rs9270320 (variation viewer)

Variant score: 0.860

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.86013794; CADD: 0.860 (8.543)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590629T>A [1|1] rs9270399 (variation viewer)

Variant score: 0.854

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.85364753; CADD: 0.854 (8.346)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577495A>C [0|1] rs41284942 (variation viewer)

Variant score: 0.852

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.85215724; CADD: 0.852 (8.302)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576140T>C [0|1] rs41284619 (variation viewer)

Variant score: 0.845

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.84533215; CADD: 0.845 (8.106)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583244T>TGA [1|1] rs9281870 (variation viewer)

Variant score: 0.843

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+864_370+865insTC:p.(=)

Pathogenicity Data:: Best Score: 0.8431444; CADD: 0.843 (8.045)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32589989TTTAA>T [0|1] rs112597642 (variation viewer)

Variant score: 0.840

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.83982307; CADD: 0.840 (7.954)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587668G>A [0/1] rs41287343 (variation viewer)

Variant score: 0.838

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1975C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8377069; CADD: 0.838 (7.897)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587053A>T [0/1] rs9270110 (variation viewer)

Variant score: 0.837

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2590T>A:p.(=)

Pathogenicity Data:: Best Score: 0.83725786; CADD: 0.837 (7.885)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581472G>C [0/1] rs9269794 (variation viewer)

Variant score: 0.833

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+85C>G:p.(=)

Pathogenicity Data:: Best Score: 0.8327755; CADD: 0.833 (7.767)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575111A>G [0|1] rs41294119 (variation viewer)

Variant score: 0.830

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.82974494; CADD: 0.830 (7.689)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573688T>C [0|1] rs9269414 (variation viewer)

Variant score: 0.829

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.8290772; CADD: 0.829 (7.672)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590185A>G [1|1] rs7771916 (variation viewer)

Variant score: 0.827

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.827098; CADD: 0.827 (7.622)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584496C>G [0/1] rs9269970 (variation viewer)

Variant score: 0.816

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-118G>C:p.(=)

Pathogenicity Data:: Best Score: 0.8156683; CADD: 0.816 (7.344)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588810T>C [0|1] rs9270217 (variation viewer)

Variant score: 0.813

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+833A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8127163; CADD: 0.813 (7.275)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585184A>T [0|1] rs368271637 (variation viewer)

Variant score: 0.812

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-806T>A:p.(=)

Pathogenicity Data:: Best Score: 0.81167847; CADD: 0.812 (7.251)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585710A>C [0|1] rs9270037 (variation viewer)

Variant score: 0.810

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1332T>G:p.(=)

Pathogenicity Data:: Best Score: 0.8099797; CADD: 0.810 (7.212)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589456TCTC>T [0|1]

Variant score: 0.801

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+184_100+186del:p.(=)

Pathogenicity Data:: Best Score: 0.80070335; CADD: 0.801 (7.005)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573704T>C [0/1] rs41291822 (variation viewer)

Variant score: 0.799

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.79922944; CADD: 0.799 (6.973)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574584C>T [0/1] rs41293680 (variation viewer)

Variant score: 0.792

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.7922218; CADD: 0.792 (6.824)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586185C>T [0|1] rs879752098 (variation viewer)

Variant score: 0.790

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1807G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7899126; CADD: 0.790 (6.776)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573758A>G [0|1] rs9269423 (variation viewer)

Variant score: 0.786

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.78585887; CADD: 0.786 (6.693)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573760A>G [0/1] rs41291825 (variation viewer)

Variant score: 0.786

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.7855629; CADD: 0.786 (6.687)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585946A>C [0/1] rs115609091 (variation viewer)

Variant score: 0.783

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1568T>G:p.(=)

Pathogenicity Data:: Best Score: 0.78332937; CADD: 0.783 (6.642)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574176T>C [0|1] rs988088752 (variation viewer)

Variant score: 0.774

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.77431643; CADD: 0.774 (6.465)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574899A>T [0|1] rs41293720 (variation viewer)

Variant score: 0.771

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.7711241; CADD: 0.771 (6.404)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588632T>G [0|1] rs41288872 (variation viewer)

Variant score: 0.771

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1011A>C:p.(=)

Pathogenicity Data:: Best Score: 0.77075493; CADD: 0.771 (6.397)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584901A>C [0/1] rs9269994 (variation viewer)

Variant score: 0.770

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-523T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7696438; CADD: 0.770 (6.376)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582707T>C [0|1] rs41293559 (variation viewer)

Variant score: 0.765

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-869A>G:p.(=)

Pathogenicity Data:: Best Score: 0.76476604; CADD: 0.765 (6.285)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581313A>G [1|1] rs9269789 (variation viewer)

Variant score: 0.762

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+244T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7618229; CADD: 0.762 (6.231)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573800T>C [1|1] rs41291831 (variation viewer)

Variant score: 0.755

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.7554881; CADD: 0.755 (6.117)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581032A>C [0/1] rs6938892 (variation viewer)

Variant score: 0.755

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-176T>G:p.(=)

Pathogenicity Data:: Best Score: 0.75486803; CADD: 0.755 (6.106)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585939T>C [1|1] rs9270049 (variation viewer)

Variant score: 0.750

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1561A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7501381; CADD: 0.750 (6.023)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587233T>G [0|1] rs34047827 (variation viewer)

Variant score: 0.750

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2410A>C:p.(=)

Pathogenicity Data:: Best Score: 0.7501381; CADD: 0.750 (6.023)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581501T>G [0/1] rs9269796 (variation viewer)

Variant score: 0.748

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+56A>C:p.(=)

Pathogenicity Data:: Best Score: 0.74771; CADD: 0.748 (5.981)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585834T>C [0|1] rs200312712 (variation viewer)

Variant score: 0.746

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1456A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7463704; CADD: 0.746 (5.958)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575778T>C [0/1] rs34419764 (variation viewer)

Variant score: 0.742

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.74242723; CADD: 0.742 (5.891)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581994T>C [0/1] rs9269818 (variation viewer)

Variant score: 0.742

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-156A>G:p.(=)

Pathogenicity Data:: Best Score: 0.74171454; CADD: 0.742 (5.879)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590058C>CCCAATTATTTT [0|1] rs9281901 (variation viewer)

Variant score: 0.740

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.74028325; CADD: 0.740 (5.855)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575598T>A [0/1] rs74453993 (variation viewer)

Variant score: 0.739

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.73902434; CADD: 0.739 (5.834)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584671A>C [0/1] rs11753207 (variation viewer)

Variant score: 0.737

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-293T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7367308; CADD: 0.737 (5.796)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582303A>G [0/1] rs9469171 (variation viewer)

Variant score: 0.736

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-465T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7361239; CADD: 0.736 (5.786)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585195T>C [0|1] rs9270013 (variation viewer)

Variant score: 0.733

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-817A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7334983; CADD: 0.733 (5.743)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589507G>C [0|1] rs112117993 (variation viewer)

Variant score: 0.724

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+136C>G:p.(=)

Pathogenicity Data:: Best Score: 0.7236879; CADD: 0.724 (5.586)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_EXON_VARIANT chr6:g.32589807A>AC [0/1] rs1554131664 (variation viewer)

Variant score: 0.722

Transcripts:: HLA-DRB1:ENST00000360004.5:c.-66_-65insG:p.(=)

Pathogenicity Data:: Best Score: 0.7223486; CADD: 0.722 (5.565)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576169A>G [0/1] rs9269538 (variation viewer)

Variant score: 0.720

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.71997297; CADD: 0.720 (5.528)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585399A>G [0|1] rs34776852 (variation viewer)

Variant score: 0.719

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1021T>C:p.(=)

Pathogenicity Data:: Best Score: 0.71913344; CADD: 0.719 (5.515)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584525A>G [1|1] rs9269972 (variation viewer)

Variant score: 0.718

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-147T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7183564; CADD: 0.718 (5.503)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590221CT>C [1|1] rs879904224 (variation viewer)

Variant score: 0.718

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.71822655; CADD: 0.718 (5.501)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589250G>A [0/1] rs9270255 (variation viewer)

Variant score: 0.718

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+393C>T:p.(=)

Pathogenicity Data:: Best Score: 0.717512; CADD: 0.718 (5.490)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586532T>G [0|1] rs34938170 (variation viewer)

Variant score: 0.716

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2154A>C:p.(=)

Pathogenicity Data:: Best Score: 0.71568483; CADD: 0.716 (5.462)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574661A>G [0|1] rs41293696 (variation viewer)

Variant score: 0.714

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.7143067; CADD: 0.714 (5.441)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573545C>T [1/1] rs9269400 (variation viewer)

Variant score: 0.702

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.7020798; CADD: 0.702 (5.259)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584724C>CCTT [0/1] rs28986203 (variation viewer)

Variant score: 0.700

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-347_101-346insAAG:p.(=)

Pathogenicity Data:: Best Score: 0.7003598; CADD: 0.700 (5.234)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575468T>A [0|1] rs111897085 (variation viewer)

Variant score: 0.699

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6985606; CADD: 0.699 (5.208)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574188T>C [0|1] rs41293322 (variation viewer)

Variant score: 0.698

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.69800484; CADD: 0.698 (5.200)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586614G>A [0/1] rs72850291 (variation viewer)

Variant score: 0.698

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2236C>T:p.(=)

Pathogenicity Data:: Best Score: 0.69751763; CADD: 0.698 (5.193)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590163T>C [1|1] rs9270337 (variation viewer)

Variant score: 0.697

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.6970297; CADD: 0.697 (5.186)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574203T>G [0|1] rs9269445 (variation viewer)

Variant score: 0.696

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6963313; CADD: 0.696 (5.176)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585392A>G [0|1] rs973383647 (variation viewer)

Variant score: 0.694

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1014T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6940151; CADD: 0.694 (5.143)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588555T>TAAGAG [0/1] rs149343040 (variation viewer)

Variant score: 0.693

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1087_100+1088insCTCTT:p.(=)

Pathogenicity Data:: Best Score: 0.6934509; CADD: 0.693 (5.135)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588534G>A [0/1] rs9270205 (variation viewer)

Variant score: 0.693

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1109C>T:p.(=)

Pathogenicity Data:: Best Score: 0.692815; CADD: 0.693 (5.126)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588556A>AAGAGG [0/1] rs9281887 (variation viewer)

Variant score: 0.693

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1086_100+1087insCCTCT:p.(=)

Pathogenicity Data:: Best Score: 0.69253194; CADD: 0.693 (5.122)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582545A>C [1|1] rs9269853 (variation viewer)

Variant score: 0.692

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-707T>G:p.(=)

Pathogenicity Data:: Best Score: 0.6923903; CADD: 0.692 (5.120)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586216A>T [0|1] rs9270061 (variation viewer)

Variant score: 0.692

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1838T>A:p.(=)

Pathogenicity Data:: Best Score: 0.6917522; CADD: 0.692 (5.111)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587299T>C [0|1] rs9270128 (variation viewer)

Variant score: 0.691

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2344A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6910416; CADD: 0.691 (5.101)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588601C>T [0/1] rs9270207 (variation viewer)

Variant score: 0.690

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1042G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6902581; CADD: 0.690 (5.090)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587632C>T [0|1] rs17203657 (variation viewer)

Variant score: 0.690

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2011G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6897584; CADD: 0.690 (5.083)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582806T>C [0/1] rs9269862 (variation viewer)

Variant score: 0.686

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-968A>G:p.(=)

Pathogenicity Data:: Best Score: 0.68594915; CADD: 0.686 (5.030)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574998C>T [0/1] rs41294107 (variation viewer)

Variant score: 0.683

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.68253195; CADD: 0.683 (4.983)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585534A>C [0/1] rs201112890 (variation viewer)

Variant score: 0.681

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1156T>G:p.(=)

Pathogenicity Data:: Best Score: 0.6812135; CADD: 0.681 (4.965)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575832T>A [0/1] rs12183302 (variation viewer)

Variant score: 0.680

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6796682; CADD: 0.680 (4.944)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585049C>A [1/1] rs9270005 (variation viewer)

Variant score: 0.676

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-671G>T:p.(=)

Pathogenicity Data:: Best Score: 0.6763319; CADD: 0.676 (4.899)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586540C>T [0|1] rs777411444 (variation viewer)

Variant score: 0.676

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2162G>A:p.(=)

Pathogenicity Data:: Best Score: 0.67588437; CADD: 0.676 (4.893)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589207C>T [0/1] rs147492518 (variation viewer)

Variant score: 0.672

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+436G>A:p.(=)

Pathogenicity Data:: Best Score: 0.67243314; CADD: 0.672 (4.847)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583253T>C [0/1] rs9469173 (variation viewer)

Variant score: 0.672

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+856A>G:p.(=)

Pathogenicity Data:: Best Score: 0.67160237; CADD: 0.672 (4.836)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585533T>A [0/1] rs9270028 (variation viewer)

Variant score: 0.671

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1155A>T:p.(=)

Pathogenicity Data:: Best Score: 0.6710726; CADD: 0.671 (4.829)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582952A>T [0|1] rs41283787 (variation viewer)

Variant score: 0.667

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1114T>A:p.(=)

Pathogenicity Data:: Best Score: 0.66741705; CADD: 0.667 (4.781)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576220T>G [0|1] rs41284627 (variation viewer)

Variant score: 0.665

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.66526586; CADD: 0.665 (4.753)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581157C>T [0/1] rs41286841 (variation viewer)

Variant score: 0.663

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-301G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6629456; CADD: 0.663 (4.723)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575033T>C [0|1] rs9269488 (variation viewer)

Variant score: 0.661

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6607655; CADD: 0.661 (4.695)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589215G>T [0/1] rs9270247 (variation viewer)

Variant score: 0.659

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+428C>A:p.(=)

Pathogenicity Data:: Best Score: 0.6588071; CADD: 0.659 (4.670)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573757C>A [0|1] rs9269422 (variation viewer)

Variant score: 0.655

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6554121; CADD: 0.655 (4.627)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573848C>T [0/1] rs9269429 (variation viewer)

Variant score: 0.655

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6545383; CADD: 0.655 (4.616)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586283C>T [0/1] rs6457605 (variation viewer)

Variant score: 0.652

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1905G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6522237; CADD: 0.652 (4.587)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588007G>A [0/1] rs9270178 (variation viewer)

Variant score: 0.652

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1636C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6515825; CADD: 0.652 (4.579)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576117T>C [0|1] rs41284611 (variation viewer)

Variant score: 0.650

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6500548; CADD: 0.650 (4.560)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573630C>A [0/1] rs146053842 (variation viewer)

Variant score: 0.649

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6491673; CADD: 0.649 (4.549)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573761A>G [0/1] rs41291828 (variation viewer)

Variant score: 0.649

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6488441; CADD: 0.649 (4.545)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584463G>C [1|1] rs28724111 (variation viewer)

Variant score: 0.644

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-85C>G:p.(=)

Pathogenicity Data:: Best Score: 0.64420485; CADD: 0.644 (4.488)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587133A>T [0|1] rs9270113 (variation viewer)

Variant score: 0.641

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2510T>A:p.(=)

Pathogenicity Data:: Best Score: 0.6411607; CADD: 0.641 (4.451)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574374T>C [0|1] rs9269459 (variation viewer)

Variant score: 0.640

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.640085; CADD: 0.640 (4.438)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585198T>A [0|1] rs9270014 (variation viewer)

Variant score: 0.640

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-820A>T:p.(=)

Pathogenicity Data:: Best Score: 0.63991916; CADD: 0.640 (4.436)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573714C>A [0|1] rs9269417 (variation viewer)

Variant score: 0.639

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6385901; CADD: 0.639 (4.420)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584707C>CACCCG [0|1] rs41288201 (variation viewer)

Variant score: 0.638

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-330_101-329insCGGGT:p.(=)

Pathogenicity Data:: Best Score: 0.6375067; CADD: 0.638 (4.407)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574593T>A [1|1] rs9269474 (variation viewer)

Variant score: 0.637

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.63700557; CADD: 0.637 (4.401)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584705C>CT [0|1] rs9281876 (variation viewer)

Variant score: 0.635

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-328_101-327insA:p.(=)

Pathogenicity Data:: Best Score: 0.635414; CADD: 0.635 (4.382)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585599G>C [0/1] rs9270032 (variation viewer)

Variant score: 0.635

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1221C>G:p.(=)

Pathogenicity Data:: Best Score: 0.6353301; CADD: 0.635 (4.381)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584739GC>G [1|1] rs9279739 (variation viewer)

Variant score: 0.630

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-362del:p.(=)

Pathogenicity Data:: Best Score: 0.62957525; CADD: 0.630 (4.313)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573871A>G [0/1] rs7768620 (variation viewer)

Variant score: 0.628

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.62812245; CADD: 0.628 (4.296)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr6:g.32604809G>A [1|1] rs9270932 (variation viewer)

Variant score: 0.626

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.6263199; CADD: 0.626 (4.275)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574551A>G [0|1] rs41293672 (variation viewer)

Variant score: 0.625

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6245086; CADD: 0.625 (4.254)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582372C>G [1|1] rs9269839 (variation viewer)

Variant score: 0.622

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-534G>C:p.(=)

Pathogenicity Data:: Best Score: 0.62207985; CADD: 0.622 (4.226)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574391C>G [0|1] rs41293648 (variation viewer)

Variant score: 0.622

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.62173164; CADD: 0.622 (4.222)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585451A>G [0|1] rs9270023 (variation viewer)

Variant score: 0.621

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1073T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6208596; CADD: 0.621 (4.212)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590050A>AT [0|1] rs1317326582 (variation viewer)

Variant score: 0.617

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.6169107; CADD: 0.617 (4.167)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585340T>C [-/1] rs9270021 (variation viewer)

Variant score: 0.616

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-962A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6162927; CADD: 0.616 (4.160)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588026T>C [0/1] rs9270179 (variation viewer)

Variant score: 0.614

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1617A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6142553; CADD: 0.614 (4.137)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576120A>G [0|1] rs34007275 (variation viewer)

Variant score: 0.612

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.61211765; CADD: 0.612 (4.113)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577652A>T [0|1] rs111402307 (variation viewer)

Variant score: 0.612

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.611939; CADD: 0.612 (4.111)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574262C>T [0/1] rs7769664 (variation viewer)

Variant score: 0.611

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.61050665; CADD: 0.611 (4.095)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574843T>TA [0|1] rs879542378 (variation viewer)

Variant score: 0.603

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.6031741; CADD: 0.603 (4.014)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582350T>A [0|1] rs9269838 (variation viewer)

Variant score: 0.602

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-512A>T:p.(=)

Pathogenicity Data:: Best Score: 0.60180116; CADD: 0.602 (3.999)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589189A>AGAG [1/1] rs34124973 (variation viewer)

Variant score: 0.602

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+453_100+454insCTC:p.(=)

Pathogenicity Data:: Best Score: 0.6017095; CADD: 0.602 (3.998)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_EXON_VARIANT chr6:g.32589828AGTT>A [0|1] rs1384956282 (variation viewer)

Variant score: 0.601

Transcripts:: HLA-DRB1:ENST00000360004.5:c.-89_-87del:p.(=)

Pathogenicity Data:: Best Score: 0.60115886; CADD: 0.601 (3.992)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576130C>T [0|1] rs41284615 (variation viewer)

Variant score: 0.597

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5970975; CADD: 0.597 (3.948)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574592T>C [1|1] rs9269473 (variation viewer)

Variant score: 0.596

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.59616864; CADD: 0.596 (3.938)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588811T>TCA [0|1] rs1281992265 (variation viewer)

Variant score: 0.593

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+831_100+832insTG:p.(=)

Pathogenicity Data:: Best Score: 0.5933695; CADD: 0.593 (3.908)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574615T>TA [-/1] rs9281858 (variation viewer)

Variant score: 0.593

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.59318215; CADD: 0.593 (3.906)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574615T>TG [-/1] rs1554286259 (variation viewer)

Variant score: 0.593

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.59318215; CADD: 0.593 (3.906)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584930C>G [1/1] rs9269996 (variation viewer)

Variant score: 0.592

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-552G>C:p.(=)

Pathogenicity Data:: Best Score: 0.59186864; CADD: 0.592 (3.892)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585186G>A [0|1] rs1254156209 (variation viewer)

Variant score: 0.590

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-808C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5899848; CADD: 0.590 (3.872)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581395TAGAA>T [0|1] rs1314988413 (variation viewer)

Variant score: 0.590

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+158_652+161del:p.(=)

Pathogenicity Data:: Best Score: 0.58960694; CADD: 0.590 (3.868)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573733T>G [0|1] rs9269420 (variation viewer)

Variant score: 0.589

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5891342; CADD: 0.589 (3.863)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32589972C>A [0|1] rs941422174 (variation viewer)

Variant score: 0.589

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.5891342; CADD: 0.589 (3.863)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586921C>G [0/1] rs117528258 (variation viewer)

Variant score: 0.589

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2543G>C:p.(=)

Pathogenicity Data:: Best Score: 0.5887556; CADD: 0.589 (3.859)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587921G>A [0/1] rs9270173 (variation viewer)

Variant score: 0.586

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1722C>T:p.(=)

Pathogenicity Data:: Best Score: 0.58561885; CADD: 0.586 (3.826)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585340T>G [-/1] rs9270021 (variation viewer)

Variant score: 0.582

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-962A>C:p.(=)

Pathogenicity Data:: Best Score: 0.58236206; CADD: 0.582 (3.792)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573985T>G [0|1] rs9269434 (variation viewer)

Variant score: 0.582

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.58216965; CADD: 0.582 (3.790)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589010C>T [-/1] rs9270230 (variation viewer)

Variant score: 0.582

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+633G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5820734; CADD: 0.582 (3.789)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590048C>G [0|1] rs9270329 (variation viewer)

Variant score: 0.578

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.5777205; CADD: 0.578 (3.744)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579228T>A [1|1] rs33962457 (variation viewer)

Variant score: 0.571

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-124A>T:p.(=)

Pathogenicity Data:: Best Score: 0.5712541; CADD: 0.571 (3.678)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579171C>G [0|1] rs41287215 (variation viewer)

Variant score: 0.568

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-67G>C:p.(=)

Pathogenicity Data:: Best Score: 0.5682821; CADD: 0.568 (3.648)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575504T>C [0|1] rs41294250 (variation viewer)

Variant score: 0.566

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5657898; CADD: 0.566 (3.623)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574408C>A [0|1] rs41293656 (variation viewer)

Variant score: 0.564

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5639864; CADD: 0.564 (3.605)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582367G>A [0|1] rs41293206 (variation viewer)

Variant score: 0.561

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-529C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5614693; CADD: 0.561 (3.580)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575121T>TGCAGTG [0/1] rs9281859 (variation viewer)

Variant score: 0.560

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5601547; CADD: 0.560 (3.567)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583081T>C [0/1] rs9269875 (variation viewer)

Variant score: 0.558

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+1028A>G:p.(=)

Pathogenicity Data:: Best Score: 0.55781907; CADD: 0.558 (3.544)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590199T>C [1|1] rs9270343 (variation viewer)

Variant score: 0.557

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.5566977; CADD: 0.557 (3.533)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589449ACACAAG>A [0|1] rs1279731642 (variation viewer)

Variant score: 0.555

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+188_100+193del:p.(=)

Pathogenicity Data:: Best Score: 0.554549; CADD: 0.555 (3.512)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577144T>TTC [0|1] rs34873314 (variation viewer)

Variant score: 0.554

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.55444634; CADD: 0.554 (3.511)

Frequency Data:: No frequency data

MISSENSE_VARIANT chr6:g.32580779C>T [0/1] rs3830125 (variation viewer)

Variant score: 0.553

Transcripts:: HLA-DRB1:ENST00000360004.5:c.730G>A:p.(Ala244Thr)

Pathogenicity Data:: Best Score: 0.995; Polyphen2: 0.995 (D); SIFT: 0.023 (D); CADD: 0.994 (22.000)

Frequency Data:: gnomAD_E_AFR: 1.4539%; gnomAD_E_AMR: 0.0158%; gnomAD_E_ASJ: 0.2859%; gnomAD_E_EAS: 0.0689%; gnomAD_E_FIN: 0.0228%; gnomAD_E_NFE: 0.5768%; gnomAD_E_OTH: 0.2122%; gnomAD_E_SAS: 0.0585%; gnomAD_G_AFR: 0.5981%; gnomAD_G_AMR: 0.4886%; gnomAD_G_ASJ: 0.9524%; gnomAD_G_EAS: 1.1257%; gnomAD_G_FIN: 0.4244%; gnomAD_G_NFE: 0.3210%; gnomAD_G_OTH: 0.5917%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582489G>A [0/1] rs41293224 (variation viewer)

Variant score: 0.553

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-651C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5530077; CADD: 0.553 (3.497)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584941A>C [1/1] rs9269997 (variation viewer)

Variant score: 0.549

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-563T>G:p.(=)

Pathogenicity Data:: Best Score: 0.5492871; CADD: 0.549 (3.461)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573903T>C [0/1] rs41293290 (variation viewer)

Variant score: 0.548

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.54814404; CADD: 0.548 (3.450)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582938G>A [1|1] rs9269869 (variation viewer)

Variant score: 0.542

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1100C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5424906; CADD: 0.542 (3.396)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577528G>A [0|1] rs41286399 (variation viewer)

Variant score: 0.539

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.539001; CADD: 0.539 (3.363)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580945C>A [1|1] rs9269767 (variation viewer)

Variant score: 0.533

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-89G>T:p.(=)

Pathogenicity Data:: Best Score: 0.5334481; CADD: 0.533 (3.311)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575477T>G [0|1] rs41294244 (variation viewer)

Variant score: 0.533

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.53312564; CADD: 0.533 (3.308)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582799G>A [0|1] rs41283757 (variation viewer)

Variant score: 0.533

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-961C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5326954; CADD: 0.533 (3.304)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588925T>G [0/1] rs9270228 (variation viewer)

Variant score: 0.532

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+718A>C:p.(=)

Pathogenicity Data:: Best Score: 0.53172606; CADD: 0.532 (3.295)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32589961AAC>A [0|1] rs1347803207 (variation viewer)

Variant score: 0.531

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.5307546; CADD: 0.531 (3.286)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585726C>T [0|1] rs199754940 (variation viewer)

Variant score: 0.528

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1348G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5281543; CADD: 0.528 (3.262)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583349A>C [1|1] rs9269898 (variation viewer)

Variant score: 0.528

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+760T>G:p.(=)

Pathogenicity Data:: Best Score: 0.5276108; CADD: 0.528 (3.257)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584686G>C [0|1] rs41287319 (variation viewer)

Variant score: 0.528

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-308C>G:p.(=)

Pathogenicity Data:: Best Score: 0.5276108; CADD: 0.528 (3.257)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575938T>A [0/1] rs9269528 (variation viewer)

Variant score: 0.526

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5264127; CADD: 0.526 (3.246)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588644C>G [0/1] rs41288876 (variation viewer)

Variant score: 0.525

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+999G>C:p.(=)

Pathogenicity Data:: Best Score: 0.525321; CADD: 0.525 (3.236)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574804C>T [0/1] rs41293700 (variation viewer)

Variant score: 0.524

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5240076; CADD: 0.524 (3.224)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582341G>T [0|1] rs9269837 (variation viewer)

Variant score: 0.520

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-503C>A:p.(=)

Pathogenicity Data:: Best Score: 0.520377; CADD: 0.520 (3.191)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589186ACT>A [1/1] rs1434471883 (variation viewer)

Variant score: 0.519

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+455_100+456del:p.(=)

Pathogenicity Data:: Best Score: 0.519382; CADD: 0.519 (3.182)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587309G>A [0|1] rs9270129 (variation viewer)

Variant score: 0.519

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2334C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5192714; CADD: 0.519 (3.181)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574439G>A [0/1] rs41293660 (variation viewer)

Variant score: 0.519

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5191606; CADD: 0.519 (3.180)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581076A>G [1|1] rs9269777 (variation viewer)

Variant score: 0.519

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-220T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5190499; CADD: 0.519 (3.179)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577566C>A [0|1] rs41286411 (variation viewer)

Variant score: 0.518

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5176081; CADD: 0.518 (3.166)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573572C>T [1|1] rs41291816 (variation viewer)

Variant score: 0.515

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5152699; CADD: 0.515 (3.145)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575371T>C [0/1] rs41294138 (variation viewer)

Variant score: 0.515

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5147115; CADD: 0.515 (3.140)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585452G>A [0|1] rs9270024 (variation viewer)

Variant score: 0.513

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1074C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5134808; CADD: 0.513 (3.129)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584460A>G [1|1] rs9269966 (variation viewer)

Variant score: 0.512

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-82T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5121347; CADD: 0.512 (3.117)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575540A>T [0/1] rs12181113 (variation viewer)

Variant score: 0.504

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.5043216; CADD: 0.504 (3.048)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587612A>T [-/1] rs9270154 (variation viewer)

Variant score: 0.503

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2031T>A:p.(=)

Pathogenicity Data:: Best Score: 0.5027211; CADD: 0.503 (3.034)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587699T>C [0|1] rs17203664 (variation viewer)

Variant score: 0.501

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1944A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5013452; CADD: 0.501 (3.022)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573678C>T [0|1] rs9269412 (variation viewer)

Variant score: 0.499

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.49938947; CADD: 0.499 (3.005)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581342AGTCTCTCCCGCCTGG>A [0|1] rs1186602109 (variation viewer)

Variant score: 0.499

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+200_652+214del:p.(=)

Pathogenicity Data:: Best Score: 0.49927413; CADD: 0.499 (3.004)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575855T>C [0/1] rs41295455 (variation viewer)

Variant score: 0.496

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.49615145; CADD: 0.496 (2.977)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581199C>T [0|1] rs28732307 (variation viewer)

Variant score: 0.494

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-343G>A:p.(=)

Pathogenicity Data:: Best Score: 0.49405885; CADD: 0.494 (2.959)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586781C>A [0/1] rs9270100 (variation viewer)

Variant score: 0.492

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2403G>T:p.(=)

Pathogenicity Data:: Best Score: 0.49242526; CADD: 0.492 (2.945)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582175TTTTACTGGTTGATCCTG>T [0/1] rs1367768660 (variation viewer)

Variant score: 0.492

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-354_371-338del:p.(=)

Pathogenicity Data:: Best Score: 0.4921915; CADD: 0.492 (2.943)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582176TTTACTGGTTGATCCTGG>T [0/1] rs1346651393 (variation viewer)

Variant score: 0.492

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-355_371-339del:p.(=)

Pathogenicity Data:: Best Score: 0.49172354; CADD: 0.492 (2.939)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32597734T>TTTTTTTTTCTTTTCTTTTTTTCTTTTA [1/1] rs1554134388 (variation viewer)

Variant score: 0.490

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.49031717; CADD: 0.490 (2.927)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584476T>TG [1|1] rs9281874 (variation viewer)

Variant score: 0.489

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-99_101-98insC:p.(=)

Pathogenicity Data:: Best Score: 0.4885537; CADD: 0.489 (2.912)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573667G>A [0/1] rs41291819 (variation viewer)

Variant score: 0.487

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.4872567; CADD: 0.487 (2.901)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582454A>G [1/1] rs9269844 (variation viewer)

Variant score: 0.486

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-616T>C:p.(=)

Pathogenicity Data:: Best Score: 0.486193; CADD: 0.486 (2.892)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586193C>T [0|1] rs200032445 (variation viewer)

Variant score: 0.486

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1815G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4860747; CADD: 0.486 (2.891)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582029AGGT>A [0|1] rs200474978 (variation viewer)

Variant score: 0.480

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-194_371-192del:p.(=)

Pathogenicity Data:: Best Score: 0.47964466; CADD: 0.480 (2.837)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577846G>GC [0|1] rs140730890 (variation viewer)

Variant score: 0.478

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.4782049; CADD: 0.478 (2.825)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585711T>C [0|1] rs9270038 (variation viewer)

Variant score: 0.478

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1333A>G:p.(=)

Pathogenicity Data:: Best Score: 0.47784436; CADD: 0.478 (2.822)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586908C>G [0/1] rs9270103 (variation viewer)

Variant score: 0.477

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2530G>C:p.(=)

Pathogenicity Data:: Best Score: 0.47700202; CADD: 0.477 (2.815)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574555C>T [0|1] rs41293676 (variation viewer)

Variant score: 0.477

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.47676116; CADD: 0.477 (2.813)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588561C>A [0|1] rs35399335 (variation viewer)

Variant score: 0.477

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1082G>T:p.(=)

Pathogenicity Data:: Best Score: 0.47652012; CADD: 0.477 (2.811)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587977A>G [1/1] rs9270176 (variation viewer)

Variant score: 0.474

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1666T>C:p.(=)

Pathogenicity Data:: Best Score: 0.47422493; CADD: 0.474 (2.792)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590046A>C [0|1] rs9270328 (variation viewer)

Variant score: 0.473

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.47264874; CADD: 0.473 (2.779)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585558G>A [0|1] rs200181846 (variation viewer)

Variant score: 0.472

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1180C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4716764; CADD: 0.472 (2.771)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586853T>C [0|1] rs115208896 (variation viewer)

Variant score: 0.470

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2475A>G:p.(=)

Pathogenicity Data:: Best Score: 0.46960425; CADD: 0.470 (2.754)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573988G>A [0|1] rs41293298 (variation viewer)

Variant score: 0.468

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.46752405; CADD: 0.468 (2.737)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577532A>G [0|1] rs41286403 (variation viewer)

Variant score: 0.464

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.46445; CADD: 0.464 (2.712)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32592536T>A [1/1] rs879865869 (variation viewer)

Variant score: 0.464

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.55679977; CADD: 0.557 (3.534)

Frequency Data:: gnomAD_G_AFR: 0.2778%; gnomAD_G_AMR: 0.1894%; gnomAD_G_FIN: 0.7968%; gnomAD_G_NFE: 0.0904%; gnomAD_G_OTH: 0.8013%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589562G>T [0|1] rs9270294 (variation viewer)

Variant score: 0.463

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+81C>A:p.(=)

Pathogenicity Data:: Best Score: 0.4634626; CADD: 0.463 (2.704)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573710A>G [0|1] rs9269416 (variation viewer)

Variant score: 0.463

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.46284455; CADD: 0.463 (2.699)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590498T>TA [0|1] rs1354686200 (variation viewer)

Variant score: 0.460

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.45986784; CADD: 0.460 (2.675)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573423G>GGGGGT [1/1] rs9281854 (variation viewer)

Variant score: 0.459

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.4589966; CADD: 0.459 (2.668)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588889TA>T [0/1] rs373061727 (variation viewer)

Variant score: 0.456

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+753del:p.(=)

Pathogenicity Data:: Best Score: 0.45624906; CADD: 0.456 (2.646)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590499T>TA [0|1] rs1443937067 (variation viewer)

Variant score: 0.455

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.45537192; CADD: 0.455 (2.639)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587286G>T [0|1] rs9270127 (variation viewer)

Variant score: 0.453

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2357C>A:p.(=)

Pathogenicity Data:: Best Score: 0.45298404; CADD: 0.453 (2.620)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590439G>T [-/1] rs9270374 (variation viewer)

Variant score: 0.451

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.4514705; CADD: 0.451 (2.608)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584803C>T [0/1] rs9461773 (variation viewer)

Variant score: 0.449

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-425G>A:p.(=)

Pathogenicity Data:: Best Score: 0.44906545; CADD: 0.449 (2.589)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586696T>C [0|1] rs72500541 (variation viewer)

Variant score: 0.444

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2318A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4435835; CADD: 0.444 (2.546)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582842C>T [0|1] rs41283767 (variation viewer)

Variant score: 0.443

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1004G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4433272; CADD: 0.443 (2.544)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584530A>C [1|1] rs9269973 (variation viewer)

Variant score: 0.443

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-152T>G:p.(=)

Pathogenicity Data:: Best Score: 0.4429425; CADD: 0.443 (2.541)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584627C>T [0|1] rs41287315 (variation viewer)

Variant score: 0.443

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-249G>A:p.(=)

Pathogenicity Data:: Best Score: 0.44255763; CADD: 0.443 (2.538)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589264C>T [0/1] rs9270256 (variation viewer)

Variant score: 0.439

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+379G>A:p.(=)

Pathogenicity Data:: Best Score: 0.43933946; CADD: 0.439 (2.513)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585311A>C [0|1] rs111336845 (variation viewer)

Variant score: 0.437

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-933T>G:p.(=)

Pathogenicity Data:: Best Score: 0.43701088; CADD: 0.437 (2.495)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574364C>G [0|1] rs41293341 (variation viewer)

Variant score: 0.435

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.43493295; CADD: 0.435 (2.479)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588813A>AC [-/1] rs1554130760 (variation viewer)

Variant score: 0.432

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+829_100+830insG:p.(=)

Pathogenicity Data:: Best Score: 0.4315399; CADD: 0.432 (2.453)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585257C>T [0/1] rs201889654 (variation viewer)

Variant score: 0.431

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-879G>A:p.(=)

Pathogenicity Data:: Best Score: 0.43101603; CADD: 0.431 (2.449)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585240T>A [0/1] rs35272048 (variation viewer)

Variant score: 0.430

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-862A>T:p.(=)

Pathogenicity Data:: Best Score: 0.43036062; CADD: 0.430 (2.444)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589590A>AG [0|1] rs1285965377 (variation viewer)

Variant score: 0.429

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+52_100+53insC:p.(=)

Pathogenicity Data:: Best Score: 0.4287845; CADD: 0.429 (2.432)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584536C>T [1|1] rs9269974 (variation viewer)

Variant score: 0.428

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-158G>A:p.(=)

Pathogenicity Data:: Best Score: 0.42812645; CADD: 0.428 (2.427)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574236T>C [0/1] rs41293330 (variation viewer)

Variant score: 0.426

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.4264121; CADD: 0.426 (2.414)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587149A>G [0|1] rs189754250 (variation viewer)

Variant score: 0.423

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2494T>C:p.(=)

Pathogenicity Data:: Best Score: 0.4234991; CADD: 0.423 (2.392)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589589A>ATTT [0|1] rs1246188251 (variation viewer)

Variant score: 0.423

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+53_100+54insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.42270207; CADD: 0.423 (2.386)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582488G>C [0|1] rs9269848 (variation viewer)

Variant score: 0.422

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-650C>G:p.(=)

Pathogenicity Data:: Best Score: 0.4217708; CADD: 0.422 (2.379)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585230G>A [0/1] rs9270017 (variation viewer)

Variant score: 0.422

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-852C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4215045; CADD: 0.422 (2.377)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588813A>ATAC [-/1] rs147921080 (variation viewer)

Variant score: 0.420

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+829_100+830insGTA:p.(=)

Pathogenicity Data:: Best Score: 0.42030442; CADD: 0.420 (2.368)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588440C>G [0/1] rs12661449 (variation viewer)

Variant score: 0.419

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1203G>C:p.(=)

Pathogenicity Data:: Best Score: 0.4192356; CADD: 0.419 (2.360)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587292G>T [0|1] rs796310820 (variation viewer)

Variant score: 0.419

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2351C>A:p.(=)

Pathogenicity Data:: Best Score: 0.41910183; CADD: 0.419 (2.359)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588244C>T [0/1] rs17210209 (variation viewer)

Variant score: 0.416

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1399G>A:p.(=)

Pathogenicity Data:: Best Score: 0.41642052; CADD: 0.416 (2.339)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589588A>C [0|1] rs35574533 (variation viewer)

Variant score: 0.413

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+55T>G:p.(=)

Pathogenicity Data:: Best Score: 0.4129163; CADD: 0.413 (2.313)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584814C>T [0/1] rs9269991 (variation viewer)

Variant score: 0.411

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-436G>A:p.(=)

Pathogenicity Data:: Best Score: 0.41088516; CADD: 0.411 (2.298)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574181A>T [0|1] rs41293318 (variation viewer)

Variant score: 0.410

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.41007066; CADD: 0.410 (2.292)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581027C>G [1|1] rs9269775 (variation viewer)

Variant score: 0.409

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-171G>C:p.(=)

Pathogenicity Data:: Best Score: 0.4093911; CADD: 0.409 (2.287)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581237G>T [0/1] rs9269784 (variation viewer)

Variant score: 0.408

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+320C>A:p.(=)

Pathogenicity Data:: Best Score: 0.40843838; CADD: 0.408 (2.280)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588453CAA>C [0|1] rs796115255 (variation viewer)

Variant score: 0.408

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1188_100+1189del:p.(=)

Pathogenicity Data:: Best Score: 0.4076205; CADD: 0.408 (2.274)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586562G>C [0/1] rs111297585 (variation viewer)

Variant score: 0.405

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2184C>G:p.(=)

Pathogenicity Data:: Best Score: 0.40529716; CADD: 0.405 (2.257)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573529CA>C [1|1] rs796948092 (variation viewer)

Variant score: 0.404

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.40420067; CADD: 0.404 (2.249)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575271G>C [1/1] rs9269495 (variation viewer)

Variant score: 0.397

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.39716285; CADD: 0.397 (2.198)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586244A>C [-/1] rs9270064 (variation viewer)

Variant score: 0.397

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1866T>G:p.(=)

Pathogenicity Data:: Best Score: 0.39716285; CADD: 0.397 (2.198)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582016C>T [0/1] rs7764811 (variation viewer)

Variant score: 0.395

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-178G>A:p.(=)

Pathogenicity Data:: Best Score: 0.39465916; CADD: 0.395 (2.180)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582299T>C [0|1] rs41293191 (variation viewer)

Variant score: 0.394

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-461A>G:p.(=)

Pathogenicity Data:: Best Score: 0.39424086; CADD: 0.394 (2.177)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586818C>A [0/1] rs72850294 (variation viewer)

Variant score: 0.392

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2440G>T:p.(=)

Pathogenicity Data:: Best Score: 0.39172494; CADD: 0.392 (2.159)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581469T>C [0/1] rs41292729 (variation viewer)

Variant score: 0.389

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+88A>G:p.(=)

Pathogenicity Data:: Best Score: 0.3886358; CADD: 0.389 (2.137)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582862A>G [0|1] rs9269866 (variation viewer)

Variant score: 0.386

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1024T>C:p.(=)

Pathogenicity Data:: Best Score: 0.38623798; CADD: 0.386 (2.120)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587728CTT>C [0|1] rs34904201 (variation viewer)

Variant score: 0.384

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1913_100+1914del:p.(=)

Pathogenicity Data:: Best Score: 0.38368887; CADD: 0.384 (2.102)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588285A>C [0/1] rs17210230 (variation viewer)

Variant score: 0.384

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1358T>G:p.(=)

Pathogenicity Data:: Best Score: 0.38368887; CADD: 0.384 (2.102)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582233T>C [0|1] rs28723981 (variation viewer)

Variant score: 0.384

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-395A>G:p.(=)

Pathogenicity Data:: Best Score: 0.38354695; CADD: 0.384 (2.101)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574642A>T [-/1] rs41293684 (variation viewer)

Variant score: 0.381

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3811292; CADD: 0.381 (2.084)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587241G>GAC [0|1] rs1425537509 (variation viewer)

Variant score: 0.381

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2401_100+2402insGT:p.(=)

Pathogenicity Data:: Best Score: 0.38070154; CADD: 0.381 (2.081)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589432T>G [-/1] rs9270271 (variation viewer)

Variant score: 0.380

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+211A>C:p.(=)

Pathogenicity Data:: Best Score: 0.38027358; CADD: 0.380 (2.078)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589581GTTA>G [0|1] rs369049717 (variation viewer)

Variant score: 0.380

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+59_100+61del:p.(=)

Pathogenicity Data:: Best Score: 0.3797025; CADD: 0.380 (2.074)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573673G>T [0|1] rs9269411 (variation viewer)

Variant score: 0.377

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.37698287; CADD: 0.377 (2.055)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582431A>G [0/1] rs9469172 (variation viewer)

Variant score: 0.373

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-593T>C:p.(=)

Pathogenicity Data:: Best Score: 0.37338614; CADD: 0.373 (2.030)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586051G>A [1/1] rs9270053 (variation viewer)

Variant score: 0.372

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1673C>T:p.(=)

Pathogenicity Data:: Best Score: 0.37179703; CADD: 0.372 (2.019)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590353G>A [0|1] rs572842430 (variation viewer)

Variant score: 0.367

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.36729681; CADD: 0.367 (1.988)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578076A>G [0/1] rs9269639 (variation viewer)

Variant score: 0.367

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.36715114; CADD: 0.367 (1.987)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590053G>T [0|1] rs9270331 (variation viewer)

Variant score: 0.367

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.3670054; CADD: 0.367 (1.986)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582328G>A [1/1] rs9269836 (variation viewer)

Variant score: 0.365

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-490C>T:p.(=)

Pathogenicity Data:: Best Score: 0.36540014; CADD: 0.365 (1.975)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586244A>T [-/1] rs9270064 (variation viewer)

Variant score: 0.365

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1866T>A:p.(=)

Pathogenicity Data:: Best Score: 0.36510777; CADD: 0.365 (1.973)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581200A>G [0|1] rs41288045 (variation viewer)

Variant score: 0.362

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-344T>C:p.(=)

Pathogenicity Data:: Best Score: 0.36188346; CADD: 0.362 (1.951)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588376CATAA>C [0/1] rs376490954 (variation viewer)

Variant score: 0.362

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1263_100+1266del:p.(=)

Pathogenicity Data:: Best Score: 0.36188346; CADD: 0.362 (1.951)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574822A>C [0|1] rs41293704 (variation viewer)

Variant score: 0.360

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.36041242; CADD: 0.360 (1.941)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585621A>G [0/1] rs9270033 (variation viewer)

Variant score: 0.359

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1243T>C:p.(=)

Pathogenicity Data:: Best Score: 0.35864276; CADD: 0.359 (1.929)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587722G>T [0|1] rs17203685 (variation viewer)

Variant score: 0.358

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1921C>A:p.(=)

Pathogenicity Data:: Best Score: 0.35805178; CADD: 0.358 (1.925)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574074C>G [0|1] rs41293306 (variation viewer)

Variant score: 0.357

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.35731226; CADD: 0.357 (1.920)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573722A>C [-/1] rs9269418 (variation viewer)

Variant score: 0.357

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.35716426; CADD: 0.357 (1.919)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573743T>C [0|1] rs9269421 (variation viewer)

Variant score: 0.356

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.35568237; CADD: 0.356 (1.909)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589552T>A [0|1] rs796807088 (variation viewer)

Variant score: 0.350

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+91A>T:p.(=)

Pathogenicity Data:: Best Score: 0.34987032; CADD: 0.350 (1.870)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585718A>G [0|1] rs879545490 (variation viewer)

Variant score: 0.349

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1340T>C:p.(=)

Pathogenicity Data:: Best Score: 0.34942108; CADD: 0.349 (1.867)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574049G>A [0|1] rs41293302 (variation viewer)

Variant score: 0.349

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.34867162; CADD: 0.349 (1.862)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590224A>G [1|1] rs796672792 (variation viewer)

Variant score: 0.348

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.34837162; CADD: 0.348 (1.860)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582104G>T [1/1] rs9269828 (variation viewer)

Variant score: 0.347

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-266C>A:p.(=)

Pathogenicity Data:: Best Score: 0.3470198; CADD: 0.347 (1.851)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587032A>G [0/1] rs9270108 (variation viewer)

Variant score: 0.342

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2611T>C:p.(=)

Pathogenicity Data:: Best Score: 0.34158456; CADD: 0.342 (1.815)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573722A>T [-/1] rs9269418 (variation viewer)

Variant score: 0.341

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.34067434; CADD: 0.341 (1.809)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574856C>T [0/1] rs41293716 (variation viewer)

Variant score: 0.340

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3400668; CADD: 0.340 (1.805)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588997C>T [0/1] rs34896989 (variation viewer)

Variant score: 0.338

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+646G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3382408; CADD: 0.338 (1.793)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578722T>TTTTTC [-/1] rs141643218 (variation viewer)

Variant score: 0.338

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.33778346; CADD: 0.338 (1.790)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581284G>GC [0|1] rs34617615 (variation viewer)

Variant score: 0.338

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+272_652+273insG:p.(=)

Pathogenicity Data:: Best Score: 0.337631; CADD: 0.338 (1.789)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575431TCTTCTAAATC>T [0|1] rs369585140 (variation viewer)

Variant score: 0.337

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.33717328; CADD: 0.337 (1.786)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574072TA>T [0/1] rs562351919 (variation viewer)

Variant score: 0.335

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.33503312; CADD: 0.335 (1.772)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582456G>A [0/1] rs7765659 (variation viewer)

Variant score: 0.334

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-618C>T:p.(=)

Pathogenicity Data:: Best Score: 0.33426714; CADD: 0.334 (1.767)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587734C>CA [0|1] rs1554129854 (variation viewer)

Variant score: 0.328

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1908_100+1909insT:p.(=)

Pathogenicity Data:: Best Score: 0.32764292; CADD: 0.328 (1.724)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575756G>T [0/1] rs41294259 (variation viewer)

Variant score: 0.326

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.32562727; CADD: 0.326 (1.711)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590599C>T [1|1] rs9270393 (variation viewer)

Variant score: 0.325

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.32531667; CADD: 0.325 (1.709)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585364A>G [0|1] rs796081718 (variation viewer)

Variant score: 0.325

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-986T>C:p.(=)

Pathogenicity Data:: Best Score: 0.32485044; CADD: 0.325 (1.706)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586220T>C [0|1] rs9270063 (variation viewer)

Variant score: 0.323

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1842A>G:p.(=)

Pathogenicity Data:: Best Score: 0.32313824; CADD: 0.323 (1.695)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586490A>T [-/1] rs9270084 (variation viewer)

Variant score: 0.322

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2112T>A:p.(=)

Pathogenicity Data:: Best Score: 0.32220244; CADD: 0.322 (1.689)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575316G>A [0/1] rs9469152 (variation viewer)

Variant score: 0.321

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3209527; CADD: 0.321 (1.681)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590734T>A [1|1] rs904376607 (variation viewer)

Variant score: 0.321

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.32063997; CADD: 0.321 (1.679)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587984C>T [0/1] rs9270177 (variation viewer)

Variant score: 0.320

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1659G>A:p.(=)

Pathogenicity Data:: Best Score: 0.32032704; CADD: 0.320 (1.677)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580503G>A [1/1] rs9269761 (variation viewer)

Variant score: 0.320

Transcripts:: HLA-DRB1:ENST00000360004.5:c.764-233C>T:p.(=)

Pathogenicity Data:: Best Score: 0.32001394; CADD: 0.320 (1.675)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573132G>T [1|1] rs9269377 (variation viewer)

Variant score: 0.320

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.33717328; CADD: 0.337 (1.786)

Frequency Data:: gnomAD_G_AFR: 0.3221%; gnomAD_G_AMR: 0.3049%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.1799%; gnomAD_G_OTH: 0.2381%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585149CAT>C [0/1]

Variant score: 0.318

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-773_101-772del:p.(=)

Pathogenicity Data:: Best Score: 0.31750417; CADD: 0.318 (1.659)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574832A>G [0|1] rs35787784 (variation viewer)

Variant score: 0.310

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3102368; CADD: 0.310 (1.613)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577479C>G [0|1] rs41284941 (variation viewer)

Variant score: 0.310

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.30991912; CADD: 0.310 (1.611)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590558GC>G [0|1] rs371442426 (variation viewer)

Variant score: 0.310

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.30991912; CADD: 0.310 (1.611)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575861A>G [0/1] rs9269521 (variation viewer)

Variant score: 0.308

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.30753154; CADD: 0.308 (1.596)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574178G>A [0|1] rs9269443 (variation viewer)

Variant score: 0.307

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.30705303; CADD: 0.307 (1.593)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584861C>G [0/1] rs370336500 (variation viewer)

Variant score: 0.306

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-483G>C:p.(=)

Pathogenicity Data:: Best Score: 0.3062548; CADD: 0.306 (1.588)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578657G>A [0|1] rs41287178 (variation viewer)

Variant score: 0.306

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.30593526; CADD: 0.306 (1.586)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574639TTGACC>T [0|1] rs780509830 (variation viewer)

Variant score: 0.305

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3049757; CADD: 0.305 (1.580)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574936C>A [0|1] rs41293740 (variation viewer)

Variant score: 0.305

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3049757; CADD: 0.305 (1.580)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573860ATTAAG>A [0/1] rs149554396 (variation viewer)

Variant score: 0.304

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.30417502; CADD: 0.304 (1.575)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581336AGGG>A [0|1] rs1208984938 (variation viewer)

Variant score: 0.304

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+218_652+220del:p.(=)

Pathogenicity Data:: Best Score: 0.30385453; CADD: 0.304 (1.573)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575554TA>T [1|1] rs879347036 (variation viewer)

Variant score: 0.302

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3020891; CADD: 0.302 (1.562)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575512C>T [0|1] rs35210979 (variation viewer)

Variant score: 0.295

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.29530692; CADD: 0.295 (1.520)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585061T>TG [1/1] rs9281878 (variation viewer)

Variant score: 0.294

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-684_101-683insC:p.(=)

Pathogenicity Data:: Best Score: 0.29449517; CADD: 0.294 (1.515)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581221C>A [0|1] rs41288053 (variation viewer)

Variant score: 0.294

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+336G>T:p.(=)

Pathogenicity Data:: Best Score: 0.29400766; CADD: 0.294 (1.512)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585322T>A [1|1] rs9270020 (variation viewer)

Variant score: 0.290

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-944A>T:p.(=)

Pathogenicity Data:: Best Score: 0.2899319; CADD: 0.290 (1.487)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574839ATG>A [0|1] rs879793780 (variation viewer)

Variant score: 0.289

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.28862268; CADD: 0.289 (1.479)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573668C>T [0|1] rs9269410 (variation viewer)

Variant score: 0.287

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.28681862; CADD: 0.287 (1.468)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32572950TAG>T [1|1] rs9279702 (variation viewer)

Variant score: 0.283

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.38567245; CADD: 0.386 (2.116)

Frequency Data:: gnomAD_G_AFR: 0.5571%; gnomAD_G_AMR: 1.0870%; gnomAD_G_EAS: 0.2083%; gnomAD_G_FIN: 0.2203%; gnomAD_G_NFE: 0.4474%; gnomAD_G_OTH: 0.2475%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582739CCTAT>C [0|1] rs1259659264 (variation viewer)

Variant score: 0.281

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-905_371-902del:p.(=)

Pathogenicity Data:: Best Score: 0.28104782; CADD: 0.281 (1.433)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574395C>T [0|1] rs9269462 (variation viewer)

Variant score: 0.277

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.27656418; CADD: 0.277 (1.406)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574651G>A [0|1] rs41293688 (variation viewer)

Variant score: 0.276

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.2763976; CADD: 0.276 (1.405)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577632T>C [0|1] rs7738986 (variation viewer)

Variant score: 0.276

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.2763976; CADD: 0.276 (1.405)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576187GTTT>G [-/1] rs374587370 (variation viewer)

Variant score: 0.276

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.27573085; CADD: 0.276 (1.401)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585556C>T [0|1] rs201892461 (variation viewer)

Variant score: 0.275

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1178G>A:p.(=)

Pathogenicity Data:: Best Score: 0.27456254; CADD: 0.275 (1.394)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587226CA>C [0|1] rs41288203 (variation viewer)

Variant score: 0.274

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2416del:p.(=)

Pathogenicity Data:: Best Score: 0.273894; CADD: 0.274 (1.390)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576187GT>G [-/1] rs374587370 (variation viewer)

Variant score: 0.273

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.27305758; CADD: 0.273 (1.385)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582301TAAAAC>T [0|1] rs374058573 (variation viewer)

Variant score: 0.270

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-468_371-464del:p.(=)

Pathogenicity Data:: Best Score: 0.26987034; CADD: 0.270 (1.366)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586130C>T [0|1] rs9270057 (variation viewer)

Variant score: 0.267

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1752G>A:p.(=)

Pathogenicity Data:: Best Score: 0.26734418; CADD: 0.267 (1.351)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585199A>G [0|1] rs1456182418 (variation viewer)

Variant score: 0.266

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-821T>C:p.(=)

Pathogenicity Data:: Best Score: 0.26616234; CADD: 0.266 (1.344)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587738A>C [0|1] rs17203699 (variation viewer)

Variant score: 0.265

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1905T>G:p.(=)

Pathogenicity Data:: Best Score: 0.26531696; CADD: 0.265 (1.339)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574825TG>T [0|1] rs781500344 (variation viewer)

Variant score: 0.265

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.2648093; CADD: 0.265 (1.336)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574349C>CTTTG [0|1] rs142563472 (variation viewer)

Variant score: 0.263

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.26328415; CADD: 0.263 (1.327)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585541C>A [1|1] rs9270029 (variation viewer)

Variant score: 0.261

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1163G>T:p.(=)

Pathogenicity Data:: Best Score: 0.26141578; CADD: 0.261 (1.316)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584711G>A [0|1] rs28724130 (variation viewer)

Variant score: 0.261

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-333C>T:p.(=)

Pathogenicity Data:: Best Score: 0.26090544; CADD: 0.261 (1.313)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585398C>A [0|1] rs34016316 (variation viewer)

Variant score: 0.259

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1020G>T:p.(=)

Pathogenicity Data:: Best Score: 0.25851905; CADD: 0.259 (1.299)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587618A>G [1|1] rs9270155 (variation viewer)

Variant score: 0.258

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2025T>C:p.(=)

Pathogenicity Data:: Best Score: 0.25817752; CADD: 0.258 (1.297)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579223TC>T [1|1] rs67419769 (variation viewer)

Variant score: 0.257

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-120del:p.(=)

Pathogenicity Data:: Best Score: 0.2574939; CADD: 0.257 (1.293)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32591169G>A [1|1] rs9270467 (variation viewer)

Variant score: 0.254

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.25441015; CADD: 0.254 (1.275)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589144G>T [0/1] rs9270238 (variation viewer)

Variant score: 0.253

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+499C>A:p.(=)

Pathogenicity Data:: Best Score: 0.25337934; CADD: 0.253 (1.269)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584893C>T [0/1] rs9269993 (variation viewer)

Variant score: 0.250

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-515G>A:p.(=)

Pathogenicity Data:: Best Score: 0.24993312; CADD: 0.250 (1.249)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586874T>C [0/1] rs111375569 (variation viewer)

Variant score: 0.245

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2496A>G:p.(=)

Pathogenicity Data:: Best Score: 0.2450816; CADD: 0.245 (1.221)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584954C>A [1/1] rs9269999 (variation viewer)

Variant score: 0.241

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-576G>T:p.(=)

Pathogenicity Data:: Best Score: 0.24142241; CADD: 0.241 (1.200)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573902C>T [0/1] rs9269432 (variation viewer)

Variant score: 0.241

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.24124771; CADD: 0.241 (1.199)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582519T>C [0|1] rs9269851 (variation viewer)

Variant score: 0.240

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-681A>G:p.(=)

Pathogenicity Data:: Best Score: 0.24037367; CADD: 0.240 (1.194)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588817A>G [0|1] rs28724211 (variation viewer)

Variant score: 0.238

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+826T>C:p.(=)

Pathogenicity Data:: Best Score: 0.23809648; CADD: 0.238 (1.181)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574298C>A [0/1] rs9269453 (variation viewer)

Variant score: 0.237

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.23739439; CADD: 0.237 (1.177)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586230C>T [0/1] rs34891954 (variation viewer)

Variant score: 0.237

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1852G>A:p.(=)

Pathogenicity Data:: Best Score: 0.23686743; CADD: 0.237 (1.174)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577586C>A [0/1] rs2894271 (variation viewer)

Variant score: 0.234

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.23369795; CADD: 0.234 (1.156)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587120C>T [-/1] rs76533559 (variation viewer)

Variant score: 0.233

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2523G>A:p.(=)

Pathogenicity Data:: Best Score: 0.23299181; CADD: 0.233 (1.152)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578092A>G [0/1] rs9269641 (variation viewer)

Variant score: 0.229

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.22945148; CADD: 0.229 (1.132)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585973C>G [0|1] rs879909843 (variation viewer)

Variant score: 0.228

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1595G>C:p.(=)

Pathogenicity Data:: Best Score: 0.227853; CADD: 0.228 (1.123)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579360C>CA [0|1] rs9281865 (variation viewer)

Variant score: 0.227

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-257_788-256insT:p.(=)

Pathogenicity Data:: Best Score: 0.22696352; CADD: 0.227 (1.118)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587622C>G [-/1] rs9270156 (variation viewer)

Variant score: 0.226

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2021G>C:p.(=)

Pathogenicity Data:: Best Score: 0.22625118; CADD: 0.226 (1.114)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579416C>CAAGA [1|1] rs1320933846 (variation viewer)

Variant score: 0.225

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-313_788-312insTCTT:p.(=)

Pathogenicity Data:: Best Score: 0.22464603; CADD: 0.225 (1.105)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574209T>C [0|1] rs9269446 (variation viewer)

Variant score: 0.223

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.22321647; CADD: 0.223 (1.097)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574902C>G [0/1] rs9269483 (variation viewer)

Variant score: 0.220

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.2201699; CADD: 0.220 (1.080)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588221C>T [0/1] rs17203853 (variation viewer)

Variant score: 0.219

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1422G>A:p.(=)

Pathogenicity Data:: Best Score: 0.21855211; CADD: 0.219 (1.071)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586225T>G [0/1] rs111734989 (variation viewer)

Variant score: 0.218

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1847A>C:p.(=)

Pathogenicity Data:: Best Score: 0.21837223; CADD: 0.218 (1.070)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590748C>A [1|1] rs9270416 (variation viewer)

Variant score: 0.217

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.21747178; CADD: 0.217 (1.065)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577883G>A [0|1] rs9269631 (variation viewer)

Variant score: 0.217

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.21711135; CADD: 0.217 (1.063)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588467AAG>A [-/1] rs1310727485 (variation viewer)

Variant score: 0.217

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1174_100+1175del:p.(=)

Pathogenicity Data:: Best Score: 0.21675074; CADD: 0.217 (1.061)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588468AG>A [-/1] rs1561839237 (variation viewer)

Variant score: 0.216

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1174del:p.(=)

Pathogenicity Data:: Best Score: 0.21584845; CADD: 0.216 (1.056)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590254G>T [1|1] rs9270350 (variation viewer)

Variant score: 0.214

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.21440268; CADD: 0.214 (1.048)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585142A>AT [1|1] rs375669474 (variation viewer)

Variant score: 0.214

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-765_101-764insA:p.(=)

Pathogenicity Data:: Best Score: 0.21404082; CADD: 0.214 (1.046)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587307A>G [0|1] rs34839446 (variation viewer)

Variant score: 0.214

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2336T>C:p.(=)

Pathogenicity Data:: Best Score: 0.21404082; CADD: 0.214 (1.046)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574240T>A [0/1] rs9269449 (variation viewer)

Variant score: 0.213

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.2134977; CADD: 0.213 (1.043)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577900T>C [0|1] rs9269633 (variation viewer)

Variant score: 0.212

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.21186614; CADD: 0.212 (1.034)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587622C>A [-/1] rs9270156 (variation viewer)

Variant score: 0.210

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2021G>T:p.(=)

Pathogenicity Data:: Best Score: 0.21041298; CADD: 0.210 (1.026)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590603G>T [1|1] rs9270394 (variation viewer)

Variant score: 0.209

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.2089572; CADD: 0.209 (1.018)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579188G>A [0|1] rs41287216 (variation viewer)

Variant score: 0.208

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-84C>T:p.(=)

Pathogenicity Data:: Best Score: 0.20786357; CADD: 0.208 (1.012)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574087A>G [0/1] rs4713541 (variation viewer)

Variant score: 0.205

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.20548886; CADD: 0.205 (0.999)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578087C>CGTA [0/1] rs150855046 (variation viewer)

Variant score: 0.201

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.20053399; CADD: 0.201 (0.972)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574410C>A [0|1] rs9269463 (variation viewer)

Variant score: 0.199

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.19924438; CADD: 0.199 (0.965)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585872T>C [0/1] rs9270044 (variation viewer)

Variant score: 0.199

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1494A>G:p.(=)

Pathogenicity Data:: Best Score: 0.19924438; CADD: 0.199 (0.965)

Frequency Data:: No frequency data

MISSENSE_VARIANT chr6:g.32584171G>A [0|1] rs766169385 (variation viewer)

Variant score: 0.198

Transcripts:: HLA-DRB1:ENST00000360004.5:c.308C>T:p.(Ala103Val)

Pathogenicity Data:: Best Score: 0.926; Polyphen2: 0.038 (B); SIFT: 0.074 (T); CADD: 0.002 (0.009)

Frequency Data:: gnomAD_E_AFR: 0.9538%; gnomAD_E_AMR: 0.0374%; gnomAD_E_EAS: 0.0215%; gnomAD_E_NFE: 0.0264%; gnomAD_E_SAS: 0.0502%; gnomAD_G_AFR: 1.9182%; gnomAD_G_AMR: 0.5769%; gnomAD_G_EAS: 0.0996%; gnomAD_G_FIN: 0.3546%; gnomAD_G_NFE: 0.0576%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582894G>A [0|1] rs41283777 (variation viewer)

Variant score: 0.198

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1056C>T:p.(=)

Pathogenicity Data:: Best Score: 0.19795269; CADD: 0.198 (0.958)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573816C>CT [1|1] rs9281855 (variation viewer)

Variant score: 0.198

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.1975832; CADD: 0.198 (0.956)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581295T>C [0|1] rs28732313 (variation viewer)

Variant score: 0.197

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+262A>G:p.(=)

Pathogenicity Data:: Best Score: 0.19721359; CADD: 0.197 (0.954)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32591157ACAAAC>A [1|1] rs143735534 (variation viewer)

Variant score: 0.196

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.19591862; CADD: 0.196 (0.947)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587314G>A [0|1] rs9270130 (variation viewer)

Variant score: 0.195

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2329C>T:p.(=)

Pathogenicity Data:: Best Score: 0.19499236; CADD: 0.195 (0.942)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585125TTC>T [0/1] rs1347472633 (variation viewer)

Variant score: 0.193

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-749_101-748del:p.(=)

Pathogenicity Data:: Best Score: 0.192765; CADD: 0.193 (0.930)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577544G>A [0/1] rs9269616 (variation viewer)

Variant score: 0.186

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.18585831; CADD: 0.186 (0.893)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582864AACT>A [0/1] rs150012197 (variation viewer)

Variant score: 0.185

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1029_371-1027del:p.(=)

Pathogenicity Data:: Best Score: 0.18473274; CADD: 0.185 (0.887)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581117G>A [0/1] rs41286837 (variation viewer)

Variant score: 0.184

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-261C>T:p.(=)

Pathogenicity Data:: Best Score: 0.18360561; CADD: 0.184 (0.881)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574151T>G [0|1] rs9269440 (variation viewer)

Variant score: 0.181

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.18134671; CADD: 0.181 (0.869)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581205T>C [0|1] rs41288049 (variation viewer)

Variant score: 0.181

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-349A>G:p.(=)

Pathogenicity Data:: Best Score: 0.18134671; CADD: 0.181 (0.869)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575491A>C [0|1] rs9269510 (variation viewer)

Variant score: 0.181

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.18096966; CADD: 0.181 (0.867)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589551A>T [0|1] rs28366217 (variation viewer)

Variant score: 0.181

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+92T>A:p.(=)

Pathogenicity Data:: Best Score: 0.180781; CADD: 0.181 (0.866)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573872T>G [1|1] rs9269430 (variation viewer)

Variant score: 0.180

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.17983735; CADD: 0.180 (0.861)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575268C>T [0/1] rs115231074 (variation viewer)

Variant score: 0.178

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.17775732; CADD: 0.178 (0.850)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577541T>C [0|1] rs41286407 (variation viewer)

Variant score: 0.177

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.17718917; CADD: 0.177 (0.847)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574933T>C [0|1] rs41293736 (variation viewer)

Variant score: 0.175

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.17491251; CADD: 0.175 (0.835)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588008C>T [0/1] rs41288151 (variation viewer)

Variant score: 0.175

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1635G>A:p.(=)

Pathogenicity Data:: Best Score: 0.17491251; CADD: 0.175 (0.835)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574656T>A [0|1] rs41293692 (variation viewer)

Variant score: 0.175

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.1747225; CADD: 0.175 (0.834)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587296C>T [0|1] rs34197017 (variation viewer)

Variant score: 0.175

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2347G>A:p.(=)

Pathogenicity Data:: Best Score: 0.17453247; CADD: 0.175 (0.833)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32571910G>GAA [1|1] rs1207454137 (variation viewer)

Variant score: 0.174

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.17377186; CADD: 0.174 (0.829)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574152A>G [0|1] rs9269441 (variation viewer)

Variant score: 0.172

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.17205787; CADD: 0.172 (0.820)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578594AC>A [0|1] rs760484737 (variation viewer)

Variant score: 0.170

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.16957581; CADD: 0.170 (0.807)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583331AGG>A [0/1] rs1353644703 (variation viewer)

Variant score: 0.169

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+776_370+777del:p.(=)

Pathogenicity Data:: Best Score: 0.1688106; CADD: 0.169 (0.803)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575306GT>G [0/1] rs66908846 (variation viewer)

Variant score: 0.167

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.1670863; CADD: 0.167 (0.794)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582870T>G [0|1] rs41283772 (variation viewer)

Variant score: 0.167

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1032A>C:p.(=)

Pathogenicity Data:: Best Score: 0.16651076; CADD: 0.167 (0.791)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575569A>G [0|1] rs41294256 (variation viewer)

Variant score: 0.165

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.16516626; CADD: 0.165 (0.784)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575336AAGC>A [0|1] rs879575970 (variation viewer)

Variant score: 0.165

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.16458935; CADD: 0.165 (0.781)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582287G>T [0|1] rs41293185 (variation viewer)

Variant score: 0.162

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-449C>A:p.(=)

Pathogenicity Data:: Best Score: 0.161699; CADD: 0.162 (0.766)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582520C>G [1|1] rs9269852 (variation viewer)

Variant score: 0.161

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-682G>C:p.(=)

Pathogenicity Data:: Best Score: 0.16092652; CADD: 0.161 (0.762)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585832C>T [0|1] rs201095119 (variation viewer)

Variant score: 0.159

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1454G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15899223; CADD: 0.159 (0.752)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575328T>C [0|1] rs9269500 (variation viewer)

Variant score: 0.158

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.15802342; CADD: 0.158 (0.747)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578644C>T [-/1] rs9269670 (variation viewer)

Variant score: 0.158

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.15782952; CADD: 0.158 (0.746)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578295A>ACTCC [0|1] rs41284667 (variation viewer)

Variant score: 0.156

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.15608245; CADD: 0.156 (0.737)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585713C>G [0|1] rs9270039 (variation viewer)

Variant score: 0.156

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1335G>C:p.(=)

Pathogenicity Data:: Best Score: 0.15569377; CADD: 0.156 (0.735)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584750A>T [1|1] rs9269984 (variation viewer)

Variant score: 0.155

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-372T>A:p.(=)

Pathogenicity Data:: Best Score: 0.15511036; CADD: 0.155 (0.732)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586657C>T [0/1] rs115208602 (variation viewer)

Variant score: 0.154

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2279G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15355253; CADD: 0.154 (0.724)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578039G>A [0/1] rs3763328 (variation viewer)

Variant score: 0.153

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.15296763; CADD: 0.153 (0.721)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578211GATT>G [0/1] rs71954614 (variation viewer)

Variant score: 0.152

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.15238231; CADD: 0.152 (0.718)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582503A>AT [1|1] rs9281869 (variation viewer)

Variant score: 0.148

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-666_371-665insA:p.(=)

Pathogenicity Data:: Best Score: 0.14788151; CADD: 0.148 (0.695)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586367G>A [1|1] rs9270075 (variation viewer)

Variant score: 0.147

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1989C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14748901; CADD: 0.147 (0.693)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587740C>CAT [0|1] rs1333087978 (variation viewer)

Variant score: 0.147

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1902_100+1903insAT:p.(=)

Pathogenicity Data:: Best Score: 0.14748901; CADD: 0.147 (0.693)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574909G>A [0|1] rs41293728 (variation viewer)

Variant score: 0.146

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.14552373; CADD: 0.146 (0.683)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582497G>A [0|1] rs9269850 (variation viewer)

Variant score: 0.145

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-659C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14493328; CADD: 0.145 (0.680)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581404C>CTGT [0|1]

Variant score: 0.144

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+152_652+153insACA:p.(=)

Pathogenicity Data:: Best Score: 0.14394832; CADD: 0.144 (0.675)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575798C>T [0/1] rs41294271 (variation viewer)

Variant score: 0.138

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13841128; CADD: 0.138 (0.647)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574653C>A [0|1] rs9269475 (variation viewer)

Variant score: 0.138

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13761735; CADD: 0.138 (0.643)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586374C>G [0/1] rs35435859 (variation viewer)

Variant score: 0.137

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1996G>C:p.(=)

Pathogenicity Data:: Best Score: 0.13722014; CADD: 0.137 (0.641)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575484A>G [0|1] rs41294247 (variation viewer)

Variant score: 0.136

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13582838; CADD: 0.136 (0.634)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582745A>AG [0|1] rs377300772 (variation viewer)

Variant score: 0.134

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-908_371-907insC:p.(=)

Pathogenicity Data:: Best Score: 0.13443434; CADD: 0.134 (0.627)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588460AG>A [0/1] rs879659436 (variation viewer)

Variant score: 0.134

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1182del:p.(=)

Pathogenicity Data:: Best Score: 0.13383627; CADD: 0.134 (0.624)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588562T>TG [0|1] rs41288212 (variation viewer)

Variant score: 0.134

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1080_100+1081insC:p.(=)

Pathogenicity Data:: Best Score: 0.13363677; CADD: 0.134 (0.623)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32597847CCA>C [1/1] rs796886436 (variation viewer)

Variant score: 0.132

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.13183957; CADD: 0.132 (0.614)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575807G>A [0/1] rs41294275 (variation viewer)

Variant score: 0.131

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13143963; CADD: 0.131 (0.612)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578471TCA>T [0/1] rs768097418 (variation viewer)

Variant score: 0.131

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13083947; CADD: 0.131 (0.609)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578644C>G [-/1] rs9269670 (variation viewer)

Variant score: 0.131

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13083947; CADD: 0.131 (0.609)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574319T>C [0/1] rs9269456 (variation viewer)

Variant score: 0.131

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.13063931; CADD: 0.131 (0.608)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582804G>A [0|1] rs28724012 (variation viewer)

Variant score: 0.130

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-966C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12963784; CADD: 0.130 (0.603)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575556TA>T [1|1] rs879530039 (variation viewer)

Variant score: 0.128

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.12823385; CADD: 0.128 (0.596)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573040TC>T [1|1] rs9279703 (variation viewer)

Variant score: 0.128

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.1392045; CADD: 0.139 (0.651)

Frequency Data:: gnomAD_G_AFR: 0.3404%; gnomAD_G_EAS: 0.4739%; gnomAD_G_FIN: 0.0597%; gnomAD_G_NFE: 0.1559%; gnomAD_G_OTH: 0.2660%

DOWNSTREAM_GENE_VARIANT chr6:g.32576231C>T [0|1] rs34673067 (variation viewer)

Variant score: 0.126

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.126023; CADD: 0.126 (0.585)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590240A>C [1|1] rs9270349 (variation viewer)

Variant score: 0.124

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578470CTCA>C [0/1] rs34413789 (variation viewer)

Variant score: 0.124

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.123806536; CADD: 0.124 (0.574)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587828C>G [0|1] rs9270164 (variation viewer)

Variant score: 0.124

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1815G>C:p.(=)

Pathogenicity Data:: Best Score: 0.123604774; CADD: 0.124 (0.573)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588466A>ATATT [0|1] rs1375533963 (variation viewer)

Variant score: 0.123

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1176_100+1177insAATA:p.(=)

Pathogenicity Data:: Best Score: 0.12340295; CADD: 0.123 (0.572)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582387A>G [1|1] rs9269841 (variation viewer)

Variant score: 0.123

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-549T>C:p.(=)

Pathogenicity Data:: Best Score: 0.12259519; CADD: 0.123 (0.568)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582364T>C [0|1] rs41293201 (variation viewer)

Variant score: 0.122

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-526A>G:p.(=)

Pathogenicity Data:: Best Score: 0.12198889; CADD: 0.122 (0.565)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588467A>ACT [-/1]

Variant score: 0.122

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1175_100+1176insAG:p.(=)

Pathogenicity Data:: Best Score: 0.12178671; CADD: 0.122 (0.564)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585363C>G [0|1] rs878904795 (variation viewer)

Variant score: 0.121

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-985G>C:p.(=)

Pathogenicity Data:: Best Score: 0.120775044; CADD: 0.121 (0.559)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574407G>C [0|1] rs41293652 (variation viewer)

Variant score: 0.120

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.12037003; CADD: 0.120 (0.557)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578142AAAC>A [0/1] rs748533648 (variation viewer)

Variant score: 0.120

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.12823385; CADD: 0.128 (0.596)

Frequency Data:: UK10K: 0.3835%

DOWNSTREAM_GENE_VARIANT chr6:g.32578068CTT>C [0/1] rs1333692336 (variation viewer)

Variant score: 0.119

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.11935675; CADD: 0.119 (0.552)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586494G>T [-/1] rs9270085 (variation viewer)

Variant score: 0.119

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2116C>A:p.(=)

Pathogenicity Data:: Best Score: 0.11895114; CADD: 0.119 (0.550)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575448G>T [1|1] rs9269507 (variation viewer)

Variant score: 0.119

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.11874825; CADD: 0.119 (0.549)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582067T>G [1|1] rs9269824 (variation viewer)

Variant score: 0.118

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-229A>C:p.(=)

Pathogenicity Data:: Best Score: 0.117936194; CADD: 0.118 (0.545)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582812G>T [0|1] rs41283762 (variation viewer)

Variant score: 0.117

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-974C>A:p.(=)

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586261GC>G [0/1] rs1561827392 (variation viewer)

Variant score: 0.117

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1884del:p.(=)

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586541C>G [0|1] rs372037414 (variation viewer)

Variant score: 0.117

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2163G>C:p.(=)

Pathogenicity Data:: Best Score: 0.11651331; CADD: 0.117 (0.538)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574907C>G [0|1] rs41293724 (variation viewer)

Variant score: 0.115

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.11468053; CADD: 0.115 (0.529)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587297G>T [0|1] rs34999845 (variation viewer)

Variant score: 0.114

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2346C>A:p.(=)

Pathogenicity Data:: Best Score: 0.11427277; CADD: 0.114 (0.527)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575854A>G [0/1] rs34943833 (variation viewer)

Variant score: 0.114

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.11386478; CADD: 0.114 (0.525)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589290CT>C [0/1] rs373834506 (variation viewer)

Variant score: 0.112

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+352del:p.(=)

Pathogenicity Data:: Best Score: 0.11223096; CADD: 0.112 (0.517)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577675G>T [0|1] rs9269618 (variation viewer)

Variant score: 0.112

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.11182201; CADD: 0.112 (0.515)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576047CT>C [0|1] rs368101921 (variation viewer)

Variant score: 0.110

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.11038929; CADD: 0.110 (0.508)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578149TTTTAA>T [0/1] rs756359623 (variation viewer)

Variant score: 0.110

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.10997951; CADD: 0.110 (0.506)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575031C>T [0|1] rs9269487 (variation viewer)

Variant score: 0.108

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.1079278; CADD: 0.108 (0.496)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580435C>G [-/1] rs9269757 (variation viewer)

Variant score: 0.108

Transcripts:: HLA-DRB1:ENST00000360004.5:c.764-165G>C:p.(=)

Pathogenicity Data:: Best Score: 0.107516885; CADD: 0.108 (0.494)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582198GTTTT>G [-/1] rs141131278 (variation viewer)

Variant score: 0.107

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-364_371-361del:p.(=)

Pathogenicity Data:: Best Score: 0.10731137; CADD: 0.107 (0.493)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574357G>A [0|1] rs9269457 (variation viewer)

Variant score: 0.106

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.106077254; CADD: 0.106 (0.487)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32591133A>ATG [1|1] rs1311072552 (variation viewer)

Variant score: 0.106

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.10587138; CADD: 0.106 (0.486)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575897T>TGTTC [0/1] rs41284646 (variation viewer)

Variant score: 0.104

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.104222775; CADD: 0.104 (0.478)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575840G>A [1/1] rs9269520 (variation viewer)

Variant score: 0.104

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.10401654; CADD: 0.104 (0.477)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574913T>C [0|1] rs41293732 (variation viewer)

Variant score: 0.104

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.10381019; CADD: 0.104 (0.476)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585911T>A [0/1] rs9283900 (variation viewer)

Variant score: 0.104

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1533A>T:p.(=)

Pathogenicity Data:: Best Score: 0.10381019; CADD: 0.104 (0.476)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575873T>A [0/1] rs35144732 (variation viewer)

Variant score: 0.100

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.10008812; CADD: 0.100 (0.458)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580435C>A [-/1] rs9269757 (variation viewer)

Variant score: 0.099

Transcripts:: HLA-DRB1:ENST00000360004.5:c.764-165G>T:p.(=)

Pathogenicity Data:: Best Score: 0.099051416; CADD: 0.099 (0.453)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585706C>T [0|1] rs201604491 (variation viewer)

Variant score: 0.099

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1328G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09863645; CADD: 0.099 (0.451)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578236G>A [0/1] rs9269646 (variation viewer)

Variant score: 0.098

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09801358; CADD: 0.098 (0.448)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575793G>A [0/1] rs41294267 (variation viewer)

Variant score: 0.098

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09780586; CADD: 0.098 (0.447)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588558A>AGAG [0|1] rs28986207 (variation viewer)

Variant score: 0.098

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1084_100+1085insCTC:p.(=)

Pathogenicity Data:: Best Score: 0.097598135; CADD: 0.098 (0.446)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577649A>T [1|1] rs9269617 (variation viewer)

Variant score: 0.097

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09718245; CADD: 0.097 (0.444)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587700G>A [0|1] rs17203671 (variation viewer)

Variant score: 0.097

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1943C>T:p.(=)

Pathogenicity Data:: Best Score: 0.09676659; CADD: 0.097 (0.442)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589421A>G [1/1] rs9270268 (variation viewer)

Variant score: 0.097

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+222T>C:p.(=)

Pathogenicity Data:: Best Score: 0.09655857; CADD: 0.097 (0.441)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590747T>TGA [1|1] rs1295500679 (variation viewer)

Variant score: 0.095

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.09489286; CADD: 0.095 (0.433)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575311C>G [-/1] rs9269498 (variation viewer)

Variant score: 0.094

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09405881; CADD: 0.094 (0.429)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585368T>C [0|1] rs796753368 (variation viewer)

Variant score: 0.094

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-990A>G:p.(=)

Pathogenicity Data:: Best Score: 0.09364152; CADD: 0.094 (0.427)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582063G>A [0|1] rs11755895 (variation viewer)

Variant score: 0.093

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-225C>T:p.(=)

Pathogenicity Data:: Best Score: 0.09322405; CADD: 0.093 (0.425)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585351C>T [0|1] rs35931533 (variation viewer)

Variant score: 0.093

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-973G>A:p.(=)

Pathogenicity Data:: Best Score: 0.092597425; CADD: 0.093 (0.422)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575959G>T [0/1] rs116207907 (variation viewer)

Variant score: 0.092

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09238851; CADD: 0.092 (0.421)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574313G>T [1|1] rs9269455 (variation viewer)

Variant score: 0.091

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09071505; CADD: 0.091 (0.413)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578715T>TCTTC [0/1] rs9281861 (variation viewer)

Variant score: 0.091

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.09050566; CADD: 0.091 (0.412)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32579161T>C [0|1] rs41287214 (variation viewer)

Variant score: 0.089

Transcripts:: HLA-DRB1:ENST00000360004.5:c.788-57A>G:p.(=)

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584553C>A [1/1] rs9269975 (variation viewer)

Variant score: 0.089

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-175G>T:p.(=)

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574983A>T [0/1] rs41294103 (variation viewer)

Variant score: 0.088

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.08798915; CADD: 0.088 (0.400)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574786A>G [0/1] rs9269479 (variation viewer)

Variant score: 0.087

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.08735895; CADD: 0.087 (0.397)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585158CG>C [0/1] rs67720908 (variation viewer)

Variant score: 0.087

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-781del:p.(=)

Pathogenicity Data:: Best Score: 0.08693856; CADD: 0.087 (0.395)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575311C>A [-/1] rs9269498 (variation viewer)

Variant score: 0.087

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.086728275; CADD: 0.087 (0.394)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582837C>T [0|1] rs9269863 (variation viewer)

Variant score: 0.086

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-999G>A:p.(=)

Pathogenicity Data:: Best Score: 0.08588678; CADD: 0.086 (0.390)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575666CA>C [0/1] rs796194525 (variation viewer)

Variant score: 0.085

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.08525509; CADD: 0.085 (0.387)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr6:g.32578849C>G [1/1] rs1064715 (variation viewer)

Variant score: 0.084

Transcripts:: HLA-DRB1:ENST00000360004.5:c.*242G>C:p.(=)

Pathogenicity Data:: Best Score: 0.08441222; CADD: 0.084 (0.383)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586186T>G [0|1] rs201844920 (variation viewer)

Variant score: 0.084

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1808A>C:p.(=)

Pathogenicity Data:: Best Score: 0.083990455; CADD: 0.084 (0.381)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574634GAC>G [0|1] rs758892055 (variation viewer)

Variant score: 0.083

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.082724094; CADD: 0.083 (0.375)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578650A>T [0|1] rs9269671 (variation viewer)

Variant score: 0.080

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.08018601; CADD: 0.080 (0.363)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590231C>T [1|1] rs9270348 (variation viewer)

Variant score: 0.079

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.07870227; CADD: 0.079 (0.356)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574276T>TTA [0/1] rs9281856 (variation viewer)

Variant score: 0.078

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.07785332; CADD: 0.078 (0.352)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585205C>T [0|1] rs34954921 (variation viewer)

Variant score: 0.077

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-827G>A:p.(=)

Pathogenicity Data:: Best Score: 0.07742858; CADD: 0.077 (0.350)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585469A>C [0/1] rs116109943 (variation viewer)

Variant score: 0.077

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1091T>G:p.(=)

Pathogenicity Data:: Best Score: 0.07679105; CADD: 0.077 (0.347)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585545T>TC [1|1] rs9281881 (variation viewer)

Variant score: 0.077

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1168_101-1167insG:p.(=)

Pathogenicity Data:: Best Score: 0.07679105; CADD: 0.077 (0.347)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577592A>C [1/1] rs2894272 (variation viewer)

Variant score: 0.075

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.07487589; CADD: 0.075 (0.338)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574816C>T [0/1] rs9269482 (variation viewer)

Variant score: 0.074

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.07444978; CADD: 0.074 (0.336)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590604T>G [1|1] rs9270395 (variation viewer)

Variant score: 0.074

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.074023426; CADD: 0.074 (0.334)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586184C>G [0|1] rs9270059 (variation viewer)

Variant score: 0.074

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1806G>C:p.(=)

Pathogenicity Data:: Best Score: 0.07381016; CADD: 0.074 (0.333)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576039A>G [0|1] rs41284603 (variation viewer)

Variant score: 0.074

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.073596895; CADD: 0.074 (0.332)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586401T>A [-/1] rs9270077 (variation viewer)

Variant score: 0.072

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-2023A>T:p.(=)

Pathogenicity Data:: Best Score: 0.071888804; CADD: 0.072 (0.324)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589526G>A [0|1] rs79708010 (variation viewer)

Variant score: 0.070

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+117C>T:p.(=)

Pathogenicity Data:: Best Score: 0.070391655; CADD: 0.070 (0.317)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587238CAG>C [0|1] rs1176899647 (variation viewer)

Variant score: 0.069

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+2403_100+2404del:p.(=)

Pathogenicity Data:: Best Score: 0.0693208; CADD: 0.069 (0.312)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575057A>C [0/1] rs9269490 (variation viewer)

Variant score: 0.069

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.06867772; CADD: 0.069 (0.309)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582703C>T [0|1] rs34025368 (variation viewer)

Variant score: 0.067

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-865G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0667457; CADD: 0.067 (0.300)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587966C>G [0|1] rs9270174 (variation viewer)

Variant score: 0.066

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1677G>C:p.(=)

Pathogenicity Data:: Best Score: 0.06631583; CADD: 0.066 (0.298)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589545G>C [0/1] rs78836800 (variation viewer)

Variant score: 0.066

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+98C>G:p.(=)

Pathogenicity Data:: Best Score: 0.066100836; CADD: 0.066 (0.297)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582047T>C [0|1] rs41293169 (variation viewer)

Variant score: 0.066

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-209A>G:p.(=)

Pathogenicity Data:: Best Score: 0.06567061; CADD: 0.066 (0.295)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582954G>T [1|1] rs9269870 (variation viewer)

Variant score: 0.066

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1116C>A:p.(=)

Pathogenicity Data:: Best Score: 0.06567061; CADD: 0.066 (0.295)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582198GTTT>G [-/1] rs141131278 (variation viewer)

Variant score: 0.065

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-363_371-361del:p.(=)

Pathogenicity Data:: Best Score: 0.06502497; CADD: 0.065 (0.292)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32573141C>G [1|1] rs9269379 (variation viewer)

Variant score: 0.062

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.3553856; CADD: 0.355 (1.907)

Frequency Data:: gnomAD_G_AFR: 1.2618%; gnomAD_G_AMR: 1.9608%; gnomAD_G_EAS: 1.0460%; gnomAD_G_FIN: 1.0922%; gnomAD_G_NFE: 1.0351%; gnomAD_G_OTH: 1.0870%

DOWNSTREAM_GENE_VARIANT chr6:g.32574173TA>T [0|1] rs367924429 (variation viewer)

Variant score: 0.061

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.06114179; CADD: 0.061 (0.274)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580986A>G [-/1] rs9269772 (variation viewer)

Variant score: 0.060

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-130T>C:p.(=)

Pathogenicity Data:: Best Score: 0.060060263; CADD: 0.060 (0.269)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588894A>G [0/1] rs9270224 (variation viewer)

Variant score: 0.059

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+749T>C:p.(=)

Pathogenicity Data:: Best Score: 0.059194148; CADD: 0.059 (0.265)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32584689G>T [0|1] rs41287323 (variation viewer)

Variant score: 0.059

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-311C>A:p.(=)

Pathogenicity Data:: Best Score: 0.058977544; CADD: 0.059 (0.264)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583321C>G [1|1] rs9269896 (variation viewer)

Variant score: 0.058

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+788G>C:p.(=)

Pathogenicity Data:: Best Score: 0.058327258; CADD: 0.058 (0.261)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585323C>A [0|1] rs1051921456 (variation viewer)

Variant score: 0.058

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-945G>T:p.(=)

Pathogenicity Data:: Best Score: 0.058110416; CADD: 0.058 (0.260)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574168G>A [0|1] rs41293310 (variation viewer)

Variant score: 0.055

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.05485159; CADD: 0.055 (0.245)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575644G>T [1/1] rs9269514 (variation viewer)

Variant score: 0.055

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.054633975; CADD: 0.055 (0.244)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32591134CA>C [1|1]

Variant score: 0.054

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.053980708; CADD: 0.054 (0.241)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575017C>T [0|1] rs41294115 (variation viewer)

Variant score: 0.054

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.05354494; CADD: 0.054 (0.239)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582961T>C [0|1] rs9269871 (variation viewer)

Variant score: 0.052

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1123A>G:p.(=)

Pathogenicity Data:: Best Score: 0.052236438; CADD: 0.052 (0.233)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574221T>A [0|1] rs9269447 (variation viewer)

Variant score: 0.051

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.05114466; CADD: 0.051 (0.228)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575285G>C [0/1] rs9269496 (variation viewer)

Variant score: 0.051

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.05114466; CADD: 0.051 (0.228)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587826C>T [0|1] rs9270163 (variation viewer)

Variant score: 0.050

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1817G>A:p.(=)

Pathogenicity Data:: Best Score: 0.04961407; CADD: 0.050 (0.221)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580986A>T [-/1] rs9269772 (variation viewer)

Variant score: 0.049

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-130T>A:p.(=)

Pathogenicity Data:: Best Score: 0.049176276; CADD: 0.049 (0.219)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582865AC>A [-/1] rs869098244 (variation viewer)

Variant score: 0.048

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1028del:p.(=)

Pathogenicity Data:: Best Score: 0.047861755; CADD: 0.048 (0.213)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574047T>C [0|1] rs9269436 (variation viewer)

Variant score: 0.048

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.04764253; CADD: 0.048 (0.212)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575301C>T [0/1] rs9269497 (variation viewer)

Variant score: 0.047

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.047423184; CADD: 0.047 (0.211)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582423A>T [0|1] rs41293211 (variation viewer)

Variant score: 0.047

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-585T>A:p.(=)

Pathogenicity Data:: Best Score: 0.04720384; CADD: 0.047 (0.210)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582973A>T [0|1] rs9269872 (variation viewer)

Variant score: 0.047

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1135T>A:p.(=)

Pathogenicity Data:: Best Score: 0.04676497; CADD: 0.047 (0.208)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576230G>T [0|1] rs41284631 (variation viewer)

Variant score: 0.046

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.04610628; CADD: 0.046 (0.205)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575853G>C [0/1] rs41295451 (variation viewer)

Variant score: 0.045

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.04522729; CADD: 0.045 (0.201)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574383C>G [0|1] rs9269460 (variation viewer)

Variant score: 0.043

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.043246627; CADD: 0.043 (0.192)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582234A>C [0|1] rs28723982 (variation viewer)

Variant score: 0.043

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-396T>G:p.(=)

Pathogenicity Data:: Best Score: 0.043246627; CADD: 0.043 (0.192)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574548C>T [0/1] rs9269472 (variation viewer)

Variant score: 0.043

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.04280591; CADD: 0.043 (0.190)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574166G>A [0|1] rs9269442 (variation viewer)

Variant score: 0.042

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.042144477; CADD: 0.042 (0.187)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575618G>A [0/1] rs34423698 (variation viewer)

Variant score: 0.042

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.042144477; CADD: 0.042 (0.187)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575673A>AAGTT [1|1] rs9281860 (variation viewer)

Variant score: 0.040

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.04037845; CADD: 0.040 (0.179)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576770T>C [0/1] rs41284923 (variation viewer)

Variant score: 0.040

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.039936423; CADD: 0.040 (0.177)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582274T>C [0|1] rs41293182 (variation viewer)

Variant score: 0.040

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-436A>G:p.(=)

Pathogenicity Data:: Best Score: 0.03971535; CADD: 0.040 (0.176)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575009A>G [0|1] rs41294111 (variation viewer)

Variant score: 0.039

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.039494157; CADD: 0.039 (0.175)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575567C>T [0|1] rs35341111 (variation viewer)

Variant score: 0.039

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.039272964; CADD: 0.039 (0.174)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582838G>A [0|1] rs9269864 (variation viewer)

Variant score: 0.039

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1000C>T:p.(=)

Pathogenicity Data:: Best Score: 0.03883046; CADD: 0.039 (0.172)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575529C>G [1|1] rs9269512 (variation viewer)

Variant score: 0.038

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.037723243; CADD: 0.038 (0.167)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575864G>A [0/1] rs9269522 (variation viewer)

Variant score: 0.037

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.036836565; CADD: 0.037 (0.163)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.32572947G>T [1|1] rs9269365 (variation viewer)

Variant score: 0.036

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.070605695; CADD: 0.071 (0.318)

Frequency Data:: gnomAD_G_AFR: 0.4986%; gnomAD_G_AMR: 1.5385%; gnomAD_G_ASJ: 0.8929%; gnomAD_G_EAS: 0.2262%; gnomAD_G_FIN: 0.3425%; gnomAD_G_NFE: 0.6163%; gnomAD_G_OTH: 0.2551%

DOWNSTREAM_GENE_VARIANT chr6:g.32574484G>C [1|1] rs9269466 (variation viewer)

Variant score: 0.034

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.03417152; CADD: 0.034 (0.151)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574458C>T [0/1] rs41293664 (variation viewer)

Variant score: 0.033

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.03283626; CADD: 0.033 (0.145)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578432AG>A [-/1] rs66850812 (variation viewer)

Variant score: 0.033

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.03283626; CADD: 0.033 (0.145)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32591136GA>G [1|1] rs1581840147 (variation viewer)

Variant score: 0.032

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 0.032390773; CADD: 0.032 (0.143)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582064T>C [1|1] rs9269823 (variation viewer)

Variant score: 0.032

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-226A>G:p.(=)

Pathogenicity Data:: Best Score: 0.03172213; CADD: 0.032 (0.140)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32585440G>A [0/1] rs35637465 (variation viewer)

Variant score: 0.031

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1062C>T:p.(=)

Pathogenicity Data:: Best Score: 0.031499147; CADD: 0.031 (0.139)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589202A>C [0/1] rs28366201 (variation viewer)

Variant score: 0.031

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+441T>G:p.(=)

Pathogenicity Data:: Best Score: 0.031499147; CADD: 0.031 (0.139)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582711G>A [0|1] rs9269860 (variation viewer)

Variant score: 0.031

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-873C>T:p.(=)

Pathogenicity Data:: Best Score: 0.031053066; CADD: 0.031 (0.137)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575910G>T [0/1] rs9269526 (variation viewer)

Variant score: 0.029

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.029490054; CADD: 0.029 (0.130)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586263TC>T [0|1] rs1375573744 (variation viewer)

Variant score: 0.029

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1886del:p.(=)

Pathogenicity Data:: Best Score: 0.028819382; CADD: 0.029 (0.127)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32586253TC>T [0|1] rs1480509265 (variation viewer)

Variant score: 0.029

Transcripts:: HLA-DRB1:ENST00000360004.5:c.101-1876del:p.(=)

Pathogenicity Data:: Best Score: 0.028595746; CADD: 0.029 (0.126)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576103A>G [0|1] rs34479687 (variation viewer)

Variant score: 0.028

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.027700663; CADD: 0.028 (0.122)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581189T>A [0/1] rs9269782 (variation viewer)

Variant score: 0.027

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-333A>T:p.(=)

Pathogenicity Data:: Best Score: 0.02702874; CADD: 0.027 (0.119)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582074G>T [0/1] rs9269826 (variation viewer)

Variant score: 0.027

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-236C>A:p.(=)

Pathogenicity Data:: Best Score: 0.026580572; CADD: 0.027 (0.117)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574356C>T [0|1] rs41293338 (variation viewer)

Variant score: 0.026

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.026132226; CADD: 0.026 (0.115)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582204T>C [0/1] rs6457603 (variation viewer)

Variant score: 0.026

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-366A>G:p.(=)

Pathogenicity Data:: Best Score: 0.025907934; CADD: 0.026 (0.114)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577892T>C [0|1] rs9269632 (variation viewer)

Variant score: 0.026

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.025683641; CADD: 0.026 (0.113)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578683T>C [0|1] rs41287186 (variation viewer)

Variant score: 0.025

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.02545923; CADD: 0.025 (0.112)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583096G>C [1|1] rs9269877 (variation viewer)

Variant score: 0.025

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+1013C>G:p.(=)

Pathogenicity Data:: Best Score: 0.025234818; CADD: 0.025 (0.111)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32573974T>A [0|1] rs9269433 (variation viewer)

Variant score: 0.025

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.025010347; CADD: 0.025 (0.110)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574385A>G [0|1] rs41293644 (variation viewer)

Variant score: 0.025

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.025010347; CADD: 0.025 (0.110)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581240A>G [0/1] rs41288061 (variation viewer)

Variant score: 0.024

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+317T>C:p.(=)

Pathogenicity Data:: Best Score: 0.024336636; CADD: 0.024 (0.107)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577401C>T [0|1] rs41284938 (variation viewer)

Variant score: 0.024

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.024111927; CADD: 0.024 (0.106)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577812G>A [0|1] rs28688765 (variation viewer)

Variant score: 0.023

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.02343762; CADD: 0.023 (0.103)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582607T>G [0|1] rs28724002 (variation viewer)

Variant score: 0.023

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-769A>C:p.(=)

Pathogenicity Data:: Best Score: 0.022762775; CADD: 0.023 (0.100)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575577G>A [0|1] rs35834993 (variation viewer)

Variant score: 0.023

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.022537708; CADD: 0.023 (0.099)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582053T>C [0|1] rs28723973 (variation viewer)

Variant score: 0.022

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-215A>G:p.(=)

Pathogenicity Data:: Best Score: 0.022087514; CADD: 0.022 (0.097)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582902C>A [0|1] rs36019320 (variation viewer)

Variant score: 0.022

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1064G>T:p.(=)

Pathogenicity Data:: Best Score: 0.022087514; CADD: 0.022 (0.097)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574953G>A [0/1] rs41293844 (variation viewer)

Variant score: 0.020

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.02005881; CADD: 0.020 (0.088)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582963T>C [0|1] rs41283792 (variation viewer)

Variant score: 0.020

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1125A>G:p.(=)

Pathogenicity Data:: Best Score: 0.019833148; CADD: 0.020 (0.087)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575833T>A [1/1] rs9269519 (variation viewer)

Variant score: 0.019

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.018704057; CADD: 0.019 (0.082)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576102C>T [0|1] rs41284607 (variation viewer)

Variant score: 0.019

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.018704057; CADD: 0.019 (0.082)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581403C>CA [0|1]

Variant score: 0.019

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+153_652+154insT:p.(=)

Pathogenicity Data:: Best Score: 0.018704057; CADD: 0.019 (0.082)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580401A>G [1|1] rs9269755 (variation viewer)

Variant score: 0.018

Transcripts:: HLA-DRB1:ENST00000360004.5:c.764-131T>C:p.(=)

Pathogenicity Data:: Best Score: 0.018478096; CADD: 0.018 (0.081)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589232G>A [0/1] rs112431275 (variation viewer)

Variant score: 0.018

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+411C>T:p.(=)

Pathogenicity Data:: Best Score: 0.018478096; CADD: 0.018 (0.081)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575649AT>A [0/1] rs67519468 (variation viewer)

Variant score: 0.018

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.018025994; CADD: 0.018 (0.079)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582235C>T [0/1] rs9269831 (variation viewer)

Variant score: 0.018

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-397G>A:p.(=)

Pathogenicity Data:: Best Score: 0.018025994; CADD: 0.018 (0.079)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580475C>T [0|1] rs12110876 (variation viewer)

Variant score: 0.016

Transcripts:: HLA-DRB1:ENST00000360004.5:c.764-205G>A:p.(=)

Pathogenicity Data:: Best Score: 0.016441941; CADD: 0.016 (0.072)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582270G>A [0/1] rs9269832 (variation viewer)

Variant score: 0.016

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-432C>T:p.(=)

Pathogenicity Data:: Best Score: 0.016441941; CADD: 0.016 (0.072)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574414C>T [0|1] rs9269464 (variation viewer)

Variant score: 0.016

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.01576227; CADD: 0.016 (0.069)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582848T>G [0|1] rs9269865 (variation viewer)

Variant score: 0.016

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1010A>C:p.(=)

Pathogenicity Data:: Best Score: 0.015535653; CADD: 0.016 (0.068)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577542G>A [1/1] rs9269615 (variation viewer)

Variant score: 0.015

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.015308917; CADD: 0.015 (0.067)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576160T>A [1|1] rs9269537 (variation viewer)

Variant score: 0.015

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.01462847; CADD: 0.015 (0.064)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581344T>C [-/1] rs9269791 (variation viewer)

Variant score: 0.014

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+213A>G:p.(=)

Pathogenicity Data:: Best Score: 0.014401555; CADD: 0.014 (0.063)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580170C>A [1/1] rs9269741 (variation viewer)

Variant score: 0.013

Transcripts:: HLA-DRB1:ENST00000360004.5:c.787+77G>T:p.(=)

Pathogenicity Data:: Best Score: 0.013493419; CADD: 0.013 (0.059)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581075C>A [1|1] rs9269776 (variation viewer)

Variant score: 0.012

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-219G>T:p.(=)

Pathogenicity Data:: Best Score: 0.011674523; CADD: 0.012 (0.051)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32589280T>A [0/1] rs9270257 (variation viewer)

Variant score: 0.011

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+363A>T:p.(=)

Pathogenicity Data:: Best Score: 0.011219263; CADD: 0.011 (0.049)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582033G>A [0/1] rs9269822 (variation viewer)

Variant score: 0.011

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-195C>T:p.(=)

Pathogenicity Data:: Best Score: 0.010763824; CADD: 0.011 (0.047)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578131G>A [0/1] rs35326463 (variation viewer)

Variant score: 0.011

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.010536015; CADD: 0.011 (0.046)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582426T>G [0|1] rs34077178 (variation viewer)

Variant score: 0.010

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-588A>C:p.(=)

Pathogenicity Data:: Best Score: 0.0103081465; CADD: 0.010 (0.045)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582290C>T [1/1] rs9269833 (variation viewer)

Variant score: 0.010

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-452G>A:p.(=)

Pathogenicity Data:: Best Score: 0.00985229; CADD: 0.010 (0.043)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581312C>T [1|1] rs9269788 (variation viewer)

Variant score: 0.010

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+245G>A:p.(=)

Pathogenicity Data:: Best Score: 0.009624243; CADD: 0.010 (0.042)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32587842A>T [0/1] rs35155838 (variation viewer)

Variant score: 0.010

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1801T>A:p.(=)

Pathogenicity Data:: Best Score: 0.009624243; CADD: 0.010 (0.042)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581119A>C [1/1] rs9269778 (variation viewer)

Variant score: 0.009

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-263T>G:p.(=)

Pathogenicity Data:: Best Score: 0.009168029; CADD: 0.009 (0.040)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577485G>A [0/1] rs9269612 (variation viewer)

Variant score: 0.009

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.008939862; CADD: 0.009 (0.039)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582288C>T [0|1] rs41293188 (variation viewer)

Variant score: 0.008

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-450G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0077982545; CADD: 0.008 (0.034)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32575715A>G [1|1] rs9269516 (variation viewer)

Variant score: 0.007

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.0071126223; CADD: 0.007 (0.031)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581294G>T [0|1] rs41288074 (variation viewer)

Variant score: 0.006

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+263C>A:p.(=)

Pathogenicity Data:: Best Score: 0.006197691; CADD: 0.006 (0.027)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582101C>T [0/1] rs41293179 (variation viewer)

Variant score: 0.006

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-263G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0057399273; CADD: 0.006 (0.025)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32583099G>C [1|1] rs9269878 (variation viewer)

Variant score: 0.005

Transcripts:: HLA-DRB1:ENST00000360004.5:c.370+1010C>G:p.(=)

Pathogenicity Data:: Best Score: 0.005281925; CADD: 0.005 (0.023)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578314G>T [0/1] rs9269654 (variation viewer)

Variant score: 0.004

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.0043653846; CADD: 0.004 (0.019)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581315A>C [1|1] rs9269790 (variation viewer)

Variant score: 0.004

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+242T>G:p.(=)

Pathogenicity Data:: Best Score: 0.0043653846; CADD: 0.004 (0.019)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577387ACC>A [0|1] rs869086368 (variation viewer)

Variant score: 0.004

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.0041360855; CADD: 0.004 (0.018)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580909C>A [0/1] rs3830122 (variation viewer)

Variant score: 0.004

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-53G>T:p.(=)

Pathogenicity Data:: Best Score: 0.0041360855; CADD: 0.004 (0.018)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577857G>T [1|1] rs9269628 (variation viewer)

Variant score: 0.004

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.0036773682; CADD: 0.004 (0.016)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581934G>A [1|1] rs9269814 (variation viewer)

Variant score: 0.003

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-96C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0027592778; CADD: 0.003 (0.012)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578298T>C [0|1] rs9269652 (variation viewer)

Variant score: 0.002

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.0022999644; CADD: 0.002 (0.010)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577882C>G [0|1] rs28744492 (variation viewer)

Variant score: 0.002

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: Best Score: 0.001840353; CADD: 0.002 (0.008)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32580951G>T [0/1] rs9269769 (variation viewer)

Variant score: 0.002

Transcripts:: HLA-DRB1:ENST00000360004.5:c.653-95C>A:p.(=)

Pathogenicity Data:: Best Score: 0.001840353; CADD: 0.002 (0.008)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581335G>A [0|1] rs35325793 (variation viewer)

Variant score: 0.002

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+222C>T:p.(=)

Pathogenicity Data:: Best Score: 0.001840353; CADD: 0.002 (0.008)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590339T>C [0|1] rs550788808 (variation viewer)

Variant score: 0.001

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 9.2059374E-4; CADD: 0.001 (0.004)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.32590348G>T [0|1] rs34699174 (variation viewer)

Variant score: 0.001

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000395363.5::

Pathogenicity Data:: Best Score: 9.2059374E-4; CADD: 0.001 (0.004)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32574642A>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576048T>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32576795A>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577051T>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32577120TCAA>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.32578432AG>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5::; HLA-DRB1:ENST00000437183.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr6:g.32579026A>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.*65T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581344T>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+213A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581351C>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.652+206G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32581850AC>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-13_371-12delGTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582031G>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-193C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582865AC>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1028_371-1027delGTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32582867TA>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.371-1030_371-1029delTAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588379A>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1264T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588380A>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1263T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.32588468AG>* [-/1]

Variant score: 0.000

Transcripts:: HLA-DRB1:ENST00000360004.5:c.100+1174_100+1175delCTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PDCD6IP

Exomiser Score: 0.572

Phenotype Score: 0.505

Variant Score: 0.907

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.572

Phenotype Score: 0.505

Variant Score: 0.907

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.33860337TTTA>T [0/1] rs1317030358 (variation viewer)

Variant score: 0.907 CONTRIBUTING VARIANT

Transcripts:: PDCD6IP:ENST00000307296.8:c.2121-3668_2121-3666del:p.(=); PDCD6IP:ENST00000457054.6:c.2136-3668_2136-3666del:p.(=)

Pathogenicity Data:: Best Score: 0.91066945; CADD: 0.911 (10.490)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0267%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.319

Phenotype Score: 0.505

Variant Score: 0.793

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.33788323C>CA [1/1] rs34935271 (variation viewer)

Variant score: 0.793 CONTRIBUTING VARIANT

Transcripts:: PDCD6IP:ENST00000457054.6::; PDCD6IP:ENST00000427380.1::

Pathogenicity Data:: Best Score: 0.79322404; CADD: 0.793 (6.845)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.33805056AAT>A [0/1] rs1237067887 (variation viewer)

Variant score: 0.247

Transcripts:: PDCD6IP:ENST00000307296.8:c.209+6120_209+6121del:p.(=); PDCD6IP:ENST00000457054.6:c.209+6120_209+6121del:p.(=)

Pathogenicity Data:: Best Score: 0.24785775; CADD: 0.248 (1.237)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.33841040T>TTC [0|1] rs201445391 (variation viewer)

Variant score: 0.116

Transcripts:: PDCD6IP:ENST00000307296.8:c.1182-857_1182-856insTC:p.(=); PDCD6IP:ENST00000457054.6:c.1197-857_1197-856insTC:p.(=)

Pathogenicity Data:: Best Score: 0.11610639; CADD: 0.116 (0.536)

Frequency Data:: gnomAD_G_AFR: 0.0362%; gnomAD_G_FIN: 0.0314%; gnomAD_G_NFE: 0.0346%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.33818097G>GT [1/1] rs756780125 (variation viewer)

Variant score: 0.042

Transcripts:: PDCD6IP:ENST00000307296.8:c.335-3858_335-3857insT:p.(=); PDCD6IP:ENST00000457054.6:c.335-3858_335-3857insT:p.(=)

Pathogenicity Data:: Best Score: 0.042144477; CADD: 0.042 (0.187)

Frequency Data:: No frequency data

SYNRG

Exomiser Score: 0.568

Phenotype Score: 0.504

Variant Score: 0.906

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.568

Phenotype Score: 0.504

Variant Score: 0.906

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37577695CT>C [1/1] rs34008016 (variation viewer)

Variant score: 0.906 CONTRIBUTING VARIANT

Transcripts:: SYNRG:ENST00000612223.5:c.590-83del:p.(=); SYNRG:ENST00000614941.4:c.590-1278del:p.(=); SYNRG:ENST00000616179.4:c.590-1278del:p.(=); SYNRG:ENST00000619541.4:c.587-1278del:p.(=); SYNRG:ENST00000621136.4:c.590-1278del:p.(=); SYNRG:ENST00000622045.4:c.590-1278del:p.(=)

Pathogenicity Data:: Best Score: 0.90645945; CADD: 0.906 (10.290)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37594154TATTATTTTAATTATATTAATTACAATATTA>T [1/1] rs1381993640 (variation viewer)

Variant score: 0.851

Transcripts:: SYNRG:ENST00000612223.5:c.240+2039_240+2068del:p.(=); SYNRG:ENST00000614941.4:c.240+2039_240+2068del:p.(=); SYNRG:ENST00000616179.4:c.240+2039_240+2068del:p.(=); SYNRG:ENST00000619541.4:c.237+2039_237+2068del:p.(=); SYNRG:ENST00000621136.4:c.240+2039_240+2068del:p.(=); SYNRG:ENST00000622045.4:c.240+2039_240+2068del:p.(=)

Pathogenicity Data:: Best Score: 0.8507549; CADD: 0.851 (8.261)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37580296CT>C [1/1] rs111270719 (variation viewer)

Variant score: 0.801

Transcripts:: SYNRG:ENST00000612223.5:c.590-2684del:p.(=); SYNRG:ENST00000614941.4:c.590-3879del:p.(=); SYNRG:ENST00000616179.4:c.590-3879del:p.(=); SYNRG:ENST00000619541.4:c.587-3879del:p.(=); SYNRG:ENST00000621136.4:c.590-3879del:p.(=); SYNRG:ENST00000622045.4:c.590-3879del:p.(=)

Pathogenicity Data:: Best Score: 0.800841; CADD: 0.801 (7.008)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37565881T>C [1/1] rs11651124 (variation viewer)

Variant score: 0.586

Transcripts:: SYNRG:ENST00000612223.5:c.1481+2910A>G:p.(=); SYNRG:ENST00000614941.4:c.998+2910A>G:p.(=); SYNRG:ENST00000616179.4:c.1247+2910A>G:p.(=); SYNRG:ENST00000619541.4:c.1244+2910A>G:p.(=); SYNRG:ENST00000621136.4:c.1247+2910A>G:p.(=); SYNRG:ENST00000622045.4:c.1247+2910A>G:p.(=)

Pathogenicity Data:: Best Score: 0.58638144; CADD: 0.586 (3.834)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37566073A>G [1/1] rs1390787257 (variation viewer)

Variant score: 0.581

Transcripts:: SYNRG:ENST00000612223.5:c.1481+2718T>C:p.(=); SYNRG:ENST00000614941.4:c.998+2718T>C:p.(=); SYNRG:ENST00000616179.4:c.1247+2718T>C:p.(=); SYNRG:ENST00000619541.4:c.1244+2718T>C:p.(=); SYNRG:ENST00000621136.4:c.1247+2718T>C:p.(=); SYNRG:ENST00000622045.4:c.1247+2718T>C:p.(=)

Pathogenicity Data:: Best Score: 0.58120644; CADD: 0.581 (3.780)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37580512A>T [1/1] rs78492676 (variation viewer)

Variant score: 0.379

Transcripts:: SYNRG:ENST00000612223.5:c.590-2899T>A:p.(=); SYNRG:ENST00000614941.4:c.590-4094T>A:p.(=); SYNRG:ENST00000616179.4:c.590-4094T>A:p.(=); SYNRG:ENST00000619541.4:c.587-4094T>A:p.(=); SYNRG:ENST00000621136.4:c.590-4094T>A:p.(=); SYNRG:ENST00000622045.4:c.590-4094T>A:p.(=)

Pathogenicity Data:: Best Score: 0.37913096; CADD: 0.379 (2.070)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37607977A>AAAC [1/1] rs1479788599 (variation viewer)

Variant score: 0.347

Transcripts:: SYNRG:ENST00000612223.5:c.77+1301_77+1302insGTT:p.(=); SYNRG:ENST00000614941.4:c.77+1301_77+1302insGTT:p.(=); SYNRG:ENST00000616179.4:c.77+1301_77+1302insGTT:p.(=); SYNRG:ENST00000619541.4:c.77+1301_77+1302insGTT:p.(=); SYNRG:ENST00000621136.4:c.77+1301_77+1302insGTT:p.(=); SYNRG:ENST00000622045.4:c.77+1301_77+1302insGTT:p.(=)

Pathogenicity Data:: Best Score: 0.3470198; CADD: 0.347 (1.851)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37580478C>CGTGTGT [1/1] rs1341679385 (variation viewer)

Variant score: 0.160

Transcripts:: SYNRG:ENST00000612223.5:c.590-2866_590-2865insACACAC:p.(=); SYNRG:ENST00000614941.4:c.590-4061_590-4060insACACAC:p.(=); SYNRG:ENST00000616179.4:c.590-4061_590-4060insACACAC:p.(=); SYNRG:ENST00000619541.4:c.587-4061_587-4060insACACAC:p.(=); SYNRG:ENST00000621136.4:c.590-4061_590-4060insACACAC:p.(=); SYNRG:ENST00000622045.4:c.590-4061_590-4060insACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.15957296; CADD: 0.160 (0.755)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37604240TA>T [1/1] rs202156948 (variation viewer)

Variant score: 0.147

Transcripts:: SYNRG:ENST00000612223.5:c.78-3838del:p.(=); SYNRG:ENST00000614941.4:c.78-3838del:p.(=); SYNRG:ENST00000616179.4:c.78-3838del:p.(=); SYNRG:ENST00000619541.4:c.78-3838del:p.(=); SYNRG:ENST00000621136.4:c.78-3838del:p.(=); SYNRG:ENST00000622045.4:c.78-3838del:p.(=)

Pathogenicity Data:: Best Score: 0.14670342; CADD: 0.147 (0.689)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37588258CT>C [1/1] rs35767898 (variation viewer)

Variant score: 0.126

Transcripts:: SYNRG:ENST00000612223.5:c.241-1710del:p.(=); SYNRG:ENST00000614941.4:c.241-1710del:p.(=); SYNRG:ENST00000616179.4:c.241-1710del:p.(=); SYNRG:ENST00000619541.4:c.238-1710del:p.(=); SYNRG:ENST00000621136.4:c.241-1710del:p.(=); SYNRG:ENST00000622045.4:c.241-1710del:p.(=)

Pathogenicity Data:: Best Score: 0.126023; CADD: 0.126 (0.585)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37577865AT>A [1/1] rs1230912539 (variation viewer)

Variant score: 0.122

Transcripts:: SYNRG:ENST00000612223.5:c.590-253del:p.(=); SYNRG:ENST00000614941.4:c.590-1448del:p.(=); SYNRG:ENST00000616179.4:c.590-1448del:p.(=); SYNRG:ENST00000619541.4:c.587-1448del:p.(=); SYNRG:ENST00000621136.4:c.590-1448del:p.(=); SYNRG:ENST00000622045.4:c.590-1448del:p.(=)

Pathogenicity Data:: Best Score: 0.12239313; CADD: 0.122 (0.567)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37575457TA>T [1/1] rs72368334 (variation viewer)

Variant score: 0.118

Transcripts:: SYNRG:ENST00000612223.5:c.901+883del:p.(=); SYNRG:ENST00000614941.4:c.667+883del:p.(=); SYNRG:ENST00000616179.4:c.667+883del:p.(=); SYNRG:ENST00000619541.4:c.664+883del:p.(=); SYNRG:ENST00000621136.4:c.667+883del:p.(=); SYNRG:ENST00000622045.4:c.667+883del:p.(=)

Pathogenicity Data:: Best Score: 0.11813927; CADD: 0.118 (0.546)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37570143CTT>C [1/1] rs11320959 (variation viewer)

Variant score: 0.099

Transcripts:: SYNRG:ENST00000612223.5:c.1347+492_1347+493del:p.(=); SYNRG:ENST00000614941.4:c.865-1221_865-1220del:p.(=); SYNRG:ENST00000616179.4:c.1113+492_1113+493del:p.(=); SYNRG:ENST00000619541.4:c.1110+492_1110+493del:p.(=); SYNRG:ENST00000621136.4:c.1113+492_1113+493del:p.(=); SYNRG:ENST00000622045.4:c.1113+492_1113+493del:p.(=)

Pathogenicity Data:: Best Score: 0.09863645; CADD: 0.099 (0.451)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37593874C>G [1/1] rs9893570 (variation viewer)

Variant score: 0.077

Transcripts:: SYNRG:ENST00000612223.5:c.240+2349G>C:p.(=); SYNRG:ENST00000614941.4:c.240+2349G>C:p.(=); SYNRG:ENST00000616179.4:c.240+2349G>C:p.(=); SYNRG:ENST00000619541.4:c.237+2349G>C:p.(=); SYNRG:ENST00000621136.4:c.240+2349G>C:p.(=); SYNRG:ENST00000622045.4:c.240+2349G>C:p.(=)

Pathogenicity Data:: Best Score: 0.0770036; CADD: 0.077 (0.348)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.37529538CA>C [1/1] rs3049513 (variation viewer)

Variant score: 0.004

Transcripts:: SYNRG:ENST00000612223.5:c.3666+6440del:p.(=); SYNRG:ENST00000614941.4:c.3048+6440del:p.(=); SYNRG:ENST00000616179.4:c.3297+6440del:p.(=); SYNRG:ENST00000619541.4:c.3429+6440del:p.(=); SYNRG:ENST00000621136.4:c.3432+6440del:p.(=); SYNRG:ENST00000622045.4:c.3501+244del:p.(=)

Pathogenicity Data:: Best Score: 0.0036773682; CADD: 0.004 (0.016)

Frequency Data:: No frequency data

AFTPH

Exomiser Score: 0.561

Phenotype Score: 0.505

Variant Score: 0.902

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.312

Phenotype Score: 0.505

Variant Score: 0.789

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.64569342T>G [0|1]

Variant score: 0.789 CONTRIBUTING VARIANT

Transcripts:: AFTPH:ENST00000238855.11:c.2214+124T>G:p.(=); AFTPH:ENST00000238856.8:c.2214+124T>G:p.(=); AFTPH:ENST00000409933.5:c.2214+124T>G:p.(=); AFTPH:ENST00000422803.2:c.-40+124T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7894283; CADD: 0.789 (6.766)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.561

Phenotype Score: 0.505

Variant Score: 0.902

Variants contributing to score:

REGULATORY_REGION_VARIANT chr2:g.64212741C>CT [1/1] rs5831682 (variation viewer)

Variant score: 0.902 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.9022763; CADD: 0.902 (10.100)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.64536951CAAA>C [1/1] rs70937353 (variation viewer)

Variant score: 0.618

Transcripts:: AFTPH:ENST00000238855.11:c.-33+12340_-33+12342del:p.(=); AFTPH:ENST00000238856.8:c.-33+12340_-33+12342del:p.(=)

Pathogenicity Data:: Best Score: 0.61840737; CADD: 0.618 (4.184)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.64549308CT>C [1/1] rs34951706 (variation viewer)

Variant score: 0.410

Transcripts:: AFTPH:ENST00000238855.11:c.-32-2134del:p.(=); AFTPH:ENST00000238856.8:c.-32-2134del:p.(=)

Pathogenicity Data:: Best Score: 0.41047806; CADD: 0.410 (2.295)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.64545570TAAAAAAA>T [1/1] rs58124855 (variation viewer)

Variant score: 0.253

Transcripts:: AFTPH:ENST00000238855.11:c.-32-5872_-32-5866del:p.(=); AFTPH:ENST00000238856.8:c.-32-5872_-32-5866del:p.(=)

Pathogenicity Data:: Best Score: 0.25269133; CADD: 0.253 (1.265)

Frequency Data:: No frequency data

USH1C

Exomiser Score: 0.557

Phenotype Score: 0.518

Variant Score: 0.886

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 1 associated with USH1C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.518 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.518 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:276904 Usher syndrome, type 1C - autosomal recessive; OMIM:602092 Deafness, autosomal recessive 18A - autosomal recessive; ORPHA:231169 Usher syndrome type 1

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.121

Phenotype Score: 0.259

Variant Score: 0.938

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.17517609A>T [0|1] rs1219211541 (variation viewer)

Variant score: 0.938 CONTRIBUTING VARIANT

Transcripts:: USH1C:ENST00000005226.12:c.1211-1319T>A:p.(=); USH1C:ENST00000318024.8:c.1211-135T>A:p.(=); USH1C:ENST00000527020.5:c.1154-135T>A:p.(=); USH1C:ENST00000527720.5:c.1118-135T>A:p.(=)

Pathogenicity Data:: Best Score: 0.93777; CADD: 0.938 (12.060)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.557

Phenotype Score: 0.518

Variant Score: 0.886

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.17517609A>T [0|1] rs1219211541 (variation viewer)

Variant score: 0.938 CONTRIBUTING VARIANT

Transcripts:: USH1C:ENST00000005226.12:c.1211-1319T>A:p.(=); USH1C:ENST00000318024.8:c.1211-135T>A:p.(=); USH1C:ENST00000527020.5:c.1154-135T>A:p.(=); USH1C:ENST00000527720.5:c.1118-135T>A:p.(=)

Pathogenicity Data:: Best Score: 0.93777; CADD: 0.938 (12.060)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.17517604AG>A [0|1] rs1300472919 (variation viewer)

Variant score: 0.835 CONTRIBUTING VARIANT

Transcripts:: USH1C:ENST00000005226.12:c.1211-1315del:p.(=); USH1C:ENST00000318024.8:c.1211-131del:p.(=); USH1C:ENST00000527020.5:c.1154-131del:p.(=); USH1C:ENST00000527720.5:c.1118-131del:p.(=)

Pathogenicity Data:: Best Score: 0.8347658; CADD: 0.835 (7.819)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.17527112ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC>A [1/1] rs55983148 (variation viewer)

Variant score: 0.466

Transcripts:: USH1C:ENST00000005226.12:c.496+66_497-73del:p.(=); USH1C:ENST00000318024.8:c.496+66_497-73del:p.(=); USH1C:ENST00000527020.5:c.496+66_497-73del:p.(=); USH1C:ENST00000527720.5:c.403+66_404-73del:p.(=)

Pathogenicity Data:: Best Score: 0.46629655; CADD: 0.466 (2.727)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.17496945T>C [0/1] rs886143419 (variation viewer)

Variant score: 0.191

Transcripts:: USH1C:ENST00000005226.12:c.2491-132A>G:p.(=); USH1C:ENST00000318024.8:c.1591-132A>G:p.(=); USH1C:ENST00000527020.5:c.1534-132A>G:p.(=); USH1C:ENST00000527720.5:c.1498-132A>G:p.(=)

Pathogenicity Data:: Best Score: 0.19164896; CADD: 0.192 (0.924)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

MARCHF6

Exomiser Score: 0.556

Phenotype Score: 0.505

Variant Score: 0.900

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:613608 Epilepsy, familial adult myoclonic, 3 - autosomal dominant; ORPHA:86814 Benign adult familial myoclonic epilepsy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.556

Phenotype Score: 0.505

Variant Score: 0.900

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.10343444A>C [0/1] rs76657857 (variation viewer)

Variant score: 0.900 CONTRIBUTING VARIANT

Transcripts:: MARCHF6:ENST00000274140.10::; MARCHF6:ENST00000296658.4::

Pathogenicity Data:: Best Score: 0.90339494; CADD: 0.903 (10.150)

Frequency Data:: TOPMed: 0.0135%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.267

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.10360144G>GT [1/1] rs1164778520 (variation viewer)

Variant score: 0.267 CONTRIBUTING VARIANT

Transcripts:: MARCHF6:ENST00000274140.10:c.19+6227_19+6228insT:p.(=); MARCHF6:ENST00000449913.6:c.19+6227_19+6228insT:p.(=); MARCHF6:ENST00000503788.5:c.19+6227_19+6228insT:p.(=); MARCHF6:ENST00000640713.1:c.19+6227_19+6228insT:p.(=)

Pathogenicity Data:: Best Score: 0.2671755; CADD: 0.267 (1.350)

Frequency Data:: No frequency data

Other passed variants:

NCALD

Exomiser Score: 0.543

Phenotype Score: 0.505

Variant Score: 0.894

Phenotype matches:

Phenotypic similarity 0.383 to mouse mutant involving NCALD.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0020870, decreased thigmotaxis

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.543

Phenotype Score: 0.505

Variant Score: 0.894

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101817475G>A [0/1] rs900255636 (variation viewer)

Variant score: 0.894 CONTRIBUTING VARIANT

Transcripts:: NCALD:ENST00000311028.4:c.-20+69666C>T:p.(=); NCALD:ENST00000395923.5:c.-19-97827C>T:p.(=); NCALD:ENST00000521599.5:c.-19-97827C>T:p.(=)

Pathogenicity Data:: Best Score: 0.89453703; CADD: 0.895 (9.769)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.350

Phenotype Score: 0.505

Variant Score: 0.809

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101817475G>A [0/1] rs900255636 (variation viewer)

Variant score: 0.894 CONTRIBUTING VARIANT

Transcripts:: NCALD:ENST00000311028.4:c.-20+69666C>T:p.(=); NCALD:ENST00000395923.5:c.-19-97827C>T:p.(=); NCALD:ENST00000521599.5:c.-19-97827C>T:p.(=)

Pathogenicity Data:: Best Score: 0.89453703; CADD: 0.895 (9.769)

Frequency Data:: TOPMed: 0.0008%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101776094T>C [0/1] rs144269958 (variation viewer)

Variant score: 0.723 CONTRIBUTING VARIANT

Transcripts:: NCALD:ENST00000220931.11:c.-20+14768A>G:p.(=); NCALD:ENST00000311028.4:c.-19-56446A>G:p.(=); NCALD:ENST00000395923.5:c.-19-56446A>G:p.(=); NCALD:ENST00000521599.5:c.-19-56446A>G:p.(=); NCALD:ENST00000522951.5:c.-20+14768A>G:p.(=)

Pathogenicity Data:: Best Score: 0.76319003; CADD: 0.763 (6.256)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1131%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0573%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1333%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102030229C>T [0/1] rs957278020 (variation viewer)

Variant score: 0.417

Transcripts:: NCALD:ENST00000311028.4:c.-209-9940G>A:p.(=); NCALD:ENST00000395923.5:c.-122-9940G>A:p.(=); NCALD:ENST00000521599.5:c.-209-1133G>A:p.(=)

Pathogenicity Data:: Best Score: 0.977249; CADD: 0.977 (16.430)

Frequency Data:: TOPMed: 0.0366%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.0133%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101938655TAA>T [-/1] rs113008084 (variation viewer)

Variant score: 0.359

Transcripts:: NCALD:ENST00000311028.4:c.-156-22799_-156-22798del:p.(=); NCALD:ENST00000395923.5:c.-69-22799_-69-22798del:p.(=); NCALD:ENST00000521599.5:c.-69-22799_-69-22798del:p.(=)

Pathogenicity Data:: Best Score: 0.43009824; CADD: 0.430 (2.442)

Frequency Data:: gnomAD_G_AFR: 0.7976%; gnomAD_G_AMR: 0.1292%; gnomAD_G_EAS: 0.1253%; gnomAD_G_NFE: 0.0771%; gnomAD_G_OTH: 0.2242%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101935982T>C [0/1] rs13254309 (variation viewer)

Variant score: 0.344

Transcripts:: NCALD:ENST00000311028.4:c.-156-20124A>G:p.(=); NCALD:ENST00000395923.5:c.-69-20124A>G:p.(=); NCALD:ENST00000521599.5:c.-69-20124A>G:p.(=)

Pathogenicity Data:: Best Score: 0.41789675; CADD: 0.418 (2.350)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.4133%; UK10K: 0.8331%; gnomAD_G_AFR: 0.0690%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2018%; gnomAD_G_NFE: 0.4753%; gnomAD_G_OTH: 0.2053%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101931007C>T [0/1] rs534171107 (variation viewer)

Variant score: 0.266

Transcripts:: NCALD:ENST00000311028.4:c.-156-15149G>A:p.(=); NCALD:ENST00000395923.5:c.-69-15149G>A:p.(=); NCALD:ENST00000521599.5:c.-69-15149G>A:p.(=)

Pathogenicity Data:: Best Score: 0.26650017; CADD: 0.267 (1.346)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0024%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101839920G>C [0/1]

Variant score: 0.211

Transcripts:: NCALD:ENST00000311028.4:c.-20+47221C>G:p.(=); NCALD:ENST00000395923.5:c.-20+75889C>G:p.(=); NCALD:ENST00000521599.5:c.-20+75889C>G:p.(=)

Pathogenicity Data:: Best Score: 0.21113986; CADD: 0.211 (1.030)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102065010C>CA [0/1] rs34548051 (variation viewer)

Variant score: 0.201

Transcripts:: NCALD:ENST00000311028.4:c.-209-44722_-209-44721insT:p.(=); NCALD:ENST00000395923.5:c.-122-44722_-122-44721insT:p.(=); NCALD:ENST00000521599.5:c.-209-35915_-209-35914insT:p.(=)

Pathogenicity Data:: Best Score: 0.20126998; CADD: 0.201 (0.976)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102054660CGATAGATAGATAGATA>C [-/1] rs10617345 (variation viewer)

Variant score: 0.190

Transcripts:: NCALD:ENST00000311028.4:c.-209-34387_-209-34372del:p.(=); NCALD:ENST00000395923.5:c.-122-34387_-122-34372del:p.(=); NCALD:ENST00000521599.5:c.-209-25580_-209-25565del:p.(=)

Pathogenicity Data:: Best Score: 0.18959892; CADD: 0.190 (0.913)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101999073CA>C [1/1] rs34227411 (variation viewer)

Variant score: 0.178

Transcripts:: NCALD:ENST00000311028.4:c.-157+21163del:p.(=); NCALD:ENST00000395923.5:c.-70+21163del:p.(=); NCALD:ENST00000521599.5:c.-70+21163del:p.(=)

Pathogenicity Data:: Best Score: 0.17813593; CADD: 0.178 (0.852)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101833610G>GT [0/1] rs555031298 (variation viewer)

Variant score: 0.155

Transcripts:: NCALD:ENST00000311028.4:c.-20+53530_-20+53531insA:p.(=); NCALD:ENST00000395923.5:c.-20+82198_-20+82199insA:p.(=); NCALD:ENST00000521599.5:c.-20+82198_-20+82199insA:p.(=)

Pathogenicity Data:: Best Score: 0.15452647; CADD: 0.155 (0.729)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102108441T>C [0/1]

Variant score: 0.145

Transcripts:: NCALD:ENST00000311028.4:c.-210+15796A>G:p.(=); NCALD:ENST00000395923.5:c.-123+16129A>G:p.(=); NCALD:ENST00000521599.5:c.-210+15796A>G:p.(=)

Pathogenicity Data:: Best Score: 0.14532697; CADD: 0.145 (0.682)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr8:g.101684379C>T [0|1] rs185901197 (variation viewer)

Variant score: 0.142

Transcripts:: NCALD:ENST00000220931.11::; NCALD:ENST00000646743.1::

Pathogenicity Data:: Best Score: 0.22874147; CADD: 0.229 (1.128)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.2796%; gnomAD_G_AFR: 0.1265%; gnomAD_G_AMR: 0.4843%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_FIN: 0.0878%; gnomAD_G_NFE: 0.3135%; gnomAD_G_OTH: 0.5102%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102079713C>T [0/1] rs185935099 (variation viewer)

Variant score: 0.090

Transcripts:: NCALD:ENST00000311028.4:c.-210+44524G>A:p.(=); NCALD:ENST00000395923.5:c.-123+44857G>A:p.(=); NCALD:ENST00000521599.5:c.-210+44524G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09510124; CADD: 0.095 (0.434)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1410%; UK10K: 0.3306%; gnomAD_G_AFR: 0.0802%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1932%; gnomAD_G_OTH: 0.1018%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102004756T>C [0/1] rs77095089 (variation viewer)

Variant score: 0.086

Transcripts:: NCALD:ENST00000311028.4:c.-157+15481A>G:p.(=); NCALD:ENST00000395923.5:c.-70+15481A>G:p.(=); NCALD:ENST00000521599.5:c.-70+15481A>G:p.(=)

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: gnomAD_G_AFR: 0.0692%; gnomAD_G_FIN: 0.1435%; gnomAD_G_NFE: 0.2595%; gnomAD_G_OTH: 0.2096%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101893625C>T [0/1] rs13255167 (variation viewer)

Variant score: 0.081

Transcripts:: NCALD:ENST00000311028.4:c.-106-6398G>A:p.(=); NCALD:ENST00000395923.5:c.-20+22184G>A:p.(=); NCALD:ENST00000521599.5:c.-20+22184G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4134568; CADD: 0.413 (2.317)

Frequency Data:: gnomAD_G_AFR: 0.4135%; gnomAD_G_AMR: 1.2085%; gnomAD_G_ASJ: 1.4563%; gnomAD_G_EAS: 0.4651%; gnomAD_G_FIN: 1.5760%; gnomAD_G_NFE: 1.9371%; gnomAD_G_OTH: 1.2346%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.102080766G>A [0/1] rs190964394 (variation viewer)

Variant score: 0.078

Transcripts:: NCALD:ENST00000311028.4:c.-210+43471C>T:p.(=); NCALD:ENST00000395923.5:c.-123+43804C>T:p.(=); NCALD:ENST00000521599.5:c.-210+43471C>T:p.(=)

Pathogenicity Data:: Best Score: 0.09092438; CADD: 0.091 (0.414)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3416%; UK10K: 0.7273%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2579%; gnomAD_G_NFE: 0.4463%; gnomAD_G_OTH: 0.2037%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101957289GT>G [1/1] rs11305701 (variation viewer)

Variant score: 0.073

Transcripts:: NCALD:ENST00000311028.4:c.-156-41432del:p.(=); NCALD:ENST00000395923.5:c.-69-41432del:p.(=); NCALD:ENST00000521599.5:c.-69-41432del:p.(=)

Pathogenicity Data:: Best Score: 0.07295674; CADD: 0.073 (0.329)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101988902GA>G [1/1] rs35196499 (variation viewer)

Variant score: 0.066

Transcripts:: NCALD:ENST00000311028.4:c.-157+31334del:p.(=); NCALD:ENST00000395923.5:c.-70+31334del:p.(=); NCALD:ENST00000521599.5:c.-70+31334del:p.(=)

Pathogenicity Data:: Best Score: 0.066100836; CADD: 0.066 (0.297)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101859915C>A [0/1] rs138623516 (variation viewer)

Variant score: 0.059

Transcripts:: NCALD:ENST00000311028.4:c.-20+27226G>T:p.(=); NCALD:ENST00000395923.5:c.-20+55894G>T:p.(=); NCALD:ENST00000521599.5:c.-20+55894G>T:p.(=)

Pathogenicity Data:: Best Score: 0.27606428; CADD: 0.276 (1.403)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 1.2310%; UK10K: 1.9175%; gnomAD_G_AFR: 0.4243%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.7741%; gnomAD_G_NFE: 1.6551%; gnomAD_G_OTH: 0.9165%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.101994393GT>G [0/1] rs1423400020 (variation viewer)

Variant score: 0.006

Transcripts:: NCALD:ENST00000311028.4:c.-157+25843del:p.(=); NCALD:ENST00000395923.5:c.-70+25843del:p.(=); NCALD:ENST00000521599.5:c.-70+25843del:p.(=)

Pathogenicity Data:: Best Score: 0.0057399273; CADD: 0.006 (0.025)

Frequency Data:: TOPMed: 0.0016%

HDAC9

Exomiser Score: 0.542

Phenotype Score: 0.519

Variant Score: 0.877

Phenotype matches:

Proximity score 0.519 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.410

Phenotype Score: 0.519

Variant Score: 0.820

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18648151CTTTA>C [0/1] rs1308533521 (variation viewer)

Variant score: 0.820 CONTRIBUTING VARIANT

Transcripts:: HDAC9:ENST00000401921.5:c.1117+154_1117+157del:p.(=); HDAC9:ENST00000405010.7:c.1240+154_1240+157del:p.(=); HDAC9:ENST00000406072.5:c.1201+154_1201+157del:p.(=); HDAC9:ENST00000406451.8:c.1240+154_1240+157del:p.(=); HDAC9:ENST00000417496.6:c.1234+154_1234+157del:p.(=); HDAC9:ENST00000428307.6:c.1108+154_1108+157del:p.(=); HDAC9:ENST00000432645.6:c.1240+154_1240+157del:p.(=); HDAC9:ENST00000441542.6:c.1249+154_1249+157del:p.(=); HDAC9:ENST00000456174.6:c.1156+154_1156+157del:p.(=); HDAC9:ENST00000524023.1:c.1009+154_1009+157del:p.(=); HDAC9:ENST00000622668.4:c.1117+154_1117+157del:p.(=)

Pathogenicity Data:: Best Score: 0.8199057; CADD: 0.820 (7.445)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.542

Phenotype Score: 0.519

Variant Score: 0.877

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18331317A>T [0/1] rs183370127 (variation viewer)

Variant score: 0.935 CONTRIBUTING VARIANT

Transcripts:: HDAC9:ENST00000417496.6:c.26-127525A>T:p.(=)

Pathogenicity Data:: Best Score: 0.98775387; CADD: 0.988 (19.120)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0964%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0535%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18648151CTTTA>C [0/1] rs1308533521 (variation viewer)

Variant score: 0.820 CONTRIBUTING VARIANT

Transcripts:: HDAC9:ENST00000401921.5:c.1117+154_1117+157del:p.(=); HDAC9:ENST00000405010.7:c.1240+154_1240+157del:p.(=); HDAC9:ENST00000406072.5:c.1201+154_1201+157del:p.(=); HDAC9:ENST00000406451.8:c.1240+154_1240+157del:p.(=); HDAC9:ENST00000417496.6:c.1234+154_1234+157del:p.(=); HDAC9:ENST00000428307.6:c.1108+154_1108+157del:p.(=); HDAC9:ENST00000432645.6:c.1240+154_1240+157del:p.(=); HDAC9:ENST00000441542.6:c.1249+154_1249+157del:p.(=); HDAC9:ENST00000456174.6:c.1156+154_1156+157del:p.(=); HDAC9:ENST00000524023.1:c.1009+154_1009+157del:p.(=); HDAC9:ENST00000622668.4:c.1117+154_1117+157del:p.(=)

Pathogenicity Data:: Best Score: 0.8199057; CADD: 0.820 (7.445)

Frequency Data:: TOPMed: 0.0024%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18627908T>C [0/1] rs183583808 (variation viewer)

Variant score: 0.776

Transcripts:: HDAC9:ENST00000401921.5:c.665-6719T>C:p.(=); HDAC9:ENST00000405010.7:c.656-1442T>C:p.(=); HDAC9:ENST00000406072.5:c.749-6719T>C:p.(=); HDAC9:ENST00000406451.8:c.656-1442T>C:p.(=); HDAC9:ENST00000417496.6:c.782-6719T>C:p.(=); HDAC9:ENST00000428307.6:c.656-6719T>C:p.(=); HDAC9:ENST00000432645.6:c.656-1442T>C:p.(=); HDAC9:ENST00000441542.6:c.665-1442T>C:p.(=); HDAC9:ENST00000456174.6:c.572-1442T>C:p.(=); HDAC9:ENST00000524023.1:c.557-6719T>C:p.(=); HDAC9:ENST00000622668.4:c.665-6719T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8651658; CADD: 0.865 (8.702)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1959%; UK10K: 0.5686%; gnomAD_G_AFR: 0.1147%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.3132%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18857703T>C [0|1] rs568569418 (variation viewer)

Variant score: 0.764

Transcripts:: HDAC9:ENST00000401921.5:c.2553-16775T>C:p.(=); HDAC9:ENST00000406451.8:c.2676-16775T>C:p.(=); HDAC9:ENST00000432645.6:c.2676-16775T>C:p.(=); HDAC9:ENST00000441542.6:c.2685-16775T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7852664; CADD: 0.785 (6.681)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0799%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1199%; gnomAD_G_NFE: 0.1800%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18728402AACACACACACACAC>A [-/1] rs56281287 (variation viewer)

Variant score: 0.618

Transcripts:: HDAC9:ENST00000401921.5:c.1777+646_1777+659del:p.(=); HDAC9:ENST00000406451.8:c.1900+646_1900+659del:p.(=); HDAC9:ENST00000432645.6:c.1900+646_1900+659del:p.(=); HDAC9:ENST00000441542.6:c.1909+646_1909+659del:p.(=)

Pathogenicity Data:: Best Score: 0.6177038; CADD: 0.618 (4.176)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18768628G>C [0/1] rs1261445238 (variation viewer)

Variant score: 0.521

Transcripts:: HDAC9:ENST00000401921.5:c.2082+1473G>C:p.(=); HDAC9:ENST00000406451.8:c.2205+1473G>C:p.(=); HDAC9:ENST00000432645.6:c.2205+1473G>C:p.(=); HDAC9:ENST00000441542.6:c.2214+1473G>C:p.(=)

Pathogenicity Data:: Best Score: 0.5210391; CADD: 0.521 (3.197)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18247685A>C [0/1] rs539609264 (variation viewer)

Variant score: 0.511

Transcripts:: HDAC9:ENST00000417496.6:c.25+85336A>C:p.(=)

Pathogenicity Data:: Best Score: 0.5392132; CADD: 0.539 (3.365)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0948%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0600%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18356358G>GTTTTTT [1/1] rs5882659 (variation viewer)

Variant score: 0.418

Transcripts:: HDAC9:ENST00000417496.6:c.26-102484_26-102483insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.4180308; CADD: 0.418 (2.351)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18859811C>CAT [-/1] rs56249427 (variation viewer)

Variant score: 0.385

Transcripts:: HDAC9:ENST00000401921.5:c.2553-14667_2553-14666insAT:p.(=); HDAC9:ENST00000406451.8:c.2676-14667_2676-14666insAT:p.(=); HDAC9:ENST00000432645.6:c.2676-14667_2676-14666insAT:p.(=); HDAC9:ENST00000441542.6:c.2685-14667_2685-14666insAT:p.(=)

Pathogenicity Data:: Best Score: 0.38538945; CADD: 0.385 (2.114)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18755248A>C [0/1] rs182736827 (variation viewer)

Variant score: 0.376

Transcripts:: HDAC9:ENST00000401921.5:c.1911+6110A>C:p.(=); HDAC9:ENST00000406451.8:c.2034+6110A>C:p.(=); HDAC9:ENST00000432645.6:c.2034+6110A>C:p.(=); HDAC9:ENST00000441542.6:c.2043+6110A>C:p.(=)

Pathogenicity Data:: Best Score: 0.60088325; CADD: 0.601 (3.989)

Frequency Data:: 1000Genomes: 0.6390%; TOPMed: 0.1617%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18857335T>TTGTG [-/1] rs375575248 (variation viewer)

Variant score: 0.353

Transcripts:: HDAC9:ENST00000401921.5:c.2553-17143_2553-17142insTGTG:p.(=); HDAC9:ENST00000406451.8:c.2676-17143_2676-17142insTGTG:p.(=); HDAC9:ENST00000432645.6:c.2676-17143_2676-17142insTGTG:p.(=); HDAC9:ENST00000441542.6:c.2685-17143_2685-17142insTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.35300636; CADD: 0.353 (1.891)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18946036CAAAAAA>C [1/1] rs1171055959 (variation viewer)

Variant score: 0.344

Transcripts:: HDAC9:ENST00000401921.5:c.2806-8109_2806-8104del:p.(=); HDAC9:ENST00000406451.8:c.2929-8109_2929-8104del:p.(=); HDAC9:ENST00000432645.6:c.2929-8109_2929-8104del:p.(=); HDAC9:ENST00000441542.6:c.2938-8109_2938-8104del:p.(=)

Pathogenicity Data:: Best Score: 0.34415686; CADD: 0.344 (1.832)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18598697C>A [0/1] rs570542536 (variation viewer)

Variant score: 0.310

Transcripts:: HDAC9:ENST00000401921.5:c.664+4668C>A:p.(=); HDAC9:ENST00000405010.7:c.655+4668C>A:p.(=); HDAC9:ENST00000406072.5:c.748+4668C>A:p.(=); HDAC9:ENST00000406451.8:c.655+4668C>A:p.(=); HDAC9:ENST00000417496.6:c.781+4668C>A:p.(=); HDAC9:ENST00000428307.6:c.655+4668C>A:p.(=); HDAC9:ENST00000432645.6:c.655+4668C>A:p.(=); HDAC9:ENST00000441542.6:c.664+4668C>A:p.(=); HDAC9:ENST00000456174.6:c.571+4668C>A:p.(=); HDAC9:ENST00000524023.1:c.556+4668C>A:p.(=); HDAC9:ENST00000622668.4:c.664+4668C>A:p.(=)

Pathogenicity Data:: Best Score: 0.31118912; CADD: 0.311 (1.619)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18937030A>ATT [1/1] rs768350029 (variation viewer)

Variant score: 0.274

Transcripts:: HDAC9:ENST00000401921.5:c.2805+1088_2805+1089insTT:p.(=); HDAC9:ENST00000406451.8:c.2928+1088_2928+1089insTT:p.(=); HDAC9:ENST00000432645.6:c.2928+1088_2928+1089insTT:p.(=); HDAC9:ENST00000441542.6:c.2937+1088_2937+1089insTT:p.(=)

Pathogenicity Data:: Best Score: 0.27422833; CADD: 0.274 (1.392)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18225022T>TA [0/1] rs924201509 (variation viewer)

Variant score: 0.273

Transcripts:: HDAC9:ENST00000417496.6:c.25+62673_25+62674insA:p.(=)

Pathogenicity Data:: Best Score: 0.27789563; CADD: 0.278 (1.414)

Frequency Data:: gnomAD_G_AFR: 0.0117%; gnomAD_G_EAS: 0.1248%; gnomAD_G_FIN: 0.0606%

FIVE_PRIME_UTR_INTRON_VARIANT chr7:g.18135492C>A [0|1] rs1174356377 (variation viewer)

Variant score: 0.260

Transcripts:: HDAC9:ENST00000417496.6:c.-96-26737C>A:p.(=)

Pathogenicity Data:: Best Score: 0.2990291; CADD: 0.299 (1.543)

Frequency Data:: gnomAD_G_AFR: 0.6787%; gnomAD_G_AMR: 0.6024%; gnomAD_G_FIN: 0.5269%; gnomAD_G_NFE: 0.1596%; gnomAD_G_OTH: 0.3401%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18415295C>G [0/1] rs931491375 (variation viewer)

Variant score: 0.260

Transcripts:: HDAC9:ENST00000417496.6:c.26-43547C>G:p.(=)

Pathogenicity Data:: Best Score: 0.25971323; CADD: 0.260 (1.306)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18732562T>C [0|1] rs369437660 (variation viewer)

Variant score: 0.249

Transcripts:: HDAC9:ENST00000401921.5:c.1777+4805T>C:p.(=); HDAC9:ENST00000406451.8:c.1900+4805T>C:p.(=); HDAC9:ENST00000432645.6:c.1900+4805T>C:p.(=); HDAC9:ENST00000441542.6:c.1909+4805T>C:p.(=)

Pathogenicity Data:: Best Score: 0.4129163; CADD: 0.413 (2.313)

Frequency Data:: 1000Genomes: 0.8986%; TOPMed: 0.8986%; gnomAD_G_AFR: 0.2205%; gnomAD_G_AMR: 0.5263%; gnomAD_G_FIN: 0.8739%; gnomAD_G_NFE: 1.3689%; gnomAD_G_OTH: 1.0204%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18799038AAGAC>A [-/1] rs1428757653 (variation viewer)

Variant score: 0.228

Transcripts:: HDAC9:ENST00000401921.5:c.2190+5587_2190+5590del:p.(=); HDAC9:ENST00000406451.8:c.2313+5587_2313+5590del:p.(=); HDAC9:ENST00000432645.6:c.2313+5587_2313+5590del:p.(=); HDAC9:ENST00000441542.6:c.2322+5587_2322+5590del:p.(=)

Pathogenicity Data:: Best Score: 0.227853; CADD: 0.228 (1.123)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18482380C>CAAAAAAAA [1/1] rs566243064 (variation viewer)

Variant score: 0.210

Transcripts:: HDAC9:ENST00000417496.6:c.86-13882_86-13881insAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.20986736; CADD: 0.210 (1.023)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18272913GCTACTACTACTACTACTACTA>G [-/1] rs149171355 (variation viewer)

Variant score: 0.179

Transcripts:: HDAC9:ENST00000417496.6:c.25+110565_25+110585del:p.(=)

Pathogenicity Data:: Best Score: 0.17927057; CADD: 0.179 (0.858)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18938230C>CA [1/1] rs71553939 (variation viewer)

Variant score: 0.156

Transcripts:: HDAC9:ENST00000401921.5:c.2805+2288_2805+2289insA:p.(=); HDAC9:ENST00000406451.8:c.2928+2288_2928+2289insA:p.(=); HDAC9:ENST00000432645.6:c.2928+2288_2928+2289insA:p.(=); HDAC9:ENST00000441542.6:c.2937+2288_2937+2289insA:p.(=)

Pathogenicity Data:: Best Score: 0.15588814; CADD: 0.156 (0.736)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18779008A>G [0/1] rs150659736 (variation viewer)

Variant score: 0.146

Transcripts:: HDAC9:ENST00000401921.5:c.2082+11853A>G:p.(=); HDAC9:ENST00000406451.8:c.2205+11853A>G:p.(=); HDAC9:ENST00000432645.6:c.2205+11853A>G:p.(=); HDAC9:ENST00000441542.6:c.2214+11853A>G:p.(=)

Pathogenicity Data:: Best Score: 0.981719; CADD: 0.982 (17.380)

Frequency Data:: 1000Genomes: 0.8387%; TOPMed: 0.4731%; UK10K: 0.1058%; gnomAD_G_AFR: 0.8129%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18733186T>TACATATATACACGTGTATACATGTGTCTATACGTATATAC [0/1] rs1317022778 (variation viewer)

Variant score: 0.128

Transcripts:: HDAC9:ENST00000401921.5:c.1777+5429_1777+5430insACATATATACACGTGTATACATGTGTCTATACGTATATAC:p.(=); HDAC9:ENST00000406451.8:c.1900+5429_1900+5430insACATATATACACGTGTATACATGTGTCTATACGTATATAC:p.(=); HDAC9:ENST00000432645.6:c.1900+5429_1900+5430insACATATATACACGTGTATACATGTGTCTATACGTATATAC:p.(=); HDAC9:ENST00000441542.6:c.1909+5429_1909+5430insACATATATACACGTGTATACATGTGTCTATACGTATATAC:p.(=)

Pathogenicity Data:: Best Score: 0.25027847; CADD: 0.250 (1.251)

Frequency Data:: gnomAD_G_AFR: 1.5277%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_NFE: 0.0421%; gnomAD_G_OTH: 0.5814%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18866471G>A [0/1] rs1337810268 (variation viewer)

Variant score: 0.124

Transcripts:: HDAC9:ENST00000401921.5:c.2553-8007G>A:p.(=); HDAC9:ENST00000406451.8:c.2676-8007G>A:p.(=); HDAC9:ENST00000432645.6:c.2676-8007G>A:p.(=); HDAC9:ENST00000441542.6:c.2685-8007G>A:p.(=)

Pathogenicity Data:: Best Score: 0.124613166; CADD: 0.125 (0.578)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18303375TTGTGTGTGTGTGTGTGTGTGTGTG>T [-/1] rs71014320 (variation viewer)

Variant score: 0.122

Transcripts:: HDAC9:ENST00000417496.6:c.25+141027_25+141050del:p.(=)

Pathogenicity Data:: Best Score: 0.12178671; CADD: 0.122 (0.564)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18349307TACACACACACACACACAC>T [-/1] rs3138825 (variation viewer)

Variant score: 0.120

Transcripts:: HDAC9:ENST00000417496.6:c.26-109534_26-109517del:p.(=)

Pathogenicity Data:: Best Score: 0.120167494; CADD: 0.120 (0.556)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18789286G>GCGCGCACA [-/1] rs146066951 (variation viewer)

Variant score: 0.113

Transcripts:: HDAC9:ENST00000401921.5:c.2083-4059_2083-4058insCGCGCACA:p.(=); HDAC9:ENST00000406451.8:c.2206-4059_2206-4058insCGCGCACA:p.(=); HDAC9:ENST00000432645.6:c.2206-4059_2206-4058insCGCGCACA:p.(=); HDAC9:ENST00000441542.6:c.2215-4059_2215-4058insCGCGCACA:p.(=)

Pathogenicity Data:: Best Score: 0.112639666; CADD: 0.113 (0.519)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18244994C>CATCT [-/1] rs1554342548 (variation viewer)

Variant score: 0.104

Transcripts:: HDAC9:ENST00000417496.6:c.25+82645_25+82646insATCT:p.(=)

Pathogenicity Data:: Best Score: 0.10401654; CADD: 0.104 (0.477)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18396079A>ATTCCCTTCCCTTCCC [1/1] rs775874685 (variation viewer)

Variant score: 0.100

Transcripts:: HDAC9:ENST00000417496.6:c.26-62763_26-62762insTTCCCTTCCCTTCCC:p.(=)

Pathogenicity Data:: Best Score: 0.099880874; CADD: 0.100 (0.457)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18789286GCA>G [-/1] rs34385627 (variation viewer)

Variant score: 0.100

Transcripts:: HDAC9:ENST00000401921.5:c.2083-4058_2083-4057del:p.(=); HDAC9:ENST00000406451.8:c.2206-4058_2206-4057del:p.(=); HDAC9:ENST00000432645.6:c.2206-4058_2206-4057del:p.(=); HDAC9:ENST00000441542.6:c.2215-4058_2215-4057del:p.(=)

Pathogenicity Data:: Best Score: 0.099880874; CADD: 0.100 (0.457)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18568026GTATA>G [-/1] rs36203178 (variation viewer)

Variant score: 0.098

Transcripts:: HDAC9:ENST00000401921.5:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000405010.7:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000406072.5:c.107-17254_107-17251del:p.(=); HDAC9:ENST00000406451.8:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000417496.6:c.149-17254_149-17251del:p.(=); HDAC9:ENST00000428307.6:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000432645.6:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000441542.6:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000622668.4:c.23-17254_23-17251del:p.(=); HDAC9:ENST00000456174.6:c.-71-17254_-71-17251del:p.(=); HDAC9:ENST00000524023.1:c.-71-17254_-71-17251del:p.(=)

Pathogenicity Data:: Best Score: 0.097598135; CADD: 0.098 (0.446)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18733138CAT>C [0/1] rs751093901 (variation viewer)

Variant score: 0.091

Transcripts:: HDAC9:ENST00000401921.5:c.1777+5382_1777+5383del:p.(=); HDAC9:ENST00000406451.8:c.1900+5382_1900+5383del:p.(=); HDAC9:ENST00000432645.6:c.1900+5382_1900+5383del:p.(=); HDAC9:ENST00000441542.6:c.1909+5382_1909+5383del:p.(=)

Pathogenicity Data:: Best Score: 0.091342926; CADD: 0.091 (0.416)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0264%; gnomAD_G_FIN: 0.0406%; gnomAD_G_NFE: 0.0074%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18258951CTTTT>C [-/1] rs199607615 (variation viewer)

Variant score: 0.086

Transcripts:: HDAC9:ENST00000417496.6:c.25+96603_25+96606del:p.(=)

Pathogenicity Data:: Best Score: 0.14138198; CADD: 0.141 (0.662)

Frequency Data:: gnomAD_G_AFR: 0.0521%; gnomAD_G_AMR: 0.2762%; gnomAD_G_EAS: 1.3627%; gnomAD_G_NFE: 0.4127%; gnomAD_G_OTH: 0.2222%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18722499T>C [0/1] rs184021295 (variation viewer)

Variant score: 0.084

Transcripts:: HDAC9:ENST00000401921.5:c.1600-5081T>C:p.(=); HDAC9:ENST00000406451.8:c.1723-5081T>C:p.(=); HDAC9:ENST00000432645.6:c.1723-5081T>C:p.(=); HDAC9:ENST00000441542.6:c.1732-5081T>C:p.(=)

Pathogenicity Data:: Best Score: 0.13403565; CADD: 0.134 (0.625)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.1768%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1199%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.1668%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18435059C>CA [1/1] rs376786180 (variation viewer)

Variant score: 0.084

Transcripts:: HDAC9:ENST00000417496.6:c.26-23783_26-23782insA:p.(=)

Pathogenicity Data:: Best Score: 0.083779514; CADD: 0.084 (0.380)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18815056C>T [0/1] rs190491584 (variation viewer)

Variant score: 0.078

Transcripts:: HDAC9:ENST00000401921.5:c.2191-14105C>T:p.(=); HDAC9:ENST00000406451.8:c.2314-14105C>T:p.(=); HDAC9:ENST00000432645.6:c.2314-14105C>T:p.(=); HDAC9:ENST00000441542.6:c.2323-14105C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12481475; CADD: 0.125 (0.579)

Frequency Data:: 1000Genomes: 0.6589%; TOPMed: 0.6589%; UK10K: 0.0793%; gnomAD_G_AFR: 0.2639%; gnomAD_G_AMR: 0.2398%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.1854%; gnomAD_G_NFE: 0.0667%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18168897TTG>T [0/1] rs1201294435 (variation viewer)

Variant score: 0.071

Transcripts:: HDAC9:ENST00000417496.6:c.25+6549_25+6550del:p.(=)

Pathogenicity Data:: Best Score: 0.070605695; CADD: 0.071 (0.318)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18768879C>A [0/1] rs184153833 (variation viewer)

Variant score: 0.070

Transcripts:: HDAC9:ENST00000401921.5:c.2082+1724C>A:p.(=); HDAC9:ENST00000406451.8:c.2205+1724C>A:p.(=); HDAC9:ENST00000432645.6:c.2205+1724C>A:p.(=); HDAC9:ENST00000441542.6:c.2214+1724C>A:p.(=)

Pathogenicity Data:: Best Score: 0.11100358; CADD: 0.111 (0.511)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 0.6989%; UK10K: 0.0793%; gnomAD_G_AFR: 0.2291%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18244994C>CCTCTATCTATCTATCTATCTATCTATCT [-/1] rs71553924 (variation viewer)

Variant score: 0.064

Transcripts:: HDAC9:ENST00000417496.6:c.25+82645_25+82646insCTCTATCTATCTATCTATCTATCTATCT:p.(=)

Pathogenicity Data:: Best Score: 0.06416345; CADD: 0.064 (0.288)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18980715CTCTTCTTCTTCCTTCTTCT>C [0/1] rs756067173 (variation viewer)

Variant score: 0.064

Transcripts:: HDAC9:ENST00000401921.5:c.3038+4763_3038+4781del:p.(=); HDAC9:ENST00000406451.8:c.3161+4763_3161+4781del:p.(=); HDAC9:ENST00000441542.6:c.3170+4763_3170+4781del:p.(=)

Pathogenicity Data:: Best Score: 0.0710336; CADD: 0.071 (0.320)

Frequency Data:: gnomAD_G_AFR: 0.2115%; gnomAD_G_AMR: 0.3344%; gnomAD_G_EAS: 0.3155%; gnomAD_G_FIN: 0.3664%; gnomAD_G_NFE: 0.5781%; gnomAD_G_OTH: 0.5525%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18768292T>C [0/1] rs146531879 (variation viewer)

Variant score: 0.047

Transcripts:: HDAC9:ENST00000401921.5:c.2082+1137T>C:p.(=); HDAC9:ENST00000406451.8:c.2205+1137T>C:p.(=); HDAC9:ENST00000432645.6:c.2205+1137T>C:p.(=); HDAC9:ENST00000441542.6:c.2214+1137T>C:p.(=)

Pathogenicity Data:: Best Score: 0.07487589; CADD: 0.075 (0.338)

Frequency Data:: 1000Genomes: 1.1180%; TOPMed: 0.5407%; UK10K: 0.0793%; gnomAD_G_AFR: 1.1460%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18468406G>C [0/1] rs1315540910 (variation viewer)

Variant score: 0.046

Transcripts:: HDAC9:ENST00000417496.6:c.85+9505G>C:p.(=)

Pathogenicity Data:: Best Score: 0.046325862; CADD: 0.046 (0.206)

Frequency Data:: TOPMed: 0.0024%

FIVE_PRIME_UTR_INTRON_VARIANT chr7:g.18089209AT>A [-/1] rs79524846 (variation viewer)

Variant score: 0.046

Transcripts:: HDAC9:ENST00000417496.6:c.-97+1997del:p.(=)

Pathogenicity Data:: Best Score: 0.0487383; CADD: 0.049 (0.217)

Frequency Data:: gnomAD_G_AFR: 0.0118%; gnomAD_G_FIN: 0.3621%; gnomAD_G_NFE: 0.0416%; gnomAD_G_OTH: 0.1126%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18772690C>T [0/1] rs145068654 (variation viewer)

Variant score: 0.041

Transcripts:: HDAC9:ENST00000401921.5:c.2082+5535C>T:p.(=); HDAC9:ENST00000406451.8:c.2205+5535C>T:p.(=); HDAC9:ENST00000432645.6:c.2205+5535C>T:p.(=); HDAC9:ENST00000441542.6:c.2214+5535C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2747295; CADD: 0.275 (1.395)

Frequency Data:: 1000Genomes: 0.9385%; TOPMed: 0.5089%; UK10K: 0.1058%; gnomAD_G_AFR: 0.8937%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_NFE: 0.0801%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18806399G>A [0/1] rs149260941 (variation viewer)

Variant score: 0.040

Transcripts:: HDAC9:ENST00000401921.5:c.2190+12947G>A:p.(=); HDAC9:ENST00000406451.8:c.2313+12947G>A:p.(=); HDAC9:ENST00000432645.6:c.2313+12947G>A:p.(=); HDAC9:ENST00000441542.6:c.2322+12947G>A:p.(=)

Pathogenicity Data:: Best Score: 0.057242513; CADD: 0.057 (0.256)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.6395%; UK10K: 1.1505%; gnomAD_G_AFR: 0.2064%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.4007%; gnomAD_G_NFE: 1.1667%; gnomAD_G_OTH: 0.5112%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18991369A>T [-/1] rs10247256 (variation viewer)

Variant score: 0.038

Transcripts:: HDAC9:ENST00000401921.5:c.3039-4654A>T:p.(=); HDAC9:ENST00000406451.8:c.3162-4654A>T:p.(=); HDAC9:ENST00000441542.6:c.3171-4654A>T:p.(=)

Pathogenicity Data:: Best Score: 0.057242513; CADD: 0.057 (0.256)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.4393%; UK10K: 0.9125%; gnomAD_G_AFR: 0.2406%; gnomAD_G_AMR: 0.4808%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 0.2586%; gnomAD_G_NFE: 1.2563%; gnomAD_G_OTH: 0.7172%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18771700C>A [0/1] rs139713904 (variation viewer)

Variant score: 0.035

Transcripts:: HDAC9:ENST00000401921.5:c.2082+4545C>A:p.(=); HDAC9:ENST00000406451.8:c.2205+4545C>A:p.(=); HDAC9:ENST00000432645.6:c.2205+4545C>A:p.(=); HDAC9:ENST00000441542.6:c.2214+4545C>A:p.(=)

Pathogenicity Data:: Best Score: 0.23581237; CADD: 0.236 (1.168)

Frequency Data:: 1000Genomes: 0.8187%; TOPMed: 0.8187%; UK10K: 0.1058%; gnomAD_G_AFR: 0.6873%; gnomAD_G_AMR: 0.2398%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_NFE: 0.0800%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18821178G>A [0/1] rs188428840 (variation viewer)

Variant score: 0.024

Transcripts:: HDAC9:ENST00000401921.5:c.2191-7983G>A:p.(=); HDAC9:ENST00000406451.8:c.2314-7983G>A:p.(=); HDAC9:ENST00000432645.6:c.2314-7983G>A:p.(=); HDAC9:ENST00000441542.6:c.2323-7983G>A:p.(=)

Pathogenicity Data:: Best Score: 0.027700663; CADD: 0.028 (0.122)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.1744%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.1665%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18207539C>CTTTTTTTTTT [-/1] rs56690120 (variation viewer)

Variant score: 0.020

Transcripts:: HDAC9:ENST00000417496.6:c.25+45190_25+45191insTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.019833148; CADD: 0.020 (0.087)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18893033G>GA [-/1] rs71960483 (variation viewer)

Variant score: 0.020

Transcripts:: HDAC9:ENST00000401921.5:c.2671+18437_2671+18438insA:p.(=); HDAC9:ENST00000406451.8:c.2794+18437_2794+18438insA:p.(=); HDAC9:ENST00000432645.6:c.2794+18437_2794+18438insA:p.(=); HDAC9:ENST00000441542.6:c.2803+18437_2803+18438insA:p.(=)

Pathogenicity Data:: Best Score: 0.019833148; CADD: 0.020 (0.087)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18207539C>CTTTTTTTTTTTT [-/1] rs56690120 (variation viewer)

Variant score: 0.019

Transcripts:: HDAC9:ENST00000417496.6:c.25+45190_25+45191insTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.01915586; CADD: 0.019 (0.084)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18202950C>T [0/1] rs138461389 (variation viewer)

Variant score: 0.019

Transcripts:: HDAC9:ENST00000417496.6:c.25+40601C>T:p.(=)

Pathogenicity Data:: Best Score: 0.024785817; CADD: 0.025 (0.109)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2397%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.2466%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18893033G>GAAAA [-/1] rs71960483 (variation viewer)

Variant score: 0.019

Transcripts:: HDAC9:ENST00000401921.5:c.2671+18437_2671+18438insAAAA:p.(=); HDAC9:ENST00000406451.8:c.2794+18437_2794+18438insAAAA:p.(=); HDAC9:ENST00000432645.6:c.2794+18437_2794+18438insAAAA:p.(=); HDAC9:ENST00000441542.6:c.2803+18437_2803+18438insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.018704057; CADD: 0.019 (0.082)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18765449G>A [0/1] rs144660476 (variation viewer)

Variant score: 0.018

Transcripts:: HDAC9:ENST00000401921.5:c.2033-1657G>A:p.(=); HDAC9:ENST00000406451.8:c.2156-1657G>A:p.(=); HDAC9:ENST00000432645.6:c.2156-1657G>A:p.(=); HDAC9:ENST00000441542.6:c.2165-1657G>A:p.(=)

Pathogenicity Data:: Best Score: 0.028148293; CADD: 0.028 (0.124)

Frequency Data:: 1000Genomes: 1.1780%; TOPMed: 0.5519%; UK10K: 0.0793%; gnomAD_G_AFR: 1.2299%; gnomAD_G_AMR: 0.3597%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_NFE: 0.0667%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18600700T>A [0/1] rs146919984 (variation viewer)

Variant score: 0.016

Transcripts:: HDAC9:ENST00000401921.5:c.664+6671T>A:p.(=); HDAC9:ENST00000405010.7:c.655+6671T>A:p.(=); HDAC9:ENST00000406072.5:c.748+6671T>A:p.(=); HDAC9:ENST00000406451.8:c.655+6671T>A:p.(=); HDAC9:ENST00000417496.6:c.781+6671T>A:p.(=); HDAC9:ENST00000428307.6:c.655+6671T>A:p.(=); HDAC9:ENST00000432645.6:c.655+6671T>A:p.(=); HDAC9:ENST00000441542.6:c.664+6671T>A:p.(=); HDAC9:ENST00000456174.6:c.571+6671T>A:p.(=); HDAC9:ENST00000524023.1:c.556+6671T>A:p.(=); HDAC9:ENST00000622668.4:c.664+6671T>A:p.(=)

Pathogenicity Data:: Best Score: 0.05506921; CADD: 0.055 (0.246)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.7088%; UK10K: 1.4811%; gnomAD_G_AFR: 0.3206%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.8317%; gnomAD_G_NFE: 1.0060%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18779727G>A [0/1] rs535686169 (variation viewer)

Variant score: 0.014

Transcripts:: HDAC9:ENST00000401921.5:c.2082+12572G>A:p.(=); HDAC9:ENST00000406451.8:c.2205+12572G>A:p.(=); HDAC9:ENST00000432645.6:c.2205+12572G>A:p.(=); HDAC9:ENST00000441542.6:c.2214+12572G>A:p.(=)

Pathogenicity Data:: Best Score: 0.095517874; CADD: 0.096 (0.436)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.1864%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_NFE: 0.0734%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18802518C>G [0/1] rs181408056 (variation viewer)

Variant score: 0.013

Transcripts:: HDAC9:ENST00000401921.5:c.2190+9066C>G:p.(=); HDAC9:ENST00000406451.8:c.2313+9066C>G:p.(=); HDAC9:ENST00000432645.6:c.2313+9066C>G:p.(=); HDAC9:ENST00000441542.6:c.2322+9066C>G:p.(=)

Pathogenicity Data:: Best Score: 0.088409066; CADD: 0.088 (0.402)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.1696%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1202%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_NFE: 0.0735%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18803212CT>C [0/1] rs200393533 (variation viewer)

Variant score: 0.012

Transcripts:: HDAC9:ENST00000401921.5:c.2190+9761del:p.(=); HDAC9:ENST00000406451.8:c.2313+9761del:p.(=); HDAC9:ENST00000432645.6:c.2313+9761del:p.(=); HDAC9:ENST00000441542.6:c.2322+9761del:p.(=)

Pathogenicity Data:: Best Score: 0.09217948; CADD: 0.092 (0.420)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.5791%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1220%; gnomAD_G_ASJ: 2.0000%; gnomAD_G_NFE: 0.0737%; gnomAD_G_OTH: 0.2049%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18568026GTA>G [-/1] rs36203178 (variation viewer)

Variant score: 0.004

Transcripts:: HDAC9:ENST00000401921.5:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000405010.7:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000406072.5:c.107-17254_107-17253del:p.(=); HDAC9:ENST00000406451.8:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000417496.6:c.149-17254_149-17253del:p.(=); HDAC9:ENST00000428307.6:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000432645.6:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000441542.6:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000622668.4:c.23-17254_23-17253del:p.(=); HDAC9:ENST00000456174.6:c.-71-17254_-71-17253del:p.(=); HDAC9:ENST00000524023.1:c.-71-17254_-71-17253del:p.(=)

Pathogenicity Data:: Best Score: 0.0041360855; CADD: 0.004 (0.018)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18753597T>G [0/1] rs117842938 (variation viewer)

Variant score: 0.003

Transcripts:: HDAC9:ENST00000401921.5:c.1911+4459T>G:p.(=); HDAC9:ENST00000406451.8:c.2034+4459T>G:p.(=); HDAC9:ENST00000432645.6:c.2034+4459T>G:p.(=); HDAC9:ENST00000441542.6:c.2043+4459T>G:p.(=)

Pathogenicity Data:: Best Score: 0.007341206; CADD: 0.007 (0.032)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.9772%; UK10K: 1.6794%; gnomAD_G_AFR: 0.3554%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.3721%; gnomAD_G_NFE: 1.6426%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18257293T>* [-/1]

Variant score: 0.000

Transcripts:: HDAC9:ENST00000417496.6:c.25+94944T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18332361ATG>* [-/1]

Variant score: 0.000

Transcripts:: HDAC9:ENST00000417496.6:c.26-126481_26-126479delATGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18725476C>CT [0|1] rs397799478 (variation viewer)

Variant score: 0.000

Transcripts:: HDAC9:ENST00000401921.5:c.1600-2104_1600-2103insT:p.(=); HDAC9:ENST00000406451.8:c.1723-2104_1723-2103insT:p.(=); HDAC9:ENST00000432645.6:c.1723-2104_1723-2103insT:p.(=); HDAC9:ENST00000441542.6:c.1732-2104_1732-2103insT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18732735ATGTGTGCGTATGTGTACACACACGTGTATGTGTGCGTATGTGTACACACACGTGTGTT>A [1|1] rs536041028 (variation viewer)

Variant score: 0.000

Transcripts:: HDAC9:ENST00000401921.5:c.1777+4979_1777+5036del:p.(=); HDAC9:ENST00000406451.8:c.1900+4979_1900+5036del:p.(=); HDAC9:ENST00000432645.6:c.1900+4979_1900+5036del:p.(=); HDAC9:ENST00000441542.6:c.1909+4979_1909+5036del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: gnomAD_G_AFR: 0.0565%; gnomAD_G_EAS: 0.2066%; gnomAD_G_FIN: 0.1674%; gnomAD_G_NFE: 0.0431%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18786463TTCCTTTCG>* [-/1]

Variant score: 0.000

Transcripts:: HDAC9:ENST00000401921.5:c.2083-6882_2083-6874delTTCCTTTCGins*:p.(=); HDAC9:ENST00000406451.8:c.2206-6882_2206-6874delTTCCTTTCGins*:p.(=); HDAC9:ENST00000432645.6:c.2206-6882_2206-6874delTTCCTTTCGins*:p.(=); HDAC9:ENST00000441542.6:c.2215-6882_2215-6874delTTCCTTTCGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.18792268A>* [-/1]

Variant score: 0.000

Transcripts:: HDAC9:ENST00000401921.5:c.2083-1077A>*:p.(=); HDAC9:ENST00000406451.8:c.2206-1077A>*:p.(=); HDAC9:ENST00000432645.6:c.2206-1077A>*:p.(=); HDAC9:ENST00000441542.6:c.2215-1077A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PLAA

Exomiser Score: 0.537

Phenotype Score: 0.506

Variant Score: 0.891

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617527 Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.171

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.26942877C>CAAAA [0/1] rs34134451 (variation viewer)

Variant score: 0.171 CONTRIBUTING VARIANT

Transcripts:: PLAA:ENST00000397292.8:c.149+4019_149+4020insTTTT:p.(=); PLAA:ENST00000520884.5:c.149+4019_149+4020insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.17091322; CADD: 0.171 (0.814)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.537

Phenotype Score: 0.506

Variant Score: 0.891

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.26917695G>C [0|1] rs1037076323 (variation viewer)

Variant score: 0.904 CONTRIBUTING VARIANT

Transcripts:: PLAA:ENST00000397292.8:c.1418-530C>G:p.(=); PLAA:ENST00000520884.5:c.1418-530C>G:p.(=)

Pathogenicity Data:: Best Score: 0.9172058; CADD: 0.917 (10.820)

Frequency Data:: TOPMed: 0.0374%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.26919826T>C [0/1] rs545829280 (variation viewer)

Variant score: 0.878 CONTRIBUTING VARIANT

Transcripts:: PLAA:ENST00000397292.8:c.1198-297A>G:p.(=); PLAA:ENST00000520884.5:c.1198-297A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8904531; CADD: 0.890 (9.604)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0358%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.1020%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.26921371T>A [0/1] rs150112670 (variation viewer)

Variant score: 0.129

Transcripts:: PLAA:ENST00000397292.8:c.1040-987A>T:p.(=); PLAA:ENST00000520884.5:c.1040-987A>T:p.(=)

Pathogenicity Data:: Best Score: 0.18698233; CADD: 0.187 (0.899)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.8489%; UK10K: 1.1902%; gnomAD_G_AFR: 0.1946%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 1.0794%; gnomAD_G_OTH: 0.7128%

RRM1

Exomiser Score: 0.536

Phenotype Score: 0.504

Variant Score: 0.892

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.262

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4113546T>C [0/1] rs1171594315 (variation viewer)

Variant score: 0.262 CONTRIBUTING VARIANT

Transcripts:: RRM1:ENST00000300738.10:c.650+1484T>C:p.(=)

Pathogenicity Data:: Best Score: 0.26209575; CADD: 0.262 (1.320)

Frequency Data:: gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.536

Phenotype Score: 0.504

Variant Score: 0.892

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4137972T>C [1|1] rs193149995 (variation viewer)

Variant score: 0.892 CONTRIBUTING VARIANT

Transcripts:: RRM1:ENST00000300738.10:c.2191-223T>C:p.(=); RRM1:ENST00000534285.5:c.1525-223T>C:p.(=)

Pathogenicity Data:: Best Score: 0.89205563; CADD: 0.892 (9.668)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4133980A>AT [1/1] rs34715101 (variation viewer)

Variant score: 0.279

Transcripts:: RRM1:ENST00000300738.10:c.2001+322_2001+323insT:p.(=); RRM1:ENST00000534285.5:c.1335+322_1335+323insT:p.(=)

Pathogenicity Data:: Best Score: 0.27905858; CADD: 0.279 (1.421)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.4101557A>ACCCCCCC [1/1]

Variant score: 0.119

Transcripts:: RRM1:ENST00000300738.10:c.20-436_20-435insCCCCCCC:p.(=)

Pathogenicity Data:: Best Score: 0.11895114; CADD: 0.119 (0.550)

Frequency Data:: No frequency data

UBOX5

Exomiser Score: 0.535

Phenotype Score: 0.505

Variant Score: 0.891

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.028

Phenotype Score: 0.505

Variant Score: 0.490

Variants contributing to score:

REGULATORY_REGION_VARIANT chr20:g.3093904C>CA [0/1] rs33990677 (variation viewer)

Variant score: 0.490 CONTRIBUTING VARIANT

Transcripts:: UBOX5:ENST00000217173.7::

Pathogenicity Data:: Best Score: 0.48973006; CADD: 0.490 (2.922)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.535

Phenotype Score: 0.505

Variant Score: 0.891

Variants contributing to score:

REGULATORY_REGION_VARIANT chr20:g.3175875CTTTTTTTTTTTTT>C [1/1] rs11477220 (variation viewer)

Variant score: 0.891 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.8906799; CADD: 0.891 (9.613)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.3124998C>T [0/1] rs184703225 (variation viewer)

Variant score: 0.431

Transcripts:: UBOX5:ENST00000217173.7:c.-41-1592G>A:p.(=); UBOX5:ENST00000348031.6:c.-41-1592G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5258672; CADD: 0.526 (3.241)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.5391%; UK10K: 0.8463%; gnomAD_G_AFR: 0.1626%; gnomAD_G_AMR: 0.7160%; gnomAD_G_FIN: 0.1726%; gnomAD_G_NFE: 0.6874%; gnomAD_G_OTH: 0.3080%

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.3156235G>A [0/1] rs142128690 (variation viewer)

Variant score: 0.403

Transcripts:: UBOX5:ENST00000217173.7:c.-42+3531C>T:p.(=); UBOX5:ENST00000348031.6:c.-42+3531C>T:p.(=); UBOX5:ENST00000380266.4:c.-191+3531C>T:p.(=)

Pathogenicity Data:: Best Score: 0.48961252; CADD: 0.490 (2.921)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.5990%; gnomAD_G_AFR: 0.2214%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1765%; gnomAD_G_NFE: 0.7602%; gnomAD_G_OTH: 0.5187%

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.3140771G>A [0/1] rs113299095 (variation viewer)

Variant score: 0.160

Transcripts:: UBOX5:ENST00000217173.7:c.-41-17365C>T:p.(=); UBOX5:ENST00000348031.6:c.-41-17365C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3904631; CADD: 0.390 (2.150)

Frequency Data:: 1000Genomes: 1.5180%; TOPMed: 1.2570%; UK10K: 1.4414%; gnomAD_G_AFR: 0.9336%; gnomAD_G_AMR: 1.6787%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 0.2298%; gnomAD_G_NFE: 1.2238%; gnomAD_G_OTH: 0.8197%

DGCR6

Exomiser Score: 0.520

Phenotype Score: 0.504

Variant Score: 0.886

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.520

Phenotype Score: 0.504

Variant Score: 0.886

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.18896533T>C [0|1] rs75068088 (variation viewer)

Variant score: 0.886 CONTRIBUTING VARIANT

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.88558054; CADD: 0.886 (9.415)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.509

Phenotype Score: 0.504

Variant Score: 0.881

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.18896533T>C [0|1] rs75068088 (variation viewer)

Variant score: 0.886 CONTRIBUTING VARIANT

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.88558054; CADD: 0.886 (9.415)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896541A>G [0|1]

Variant score: 0.876 CONTRIBUTING VARIANT

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.8756058; CADD: 0.876 (9.052)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr22:g.18893043A>G [1/1] rs78199573 (variation viewer)

Variant score: 0.879

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.8790238; CADD: 0.879 (9.173)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896367T>G [1|1] rs79424639 (variation viewer)

Variant score: 0.871

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.8708186; CADD: 0.871 (8.888)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896398T>A [0|1]

Variant score: 0.871

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.87061024; CADD: 0.871 (8.881)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896406C>T [0|1]

Variant score: 0.838

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.83752; CADD: 0.838 (7.892)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896394G>T [1|1] rs201037617 (variation viewer)

Variant score: 0.822

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.82229483; CADD: 0.822 (7.503)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896306T>G [1|1] rs78706153 (variation viewer)

Variant score: 0.797

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.79699814; CADD: 0.797 (6.925)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.18896535G>A [0|1]

Variant score: 0.759

Transcripts:: DGCR6:ENST00000413981.5::

Pathogenicity Data:: Best Score: 0.7590094; CADD: 0.759 (6.180)

Frequency Data:: No frequency data

USP22

Exomiser Score: 0.518

Phenotype Score: 0.504

Variant Score: 0.884

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.319

Phenotype Score: 0.504

Variant Score: 0.793

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.21009091CAAAAA>C [0|1] rs56665164 (variation viewer)

Variant score: 0.793 CONTRIBUTING VARIANT

Transcripts:: USP22:ENST00000261497.9:c.1104-1100_1104-1096del:p.(=); USP22:ENST00000537526.6:c.1068-1100_1068-1096del:p.(=)

Pathogenicity Data:: Best Score: 0.7934144; CADD: 0.793 (6.849)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.518

Phenotype Score: 0.504

Variant Score: 0.884

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.21043112G>A [1/1] rs866440130 (variation viewer)

Variant score: 0.884 CONTRIBUTING VARIANT

Transcripts:: USP22:ENST00000537526.6:c.135+514C>T:p.(=)

Pathogenicity Data:: Best Score: 0.97135824; CADD: 0.971 (15.430)

Frequency Data:: gnomAD_G_ASJ: 0.5102%; gnomAD_G_NFE: 0.0196%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.21007026A>T [0/1] rs779884520 (variation viewer)

Variant score: 0.403

Transcripts:: USP22:ENST00000261497.9:c.1231-39T>A:p.(=); USP22:ENST00000537526.6:c.1195-39T>A:p.(=)

Pathogenicity Data:: Best Score: 0.40488625; CADD: 0.405 (2.254)

Frequency Data:: ExAC NFE: 0.0066%; ExAC SAS: 0.0304%; gnomAD_E_NFE: 0.0017%; gnomAD_E_SAS: 0.0242%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.21032922CAAAAAAAAAAAAAA>C [0/1] rs753804890 (variation viewer)

Variant score: 0.149

Transcripts:: USP22:ENST00000261497.9:c.172-4262_172-4249del:p.(=); USP22:ENST00000537526.6:c.136-4262_136-4249del:p.(=)

Pathogenicity Data:: Best Score: 0.14866596; CADD: 0.149 (0.699)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr17:g.20999066G>A [0/1]

Variant score: 0.138

Transcripts:: USP22:ENST00000261497.9::; USP22:ENST00000582896.1::

Pathogenicity Data:: Best Score: 0.13821286; CADD: 0.138 (0.646)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.21036030CA>C [0/1] rs35324126 (variation viewer)

Variant score: 0.131

Transcripts:: USP22:ENST00000261497.9:c.171+6634del:p.(=); USP22:ENST00000537526.6:c.136-7357del:p.(=)

Pathogenicity Data:: Best Score: 0.13143963; CADD: 0.131 (0.612)

Frequency Data:: No frequency data

VDAC3

Exomiser Score: 0.505

Phenotype Score: 0.516

Variant Score: 0.865

Phenotype matches:

Proximity score 0.516 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.505

Phenotype Score: 0.516

Variant Score: 0.865

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr8:g.42391747C>A [0/1] rs7017321 (variation viewer)

Variant score: 0.865 CONTRIBUTING VARIANT

Transcripts:: VDAC3:ENST00000522572.5::; VDAC3:ENST00000220812.3::

Pathogenicity Data:: Best Score: 0.8675659; CADD: 0.868 (8.780)

Frequency Data:: gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.248

Phenotype Score: 0.516

Variant Score: 0.742

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr8:g.42391747C>A [0/1] rs7017321 (variation viewer)

Variant score: 0.865 CONTRIBUTING VARIANT

Transcripts:: VDAC3:ENST00000522572.5::; VDAC3:ENST00000220812.3::

Pathogenicity Data:: Best Score: 0.8675659; CADD: 0.868 (8.780)

Frequency Data:: gnomAD_G_NFE: 0.0200%

INTERGENIC_VARIANT chr8:g.42379601C>T [0/1] rs78258271 (variation viewer)

Variant score: 0.619 CONTRIBUTING VARIANT

Transcripts:: VDAC3:ENST00000522572.5::

Pathogenicity Data:: Best Score: 0.6356658; CADD: 0.636 (4.385)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0200%; UK10K: 0.1455%; gnomAD_G_FIN: 0.1750%; gnomAD_G_NFE: 0.0536%; gnomAD_G_OTH: 0.1033%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.42400673CT>C [0/1] rs1188886241 (variation viewer)

Variant score: 0.140

Transcripts:: VDAC3:ENST00000022615.9:c.323+971del:p.(=); VDAC3:ENST00000521158.5:c.326+971del:p.(=); VDAC3:ENST00000522572.5:c.326+971del:p.(=)

Pathogenicity Data:: Best Score: 0.1403929; CADD: 0.140 (0.657)

Frequency Data:: No frequency data

ABL2

Exomiser Score: 0.502

Phenotype Score: 0.514

Variant Score: 0.867

Phenotype matches:

Phenotypic similarity 0.514 to mouse mutant involving ABL2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.502

Phenotype Score: 0.514

Variant Score: 0.867

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179163851G>A [0/1] rs751987438 (variation viewer)

Variant score: 0.867 CONTRIBUTING VARIANT

Transcripts:: ABL2:ENST00000367623.8:c.158-32370C>T:p.(=); ABL2:ENST00000392043.4:c.158-32370C>T:p.(=); ABL2:ENST00000502732.6:c.158-30477C>T:p.(=); ABL2:ENST00000507173.5:c.158-32370C>T:p.(=); ABL2:ENST00000511413.5:c.158-30477C>T:p.(=)

Pathogenicity Data:: Best Score: 0.86983323; CADD: 0.870 (8.855)

Frequency Data:: TOPMed: 0.0032%; UK10K: 0.0264%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.386

Phenotype Score: 0.514

Variant Score: 0.815

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179163851G>A [0/1] rs751987438 (variation viewer)

Variant score: 0.867 CONTRIBUTING VARIANT

Transcripts:: ABL2:ENST00000367623.8:c.158-32370C>T:p.(=); ABL2:ENST00000392043.4:c.158-32370C>T:p.(=); ABL2:ENST00000502732.6:c.158-30477C>T:p.(=); ABL2:ENST00000507173.5:c.158-32370C>T:p.(=); ABL2:ENST00000511413.5:c.158-30477C>T:p.(=)

Pathogenicity Data:: Best Score: 0.86983323; CADD: 0.870 (8.855)

Frequency Data:: TOPMed: 0.0032%; UK10K: 0.0264%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179125774G>C [0/1] rs192219602 (variation viewer)

Variant score: 0.763 CONTRIBUTING VARIANT

Transcripts:: ABL2:ENST00000344730.7:c.642+603C>G:p.(=); ABL2:ENST00000367623.8:c.624+603C>G:p.(=); ABL2:ENST00000392043.4:c.624+603C>G:p.(=); ABL2:ENST00000502732.6:c.687+603C>G:p.(=); ABL2:ENST00000504405.5:c.579+603C>G:p.(=); ABL2:ENST00000507173.5:c.624+603C>G:p.(=); ABL2:ENST00000511413.5:c.687+603C>G:p.(=); ABL2:ENST00000512653.5:c.642+603C>G:p.(=)

Pathogenicity Data:: Best Score: 0.8080448; CADD: 0.808 (7.168)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.2015%; UK10K: 0.3438%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.3000%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179147808T>C [0/1] rs954615357 (variation viewer)

Variant score: 0.741

Transcripts:: ABL2:ENST00000367623.8:c.158-16327A>G:p.(=); ABL2:ENST00000392043.4:c.158-16327A>G:p.(=); ABL2:ENST00000502732.6:c.158-14434A>G:p.(=); ABL2:ENST00000507173.5:c.158-16327A>G:p.(=); ABL2:ENST00000511413.5:c.158-14434A>G:p.(=)

Pathogenicity Data:: Best Score: 0.74088055; CADD: 0.741 (5.865)

Frequency Data:: TOPMed: 0.0008%

MISSENSE_VARIANT chr1:g.179108478T>C [0/1] rs17277288 (variation viewer)

ClinVar: BENIGN (criteria_provided,_single_submitter)

Variant score: 0.497

Transcripts:: ABL2:ENST00000344730.7:c.2435A>G:p.(Lys812Arg); ABL2:ENST00000367623.8:c.2726A>G:p.(Lys909Arg); ABL2:ENST00000502732.6:c.2789A>G:p.(Lys930Arg); ABL2:ENST00000504405.5:c.2372A>G:p.(Lys791Arg); ABL2:ENST00000507173.5:c.2417A>G:p.(Lys806Arg); ABL2:ENST00000511413.5:c.2480A>G:p.(Lys827Arg); ABL2:ENST00000512653.5:c.2744A>G:p.(Lys915Arg)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.994 (D); Mutation Taster: 1.000 (P); SIFT: 0.000 (D); CADD: 0.996 (23.600)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 1.0190%; UK10K: 1.4282%; ESP AA: 0.3858%; ESP EA: 1.4070%; ESP All: 1.0610%; ExAC AFR: 0.3267%; ExAC AMR: 0.8639%; ExAC EAS: 0.0116%; ExAC FIN: 0.1814%; ExAC NFE: 1.2590%; ExAC OTH: 0.9912%; ExAC SAS: 0.5390%; gnomAD_E_AFR: 0.2614%; gnomAD_E_AMR: 0.8695%; gnomAD_E_ASJ: 0.8327%; gnomAD_E_EAS: 0.0058%; gnomAD_E_FIN: 0.1885%; gnomAD_E_NFE: 1.3060%; gnomAD_E_OTH: 1.4776%; gnomAD_E_SAS: 0.5750%; gnomAD_G_AFR: 0.2981%; gnomAD_G_AMR: 1.5513%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.2003%; gnomAD_G_NFE: 1.1797%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179212777T>C [0/1] rs1317642152 (variation viewer)

Variant score: 0.479

Transcripts:: ABL2:ENST00000367623.8:c.157+16464A>G:p.(=); ABL2:ENST00000392043.4:c.157+16464A>G:p.(=); ABL2:ENST00000502732.6:c.157+16464A>G:p.(=); ABL2:ENST00000507173.5:c.157+16464A>G:p.(=); ABL2:ENST00000511413.5:c.157+16464A>G:p.(=)

Pathogenicity Data:: Best Score: 0.47868526; CADD: 0.479 (2.829)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179174703T>C [0/1] rs186758752 (variation viewer)

Variant score: 0.240

Transcripts:: ABL2:ENST00000367623.8:c.158-43222A>G:p.(=); ABL2:ENST00000392043.4:c.158-43222A>G:p.(=); ABL2:ENST00000502732.6:c.158-41329A>G:p.(=); ABL2:ENST00000507173.5:c.158-43222A>G:p.(=); ABL2:ENST00000511413.5:c.158-41329A>G:p.(=)

Pathogenicity Data:: Best Score: 0.2603947; CADD: 0.260 (1.310)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.2381%; UK10K: 0.4628%; gnomAD_G_AFR: 0.0810%; gnomAD_G_AMR: 0.1250%; gnomAD_G_FIN: 0.0602%; gnomAD_G_NFE: 0.3175%; gnomAD_G_OTH: 0.2096%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179124464C>CTTTTT [1/1] rs562899587 (variation viewer)

Variant score: 0.218

Transcripts:: ABL2:ENST00000344730.7:c.642+1912_642+1913insAAAAA:p.(=); ABL2:ENST00000367623.8:c.624+1912_624+1913insAAAAA:p.(=); ABL2:ENST00000392043.4:c.624+1912_624+1913insAAAAA:p.(=); ABL2:ENST00000502732.6:c.687+1912_687+1913insAAAAA:p.(=); ABL2:ENST00000504405.5:c.579+1912_579+1913insAAAAA:p.(=); ABL2:ENST00000507173.5:c.624+1912_624+1913insAAAAA:p.(=); ABL2:ENST00000511413.5:c.687+1912_687+1913insAAAAA:p.(=); ABL2:ENST00000512653.5:c.642+1912_642+1913insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.21801215; CADD: 0.218 (1.068)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179181946AT>A [0/1] rs34828452 (variation viewer)

Variant score: 0.151

Transcripts:: ABL2:ENST00000367623.8:c.157+47294del:p.(=); ABL2:ENST00000392043.4:c.157+47294del:p.(=); ABL2:ENST00000502732.6:c.157+47294del:p.(=); ABL2:ENST00000507173.5:c.157+47294del:p.(=); ABL2:ENST00000511413.5:c.157+47294del:p.(=)

Pathogenicity Data:: Best Score: 0.15121049; CADD: 0.151 (0.712)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr1:g.179101996CTTTTTTT>C [1/1] rs869095809 (variation viewer)

Variant score: 0.128

Transcripts:: ABL2:ENST00000502732.6:c.*5715_*5721del:p.(=)

Pathogenicity Data:: Best Score: 0.1280331; CADD: 0.128 (0.595)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179176702C>CTTTTTTTTTTTTTT [0/1] rs35138436 (variation viewer)

Variant score: 0.121

Transcripts:: ABL2:ENST00000367623.8:c.158-45222_158-45221insAAAAAAAAAAAAAA:p.(=); ABL2:ENST00000392043.4:c.158-45222_158-45221insAAAAAAAAAAAAAA:p.(=); ABL2:ENST00000502732.6:c.158-43329_158-43328insAAAAAAAAAAAAAA:p.(=); ABL2:ENST00000507173.5:c.158-45222_158-45221insAAAAAAAAAAAAAA:p.(=); ABL2:ENST00000511413.5:c.158-43329_158-43328insAAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.12117988; CADD: 0.121 (0.561)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179174920A>T [0/1] rs6699363 (variation viewer)

Variant score: 0.119

Transcripts:: ABL2:ENST00000367623.8:c.158-43439T>A:p.(=); ABL2:ENST00000392043.4:c.158-43439T>A:p.(=); ABL2:ENST00000502732.6:c.158-41546T>A:p.(=); ABL2:ENST00000507173.5:c.158-43439T>A:p.(=); ABL2:ENST00000511413.5:c.158-41546T>A:p.(=)

Pathogenicity Data:: Best Score: 0.11874825; CADD: 0.119 (0.549)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179143720G>A [0/1] rs879418237 (variation viewer)

Variant score: 0.092

Transcripts:: ABL2:ENST00000367623.8:c.158-12239C>T:p.(=); ABL2:ENST00000392043.4:c.158-12239C>T:p.(=); ABL2:ENST00000502732.6:c.158-10346C>T:p.(=); ABL2:ENST00000507173.5:c.158-12239C>T:p.(=); ABL2:ENST00000511413.5:c.158-10346C>T:p.(=)

Pathogenicity Data:: Best Score: 0.09217948; CADD: 0.092 (0.420)

Frequency Data:: TOPMed: 0.0143%; gnomAD_G_FIN: 0.0288%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179191413CT>C [1/1] rs35362624 (variation viewer)

Variant score: 0.031

Transcripts:: ABL2:ENST00000367623.8:c.157+37827del:p.(=); ABL2:ENST00000392043.4:c.157+37827del:p.(=); ABL2:ENST00000502732.6:c.157+37827del:p.(=); ABL2:ENST00000507173.5:c.157+37827del:p.(=); ABL2:ENST00000511413.5:c.157+37827del:p.(=)

Pathogenicity Data:: Best Score: 0.030829906; CADD: 0.031 (0.136)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.179214519C>CATAT [-/1] rs59744061 (variation viewer)

Variant score: 0.010

Transcripts:: ABL2:ENST00000367623.8:c.157+14721_157+14722insATAT:p.(=); ABL2:ENST00000392043.4:c.157+14721_157+14722insATAT:p.(=); ABL2:ENST00000502732.6:c.157+14721_157+14722insATAT:p.(=); ABL2:ENST00000507173.5:c.157+14721_157+14722insATAT:p.(=); ABL2:ENST00000511413.5:c.157+14721_157+14722insATAT:p.(=)

Pathogenicity Data:: Best Score: 0.010080218; CADD: 0.010 (0.044)

Frequency Data:: No frequency data

PLPP1

Exomiser Score: 0.502

Phenotype Score: 0.505

Variant Score: 0.876

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.502

Phenotype Score: 0.505

Variant Score: 0.876

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.55498172C>A [0/1] rs139734878 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: PLPP1:ENST00000264775.9:c.59-7058G>T:p.(=); PLPP1:ENST00000307259.9:c.59-22722G>T:p.(=)

Pathogenicity Data:: Best Score: 0.942456; CADD: 0.942 (12.400)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1242%; UK10K: 0.1719%; gnomAD_G_NFE: 0.0667%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.55449680AAGGAAGTCAAATTACAACATG>A [0/1] rs764820773 (variation viewer)

Variant score: 0.834 CONTRIBUTING VARIANT

Transcripts:: PLPP1:ENST00000264775.9:c.495-7793_495-7773del:p.(=); PLPP1:ENST00000307259.9:c.492-7793_492-7773del:p.(=)

Pathogenicity Data:: Best Score: 0.84621996; CADD: 0.846 (8.131)

Frequency Data:: UK10K: 0.0926%; gnomAD_G_NFE: 0.0666%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.55499599TAA>T [0/1] rs530484090 (variation viewer)

Variant score: 0.387

Transcripts:: PLPP1:ENST00000264775.9:c.59-8487_59-8486del:p.(=); PLPP1:ENST00000307259.9:c.59-24151_59-24150del:p.(=)

Pathogenicity Data:: Best Score: 0.9075302; CADD: 0.908 (10.340)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4930%; UK10K: 0.6083%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.4796%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0864%; gnomAD_G_NFE: 0.5268%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.55526931C>CA [1/1] rs34267008 (variation viewer)

Variant score: 0.278

Transcripts:: PLPP1:ENST00000264775.9:c.58+7640_58+7641insT:p.(=); PLPP1:ENST00000307259.9:c.58+7640_58+7641insT:p.(=)

Pathogenicity Data:: Best Score: 0.27756298; CADD: 0.278 (1.412)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.55444743T>TGTGTGTGTGTGTGTG [1|1] rs368045819 (variation viewer)

Variant score: 0.113

Transcripts:: PLPP1:ENST00000264775.9:c.495-2836_495-2835insCACACACACACACAC:p.(=); PLPP1:ENST00000307259.9:c.492-2836_492-2835insCACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.11345661; CADD: 0.113 (0.523)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.55443190A>ATATATATATAT [0/1] rs796929898 (variation viewer)

Variant score: 0.016

Transcripts:: PLPP1:ENST00000264775.9:c.495-1283_495-1282insATATATATATA:p.(=); PLPP1:ENST00000307259.9:c.492-1283_492-1282insATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.018252075; CADD: 0.018 (0.080)

Frequency Data:: gnomAD_G_AFR: 0.2291%; gnomAD_G_NFE: 0.6530%

MYH14

Exomiser Score: 0.488

Phenotype Score: 0.506

Variant Score: 0.869

Phenotype matches:

Proximity score 0.506 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:600652 Deafness, autosomal dominant 4A - autosomal dominant; OMIM:614369 ?Peripheral neuropathy, myopathy, hoarseness, and hearing loss (unconfirmed); ORPHA:397744 Peripheral neuropathy-myopathy-hoarseness-hearing loss syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.488

Phenotype Score: 0.506

Variant Score: 0.869

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50240508A>G [0/1] rs962006517 (variation viewer)

Variant score: 0.869 CONTRIBUTING VARIANT

Transcripts:: MYH14:ENST00000376970.6:c.1091-3734A>G:p.(=); MYH14:ENST00000425460.5:c.1115-3734A>G:p.(=); MYH14:ENST00000596571.5:c.1091-3734A>G:p.(=); MYH14:ENST00000598205.5:c.1115-3734A>G:p.(=); MYH14:ENST00000642316.2:c.1115-3734A>G:p.(=); MYH14:ENST00000440075.6:c.-1200-3734A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8714417; CADD: 0.871 (8.909)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.037

Phenotype Score: 0.253

Variant Score: 0.806

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50240508A>G [0/1] rs962006517 (variation viewer)

Variant score: 0.869 CONTRIBUTING VARIANT

Transcripts:: MYH14:ENST00000376970.6:c.1091-3734A>G:p.(=); MYH14:ENST00000425460.5:c.1115-3734A>G:p.(=); MYH14:ENST00000596571.5:c.1091-3734A>G:p.(=); MYH14:ENST00000598205.5:c.1115-3734A>G:p.(=); MYH14:ENST00000642316.2:c.1115-3734A>G:p.(=); MYH14:ENST00000440075.6:c.-1200-3734A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8714417; CADD: 0.871 (8.909)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50251276G>A [0/1] rs555330945 (variation viewer)

Variant score: 0.743 CONTRIBUTING VARIANT

Transcripts:: MYH14:ENST00000376970.6:c.1806+588G>A:p.(=); MYH14:ENST00000425460.5:c.1830+588G>A:p.(=); MYH14:ENST00000596571.5:c.1806+588G>A:p.(=); MYH14:ENST00000598205.5:c.1830+588G>A:p.(=); MYH14:ENST00000642316.2:c.1830+588G>A:p.(=); MYH14:ENST00000440075.6:c.-728+1522G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7835787; CADD: 0.784 (6.647)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.3225%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.2401%

Other passed variants:

UPSTREAM_GENE_VARIANT chr19:g.50184717A>T [1/1] rs55738249 (variation viewer)

Variant score: 0.606

Transcripts:: MYH14:ENST00000598205.5::; MYH14:ENST00000293405.7::

Pathogenicity Data:: Best Score: 0.6056335; CADD: 0.606 (4.041)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50297491C>CTTTTT [1/1] rs869049808 (variation viewer)

Variant score: 0.515

Transcripts:: MYH14:ENST00000376970.6:c.5346+3804_5346+3805insTTTTT:p.(=); MYH14:ENST00000425460.5:c.5370+3804_5370+3805insTTTTT:p.(=); MYH14:ENST00000440075.6:c.1275+3804_1275+3805insTTTTT:p.(=); MYH14:ENST00000596571.5:c.5346+3804_5346+3805insTTTTT:p.(=); MYH14:ENST00000598205.5:c.5370+3804_5370+3805insTTTTT:p.(=); MYH14:ENST00000642316.2:c.5469+3804_5469+3805insTTTTT:p.(=); MYH14:ENST00000262269.12:c.*830+3804_*830+3805insTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.5152699; CADD: 0.515 (3.145)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr19:g.50184572C>CATATATATATATATATATATATAT [0/1] rs149782571 (variation viewer)

Variant score: 0.514

Transcripts:: MYH14:ENST00000598205.5::; MYH14:ENST00000293405.7::

Pathogenicity Data:: Best Score: 0.5657898; CADD: 0.566 (3.623)

Frequency Data:: gnomAD_G_AFR: 0.5152%; gnomAD_G_NFE: 0.2592%; gnomAD_G_OTH: 0.3676%

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.50210096CA>C [1/1] rs71180680 (variation viewer)

Variant score: 0.333

Transcripts:: MYH14:ENST00000376970.6:c.-3-266del:p.(=); MYH14:ENST00000425460.5:c.-3-266del:p.(=); MYH14:ENST00000440075.6:c.-2171-266del:p.(=); MYH14:ENST00000598205.5:c.-3-266del:p.(=); MYH14:ENST00000642316.2:c.-3-266del:p.(=)

Pathogenicity Data:: Best Score: 0.33273244; CADD: 0.333 (1.757)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50213477G>C [0/1] rs141438849 (variation viewer)

Variant score: 0.186

Transcripts:: MYH14:ENST00000376970.6:c.405+2707G>C:p.(=); MYH14:ENST00000425460.5:c.405+2707G>C:p.(=); MYH14:ENST00000596571.5:c.405+2707G>C:p.(=); MYH14:ENST00000598205.5:c.405+2707G>C:p.(=); MYH14:ENST00000642316.2:c.405+2707G>C:p.(=); MYH14:ENST00000440075.6:c.-1886+2707G>C:p.(=)

Pathogenicity Data:: Best Score: 0.27656418; CADD: 0.277 (1.406)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.5113%; UK10K: 0.8992%; gnomAD_G_AFR: 0.1031%; gnomAD_G_FIN: 1.2314%; gnomAD_G_NFE: 0.8608%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50258735A>AC [0/1] rs867761309 (variation viewer)

Variant score: 0.080

Transcripts:: MYH14:ENST00000376970.6:c.2110-409_2110-408insC:p.(=); MYH14:ENST00000425460.5:c.2134-409_2134-408insC:p.(=); MYH14:ENST00000596571.5:c.2110-409_2110-408insC:p.(=); MYH14:ENST00000598205.5:c.2134-409_2134-408insC:p.(=); MYH14:ENST00000642316.2:c.2233-409_2233-408insC:p.(=); MYH14:ENST00000440075.6:c.-728+8981_-728+8982insC:p.(=)

Pathogenicity Data:: Best Score: 0.12521768; CADD: 0.125 (0.581)

Frequency Data:: gnomAD_G_AFR: 0.7947%; gnomAD_G_AMR: 1.2295%; gnomAD_G_ASJ: 1.1364%; gnomAD_G_EAS: 0.1304%; gnomAD_G_FIN: 0.6963%; gnomAD_G_NFE: 1.3070%; gnomAD_G_OTH: 0.7692%

UPSTREAM_GENE_VARIANT chr19:g.50187618G>A [0/1] rs189437908 (variation viewer)

Variant score: 0.073

Transcripts:: MYH14:ENST00000598205.5::; MYH14:ENST00000293405.7::

Pathogenicity Data:: Best Score: 0.10277784; CADD: 0.103 (0.471)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1398%; UK10K: 0.6215%; gnomAD_G_AFR: 0.1034%; gnomAD_G_FIN: 1.1481%; gnomAD_G_NFE: 0.5616%; gnomAD_G_OTH: 0.2041%

UPSTREAM_GENE_VARIANT chr19:g.50184647A>AAGTATATACATACATGAATATATATATACAAGTATATATATATTCATGTATGTATATACTTGTATATATATACG [1/1]

Variant score: 0.000

Transcripts:: MYH14:ENST00000598205.5::; MYH14:ENST00000293405.7::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.50251521TACACACACACACACAC>* [-/1]

Variant score: 0.000

Transcripts:: MYH14:ENST00000376970.6:c.1806+833_1806+849delTACACACACACACACACins*:p.(=); MYH14:ENST00000425460.5:c.1830+833_1830+849delTACACACACACACACACins*:p.(=); MYH14:ENST00000596571.5:c.1806+833_1806+849delTACACACACACACACACins*:p.(=); MYH14:ENST00000598205.5:c.1830+833_1830+849delTACACACACACACACACins*:p.(=); MYH14:ENST00000642316.2:c.1830+833_1830+849delTACACACACACACACACins*:p.(=); MYH14:ENST00000440075.6:c.-728+1767_-728+1783delTACACACACACACACACins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NDUFA10

Exomiser Score: 0.480

Phenotype Score: 0.504

Variant Score: 0.867

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFA10.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618243 Mitochondrial complex I deficiency, nuclear type 22 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.121

Phenotype Score: 0.252

Variant Score: 0.945

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.239973501T>C [0/1] rs1296243018 (variation viewer)

Variant score: 0.945 CONTRIBUTING VARIANT

Transcripts:: NDUFA10:ENST00000252711.7:c.1000-12315A>G:p.(=); NDUFA10:ENST00000404554.5:c.1104+8614A>G:p.(=); NDUFA10:ENST00000620965.4:c.1000-12315A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9466665; CADD: 0.947 (12.730)

Frequency Data:: gnomAD_G_AFR: 0.0115%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.480

Phenotype Score: 0.504

Variant Score: 0.867

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.239973501T>C [0/1] rs1296243018 (variation viewer)

Variant score: 0.945 CONTRIBUTING VARIANT

Transcripts:: NDUFA10:ENST00000252711.7:c.1000-12315A>G:p.(=); NDUFA10:ENST00000404554.5:c.1104+8614A>G:p.(=); NDUFA10:ENST00000620965.4:c.1000-12315A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9466665; CADD: 0.947 (12.730)

Frequency Data:: gnomAD_G_AFR: 0.0115%

REGULATORY_REGION_VARIANT chr2:g.239434158A>G [0/1] rs972332112 (variation viewer)

Variant score: 0.789 CONTRIBUTING VARIANT

Transcripts:: NDUFA10:ENST00000252711.7::

Pathogenicity Data:: Best Score: 0.7902026; CADD: 0.790 (6.782)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.239982424T>C [0/1] rs145201127 (variation viewer)

Variant score: 0.692

Transcripts:: NDUFA10:ENST00000252711.7:c.999+7650A>G:p.(=); NDUFA10:ENST00000404554.5:c.1000-205A>G:p.(=); NDUFA10:ENST00000620965.4:c.999+7650A>G:p.(=)

Pathogenicity Data:: Best Score: 0.772333; CADD: 0.772 (6.427)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.3958%; UK10K: 0.5686%; gnomAD_G_AFR: 0.1374%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.4007%; gnomAD_G_NFE: 0.4329%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.240003655C>G [0/1] rs140471200 (variation viewer)

Variant score: 0.516

Transcripts:: NDUFA10:ENST00000252711.7:c.890+1555G>C:p.(=); NDUFA10:ENST00000307300.8:c.980+1555G>C:p.(=); NDUFA10:ENST00000404554.5:c.890+1555G>C:p.(=); NDUFA10:ENST00000620965.4:c.890+1555G>C:p.(=)

Pathogenicity Data:: Best Score: 0.635414; CADD: 0.635 (4.382)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.5487%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1603%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.7155%; gnomAD_G_NFE: 0.7066%; gnomAD_G_OTH: 0.5092%

REGULATORY_REGION_VARIANT chr2:g.239911670A>AGTGTGTGTGT [0|1] rs146389087 (variation viewer)

Variant score: 0.267

Transcripts:: NDUFA10:ENST00000252711.7::

Pathogenicity Data:: Best Score: 0.2671755; CADD: 0.267 (1.350)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr2:g.239956729G>A [0/1] rs142763607 (variation viewer)

Variant score: 0.134

Transcripts:: NDUFA10:ENST00000252711.7::; NDUFA10:ENST00000543185.5::

Pathogenicity Data:: Best Score: 0.16516626; CADD: 0.165 (0.784)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.5057%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1605%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.7155%; gnomAD_G_NFE: 0.7131%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.239985738T>G [0/1] rs188882578 (variation viewer)

Variant score: 0.045

Transcripts:: NDUFA10:ENST00000252711.7:c.999+4336A>C:p.(=); NDUFA10:ENST00000307300.8:c.1090-2021A>C:p.(=); NDUFA10:ENST00000404554.5:c.1000-3519A>C:p.(=); NDUFA10:ENST00000620965.4:c.999+4336A>C:p.(=)

Pathogenicity Data:: Best Score: 0.0557217; CADD: 0.056 (0.249)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.5503%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1614%; gnomAD_G_AMR: 0.1199%; gnomAD_G_FIN: 0.6985%; gnomAD_G_NFE: 0.7089%; gnomAD_G_OTH: 0.5187%

CTNNA2

Exomiser Score: 0.479

Phenotype Score: 0.508

Variant Score: 0.863

Phenotype matches:

Proximity score 0.508 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618174 Cortical dysplasia, complex, with other brain malformations 9 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.081

Phenotype Score: 0.254

Variant Score: 0.896

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80420713T>A [0/1]

Variant score: 0.896 CONTRIBUTING VARIANT

Transcripts:: CTNNA2:ENST00000343114.7:c.327+1112T>A:p.(=); CTNNA2:ENST00000361291.8:c.138+1112T>A:p.(=); CTNNA2:ENST00000402739.8:c.1290+1112T>A:p.(=); CTNNA2:ENST00000466387.5:c.1290+1112T>A:p.(=); CTNNA2:ENST00000496558.5:c.1290+1112T>A:p.(=); CTNNA2:ENST00000540488.5:c.138+1112T>A:p.(=); CTNNA2:ENST00000541047.5:c.186+1112T>A:p.(=); CTNNA2:ENST00000629316.2:c.1290+1112T>A:p.(=)

Pathogenicity Data:: Best Score: 0.89555204; CADD: 0.896 (9.811)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.479

Phenotype Score: 0.508

Variant Score: 0.863

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80420713T>A [0/1]

Variant score: 0.896 CONTRIBUTING VARIANT

Transcripts:: CTNNA2:ENST00000343114.7:c.327+1112T>A:p.(=); CTNNA2:ENST00000361291.8:c.138+1112T>A:p.(=); CTNNA2:ENST00000402739.8:c.1290+1112T>A:p.(=); CTNNA2:ENST00000466387.5:c.1290+1112T>A:p.(=); CTNNA2:ENST00000496558.5:c.1290+1112T>A:p.(=); CTNNA2:ENST00000540488.5:c.138+1112T>A:p.(=); CTNNA2:ENST00000541047.5:c.186+1112T>A:p.(=); CTNNA2:ENST00000629316.2:c.1290+1112T>A:p.(=)

Pathogenicity Data:: Best Score: 0.89555204; CADD: 0.896 (9.811)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80454469G>A [0/1] rs113848529 (variation viewer)

Variant score: 0.830 CONTRIBUTING VARIANT

Transcripts:: CTNNA2:ENST00000343114.7:c.327+34868G>A:p.(=); CTNNA2:ENST00000361291.8:c.138+34868G>A:p.(=); CTNNA2:ENST00000402739.8:c.1290+34868G>A:p.(=); CTNNA2:ENST00000466387.5:c.1290+34868G>A:p.(=); CTNNA2:ENST00000496558.5:c.1290+34868G>A:p.(=); CTNNA2:ENST00000540488.5:c.138+34868G>A:p.(=); CTNNA2:ENST00000541047.5:c.186+34868G>A:p.(=); CTNNA2:ENST00000629316.2:c.1290+34868G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8350699; CADD: 0.835 (7.827)

Frequency Data:: TOPMed: 0.0199%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0266%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79931724T>C [0/1]

Variant score: 0.789

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+21927T>C:p.(=); CTNNA2:ENST00000466387.5:c.1056+21927T>C:p.(=); CTNNA2:ENST00000496558.5:c.1056+21927T>C:p.(=); CTNNA2:ENST00000629316.2:c.1056+21927T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7885051; CADD: 0.789 (6.747)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79523184T>C [0/1] rs780686450 (variation viewer)

Variant score: 0.779

Transcripts:: CTNNA2:ENST00000466387.5:c.-6+18002T>C:p.(=); CTNNA2:ENST00000496558.5:c.-6+9977T>C:p.(=); CTNNA2:ENST00000629316.2:c.-6+9977T>C:p.(=)

Pathogenicity Data:: Best Score: 0.80366397; CADD: 0.804 (7.070)

Frequency Data:: TOPMed: 0.0231%; ExAC NFE: 0.2023%; ExAC SAS: 0.0140%; gnomAD_E_AMR: 0.0232%; gnomAD_E_ASJ: 0.1094%; gnomAD_E_NFE: 0.0486%; gnomAD_E_OTH: 0.0407%; gnomAD_E_SAS: 0.0065%; gnomAD_G_AFR: 0.0114%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0466%

INTERGENIC_VARIANT chr2:g.79170005T>G [0/1] rs913910608 (variation viewer)

Variant score: 0.775

Transcripts:: CTNNA2:ENST00000466387.5::; CTNNA2:ENST00000393878.5::

Pathogenicity Data:: Best Score: 0.77576673; CADD: 0.776 (6.493)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80477316C>T [0/1]

Variant score: 0.711

Transcripts:: CTNNA2:ENST00000343114.7:c.327+57715C>T:p.(=); CTNNA2:ENST00000361291.8:c.138+57715C>T:p.(=); CTNNA2:ENST00000402739.8:c.1290+57715C>T:p.(=); CTNNA2:ENST00000466387.5:c.1290+57715C>T:p.(=); CTNNA2:ENST00000496558.5:c.1290+57715C>T:p.(=); CTNNA2:ENST00000540488.5:c.138+57715C>T:p.(=); CTNNA2:ENST00000541047.5:c.186+57715C>T:p.(=); CTNNA2:ENST00000629316.2:c.1290+57715C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7110651; CADD: 0.711 (5.392)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80116902A>AGTGTGTGT [-/1] rs112383959 (variation viewer)

Variant score: 0.678

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+207105_1056+207106insGTGTGTGT:p.(=); CTNNA2:ENST00000466387.5:c.1056+207105_1056+207106insGTGTGTGT:p.(=); CTNNA2:ENST00000496558.5:c.1056+207105_1056+207106insGTGTGTGT:p.(=); CTNNA2:ENST00000629316.2:c.1056+207105_1056+207106insGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.67774475; CADD: 0.678 (4.918)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80116902A>AGTGTGTGTGTGT [-/1] rs112383959 (variation viewer)

Variant score: 0.663

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+207105_1056+207106insGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000466387.5:c.1056+207105_1056+207106insGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000496558.5:c.1056+207105_1056+207106insGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000629316.2:c.1056+207105_1056+207106insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.6629456; CADD: 0.663 (4.723)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79218311T>TTGTGTG [0/1] rs60680995 (variation viewer)

Variant score: 0.609

Transcripts:: CTNNA2:ENST00000466387.5:c.-406+20235_-406+20236insTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.60870886; CADD: 0.609 (4.075)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80189821C>T [0/1]

Variant score: 0.593

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-203390C>T:p.(=); CTNNA2:ENST00000466387.5:c.1057-203390C>T:p.(=); CTNNA2:ENST00000496558.5:c.1057-203390C>T:p.(=); CTNNA2:ENST00000629316.2:c.1057-203390C>T:p.(=)

Pathogenicity Data:: Best Score: 0.59299475; CADD: 0.593 (3.904)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80465024A>G [0/1]

Variant score: 0.582

Transcripts:: CTNNA2:ENST00000343114.7:c.327+45423A>G:p.(=); CTNNA2:ENST00000361291.8:c.138+45423A>G:p.(=); CTNNA2:ENST00000402739.8:c.1290+45423A>G:p.(=); CTNNA2:ENST00000466387.5:c.1290+45423A>G:p.(=); CTNNA2:ENST00000496558.5:c.1290+45423A>G:p.(=); CTNNA2:ENST00000540488.5:c.138+45423A>G:p.(=); CTNNA2:ENST00000541047.5:c.186+45423A>G:p.(=); CTNNA2:ENST00000629316.2:c.1290+45423A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5819772; CADD: 0.582 (3.788)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79228239A>T [0/1] rs116675771 (variation viewer)

Variant score: 0.578

Transcripts:: CTNNA2:ENST00000466387.5:c.-406+30163A>T:p.(=)

Pathogenicity Data:: Best Score: 0.75082755; CADD: 0.751 (6.035)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.5423%; UK10K: 0.9918%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.9445%; gnomAD_G_NFE: 0.8861%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79860546G>GTTTTTTT [1/1] rs56929879 (variation viewer)

Variant score: 0.549

Transcripts:: CTNNA2:ENST00000402739.8:c.465+2367_465+2368insTTTTTTT:p.(=); CTNNA2:ENST00000466387.5:c.465+2367_465+2368insTTTTTTT:p.(=); CTNNA2:ENST00000496558.5:c.465+2367_465+2368insTTTTTTT:p.(=); CTNNA2:ENST00000629316.2:c.465+2367_465+2368insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.54887176; CADD: 0.549 (3.457)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79926763G>A [0/1] rs552702206 (variation viewer)

Variant score: 0.499

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+16966G>A:p.(=); CTNNA2:ENST00000466387.5:c.1056+16966G>A:p.(=); CTNNA2:ENST00000496558.5:c.1056+16966G>A:p.(=); CTNNA2:ENST00000629316.2:c.1056+16966G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5093181; CADD: 0.509 (3.092)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0987%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.1404%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80087603G>A [0/1] rs567928149 (variation viewer)

Variant score: 0.498

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+177806G>A:p.(=); CTNNA2:ENST00000466387.5:c.1056+177806G>A:p.(=); CTNNA2:ENST00000496558.5:c.1056+177806G>A:p.(=); CTNNA2:ENST00000629316.2:c.1056+177806G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5706613; CADD: 0.571 (3.672)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1720%; UK10K: 0.2248%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.1667%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80075567T>A [0/1] rs866546825 (variation viewer)

Variant score: 0.482

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+165770T>A:p.(=); CTNNA2:ENST00000466387.5:c.1056+165770T>A:p.(=); CTNNA2:ENST00000496558.5:c.1056+165770T>A:p.(=); CTNNA2:ENST00000629316.2:c.1056+165770T>A:p.(=)

Pathogenicity Data:: Best Score: 0.49265897; CADD: 0.493 (2.947)

Frequency Data:: gnomAD_G_NFE: 0.0149%; gnomAD_G_OTH: 0.1538%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80033972T>TA [0/1] rs70940069 (variation viewer)

Variant score: 0.468

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+124175_1056+124176insA:p.(=); CTNNA2:ENST00000466387.5:c.1056+124175_1056+124176insA:p.(=); CTNNA2:ENST00000496558.5:c.1056+124175_1056+124176insA:p.(=); CTNNA2:ENST00000629316.2:c.1056+124175_1056+124176insA:p.(=)

Pathogenicity Data:: Best Score: 0.46813673; CADD: 0.468 (2.742)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80117455A>AGTGTGTGTGT [-/1] rs59521287 (variation viewer)

Variant score: 0.438

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+207658_1056+207659insGTGTGTGTGT:p.(=); CTNNA2:ENST00000466387.5:c.1056+207658_1056+207659insGTGTGTGTGT:p.(=); CTNNA2:ENST00000496558.5:c.1056+207658_1056+207659insGTGTGTGTGT:p.(=); CTNNA2:ENST00000629316.2:c.1056+207658_1056+207659insGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.4381764; CADD: 0.438 (2.504)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80489710GTTC>G [0/1] rs935396730 (variation viewer)

Variant score: 0.436

Transcripts:: CTNNA2:ENST00000343114.7:c.328-55271_328-55269del:p.(=); CTNNA2:ENST00000361291.8:c.139-55271_139-55269del:p.(=); CTNNA2:ENST00000402739.8:c.1291-55271_1291-55269del:p.(=); CTNNA2:ENST00000466387.5:c.1291-55271_1291-55269del:p.(=); CTNNA2:ENST00000496558.5:c.1291-55271_1291-55269del:p.(=); CTNNA2:ENST00000540488.5:c.139-55271_139-55269del:p.(=); CTNNA2:ENST00000541047.5:c.187-55271_187-55269del:p.(=); CTNNA2:ENST00000629316.2:c.1291-55271_1291-55269del:p.(=)

Pathogenicity Data:: Best Score: 0.43662184; CADD: 0.437 (2.492)

Frequency Data:: TOPMed: 0.0096%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80164950T>G [0|1] rs74846394 (variation viewer)

Variant score: 0.418

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-228261T>G:p.(=); CTNNA2:ENST00000466387.5:c.1057-228261T>G:p.(=); CTNNA2:ENST00000496558.5:c.1057-228261T>G:p.(=); CTNNA2:ENST00000629316.2:c.1057-228261T>G:p.(=)

Pathogenicity Data:: Best Score: 0.4181648; CADD: 0.418 (2.352)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80149774T>TCACACACA [-/1] rs10595115 (variation viewer)

Variant score: 0.409

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+239977_1056+239978insCACACACA:p.(=); CTNNA2:ENST00000466387.5:c.1056+239977_1056+239978insCACACACA:p.(=); CTNNA2:ENST00000496558.5:c.1056+239977_1056+239978insCACACACA:p.(=); CTNNA2:ENST00000629316.2:c.1056+239977_1056+239978insCACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.4093911; CADD: 0.409 (2.287)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79930268A>G [0/1] rs61232798 (variation viewer)

Variant score: 0.401

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+20471A>G:p.(=); CTNNA2:ENST00000466387.5:c.1056+20471A>G:p.(=); CTNNA2:ENST00000496558.5:c.1056+20471A>G:p.(=); CTNNA2:ENST00000629316.2:c.1056+20471A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4801237; CADD: 0.480 (2.841)

Frequency Data:: gnomAD_G_AFR: 0.2723%; gnomAD_G_AMR: 0.5831%; gnomAD_G_ASJ: 0.7937%; gnomAD_G_EAS: 0.0804%; gnomAD_G_FIN: 0.1733%; gnomAD_G_NFE: 0.3177%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80227605T>A [0/1] rs139792066 (variation viewer)

Variant score: 0.393

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-165606T>A:p.(=); CTNNA2:ENST00000466387.5:c.1057-165606T>A:p.(=); CTNNA2:ENST00000496558.5:c.1057-165606T>A:p.(=); CTNNA2:ENST00000629316.2:c.1057-165606T>A:p.(=)

Pathogenicity Data:: Best Score: 0.42628002; CADD: 0.426 (2.413)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.1848%; UK10K: 0.0264%; gnomAD_G_AFR: 0.4579%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.0667%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80634773GTT>G [0/1] rs1420721334 (variation viewer)

Variant score: 0.380

Transcripts:: CTNNA2:ENST00000343114.7:c.1468-12811_1468-12810del:p.(=); CTNNA2:ENST00000361291.8:c.1423-12811_1423-12810del:p.(=); CTNNA2:ENST00000402739.8:c.2575-12811_2575-12810del:p.(=); CTNNA2:ENST00000466387.5:c.2431-12811_2431-12810del:p.(=); CTNNA2:ENST00000496558.5:c.2431-12811_2431-12810del:p.(=); CTNNA2:ENST00000540488.5:c.1144-12811_1144-12810del:p.(=); CTNNA2:ENST00000541047.5:c.1327-12811_1327-12810del:p.(=); CTNNA2:ENST00000629316.2:c.2296-12811_2296-12810del:p.(=)

Pathogenicity Data:: Best Score: 0.38027358; CADD: 0.380 (2.078)

Frequency Data:: TOPMed: 0.0040%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80244532TAGACTC>T [0/1] rs572213030 (variation viewer)

Variant score: 0.376

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-148678_1057-148673del:p.(=); CTNNA2:ENST00000466387.5:c.1057-148678_1057-148673del:p.(=); CTNNA2:ENST00000496558.5:c.1057-148678_1057-148673del:p.(=); CTNNA2:ENST00000629316.2:c.1057-148678_1057-148673del:p.(=)

Pathogenicity Data:: Best Score: 0.39744043; CADD: 0.397 (2.200)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0462%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0916%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0466%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80463304C>T [0/1] rs183744433 (variation viewer)

Variant score: 0.353

Transcripts:: CTNNA2:ENST00000343114.7:c.327+43703C>T:p.(=); CTNNA2:ENST00000361291.8:c.138+43703C>T:p.(=); CTNNA2:ENST00000402739.8:c.1290+43703C>T:p.(=); CTNNA2:ENST00000466387.5:c.1290+43703C>T:p.(=); CTNNA2:ENST00000496558.5:c.1290+43703C>T:p.(=); CTNNA2:ENST00000540488.5:c.138+43703C>T:p.(=); CTNNA2:ENST00000541047.5:c.186+43703C>T:p.(=); CTNNA2:ENST00000629316.2:c.1290+43703C>T:p.(=)

Pathogenicity Data:: Best Score: 0.37841576; CADD: 0.378 (2.065)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.0446%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0400%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79509000TATATATATATATAA>T [0|1] rs1445909173 (variation viewer)

Variant score: 0.341

Transcripts:: CTNNA2:ENST00000466387.5:c.-6+3819_-6+3832del:p.(=)

Pathogenicity Data:: Best Score: 0.39368266; CADD: 0.394 (2.173)

Frequency Data:: gnomAD_G_AFR: 0.0494%; gnomAD_G_AMR: 0.6849%; gnomAD_G_EAS: 0.1312%; gnomAD_G_NFE: 0.3903%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80267263A>C [0/1]

Variant score: 0.341

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-125948A>C:p.(=); CTNNA2:ENST00000466387.5:c.1057-125948A>C:p.(=); CTNNA2:ENST00000496558.5:c.1057-125948A>C:p.(=); CTNNA2:ENST00000629316.2:c.1057-125948A>C:p.(=)

Pathogenicity Data:: Best Score: 0.3408261; CADD: 0.341 (1.810)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79475679C>CATTTT [-/1] rs10626335 (variation viewer)

Variant score: 0.327

Transcripts:: CTNNA2:ENST00000466387.5:c.-134-29375_-134-29374insATTTT:p.(=)

Pathogenicity Data:: Best Score: 0.32733315; CADD: 0.327 (1.722)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80126638T>C [1|1] rs58587143 (variation viewer)

Variant score: 0.320

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+216841T>C:p.(=); CTNNA2:ENST00000466387.5:c.1056+216841T>C:p.(=); CTNNA2:ENST00000496558.5:c.1056+216841T>C:p.(=); CTNNA2:ENST00000629316.2:c.1056+216841T>C:p.(=)

Pathogenicity Data:: Best Score: 0.3204835; CADD: 0.320 (1.678)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79387446C>G [0/1] rs139398775 (variation viewer)

Variant score: 0.319

Transcripts:: CTNNA2:ENST00000466387.5:c.-135+13433C>G:p.(=)

Pathogenicity Data:: Best Score: 0.3382408; CADD: 0.338 (1.793)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1378%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1066%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80073771C>CACACACACACACTT [-/1] rs1553443664 (variation viewer)

Variant score: 0.282

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+163974_1056+163975insACACACACACACTT:p.(=); CTNNA2:ENST00000466387.5:c.1056+163974_1056+163975insACACACACACACTT:p.(=); CTNNA2:ENST00000496558.5:c.1056+163974_1056+163975insACACACACACACTT:p.(=); CTNNA2:ENST00000629316.2:c.1056+163974_1056+163975insACACACACACACTT:p.(=)

Pathogenicity Data:: Best Score: 0.28154427; CADD: 0.282 (1.436)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80591457GTT>G [1/1] rs567131551 (variation viewer)

Variant score: 0.281

Transcripts:: CTNNA2:ENST00000343114.7:c.1226+1973_1226+1974del:p.(=); CTNNA2:ENST00000361291.8:c.1037+1973_1037+1974del:p.(=); CTNNA2:ENST00000402739.8:c.2189+1973_2189+1974del:p.(=); CTNNA2:ENST00000466387.5:c.2189+1973_2189+1974del:p.(=); CTNNA2:ENST00000496558.5:c.2189+1973_2189+1974del:p.(=); CTNNA2:ENST00000540488.5:c.1037+1973_1037+1974del:p.(=); CTNNA2:ENST00000541047.5:c.1085+1973_1085+1974del:p.(=); CTNNA2:ENST00000629316.2:c.2189+1973_2189+1974del:p.(=)

Pathogenicity Data:: Best Score: 0.28121334; CADD: 0.281 (1.434)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79536574A>AGTATGTGTGTGTGTGTGTGTGT [-/1] rs34403615 (variation viewer)

Variant score: 0.275

Transcripts:: CTNNA2:ENST00000466387.5:c.-6+31392_-6+31393insGTATGTGTGTGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000496558.5:c.-6+23367_-6+23368insGTATGTGTGTGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000629316.2:c.-6+23367_-6+23368insGTATGTGTGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.27456254; CADD: 0.275 (1.394)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79839054A>G [0/1] rs568714515 (variation viewer)

Variant score: 0.258

Transcripts:: CTNNA2:ENST00000402739.8:c.299-18959A>G:p.(=); CTNNA2:ENST00000466387.5:c.299-18959A>G:p.(=); CTNNA2:ENST00000496558.5:c.299-18959A>G:p.(=); CTNNA2:ENST00000629316.2:c.299-18959A>G:p.(=)

Pathogenicity Data:: Best Score: 0.2651478; CADD: 0.265 (1.338)

Frequency Data:: TOPMed: 0.0987%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0458%; gnomAD_G_NFE: 0.1801%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80547690C>CTTTTTTT [0|1] rs61186189 (variation viewer)

Variant score: 0.242

Transcripts:: CTNNA2:ENST00000343114.7:c.577+1627_577+1628insTTTTTTT:p.(=); CTNNA2:ENST00000361291.8:c.388+1627_388+1628insTTTTTTT:p.(=); CTNNA2:ENST00000402739.8:c.1540+1627_1540+1628insTTTTTTT:p.(=); CTNNA2:ENST00000466387.5:c.1540+1627_1540+1628insTTTTTTT:p.(=); CTNNA2:ENST00000496558.5:c.1540+1627_1540+1628insTTTTTTT:p.(=); CTNNA2:ENST00000540488.5:c.388+1627_388+1628insTTTTTTT:p.(=); CTNNA2:ENST00000541047.5:c.436+1627_436+1628insTTTTTTT:p.(=); CTNNA2:ENST00000629316.2:c.1540+1627_1540+1628insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.2421208; CADD: 0.242 (1.204)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80441140G>T [0/1]

Variant score: 0.232

Transcripts:: CTNNA2:ENST00000343114.7:c.327+21539G>T:p.(=); CTNNA2:ENST00000361291.8:c.138+21539G>T:p.(=); CTNNA2:ENST00000402739.8:c.1290+21539G>T:p.(=); CTNNA2:ENST00000466387.5:c.1290+21539G>T:p.(=); CTNNA2:ENST00000496558.5:c.1290+21539G>T:p.(=); CTNNA2:ENST00000540488.5:c.138+21539G>T:p.(=); CTNNA2:ENST00000541047.5:c.186+21539G>T:p.(=); CTNNA2:ENST00000629316.2:c.1290+21539G>T:p.(=)

Pathogenicity Data:: Best Score: 0.23228502; CADD: 0.232 (1.148)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79982192CTATA>C [-/1] rs70940064 (variation viewer)

Variant score: 0.223

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+72396_1056+72399del:p.(=); CTNNA2:ENST00000466387.5:c.1056+72396_1056+72399del:p.(=); CTNNA2:ENST00000496558.5:c.1056+72396_1056+72399del:p.(=); CTNNA2:ENST00000629316.2:c.1056+72396_1056+72399del:p.(=)

Pathogenicity Data:: Best Score: 0.2230376; CADD: 0.223 (1.096)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79251523A>G [0/1] rs536665358 (variation viewer)

Variant score: 0.201

Transcripts:: CTNNA2:ENST00000466387.5:c.-406+53447A>G:p.(=)

Pathogenicity Data:: Best Score: 0.20255637; CADD: 0.203 (0.983)

Frequency Data:: TOPMed: 0.0295%; UK10K: 0.0661%; gnomAD_G_NFE: 0.0466%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79809544G>T [0|1] rs868778969 (variation viewer)

Variant score: 0.188

Transcripts:: CTNNA2:ENST00000402739.8:c.299-48469G>T:p.(=); CTNNA2:ENST00000466387.5:c.299-48469G>T:p.(=); CTNNA2:ENST00000496558.5:c.299-48469G>T:p.(=); CTNNA2:ENST00000629316.2:c.299-48469G>T:p.(=)

Pathogenicity Data:: Best Score: 0.19813734; CADD: 0.198 (0.959)

Frequency Data:: TOPMed: 0.0239%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0266%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80301756G>A [0/1] rs116077606 (variation viewer)

Variant score: 0.186

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-91455G>A:p.(=); CTNNA2:ENST00000466387.5:c.1057-91455G>A:p.(=); CTNNA2:ENST00000496558.5:c.1057-91455G>A:p.(=); CTNNA2:ENST00000629316.2:c.1057-91455G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6807727; CADD: 0.681 (4.959)

Frequency Data:: 1000Genomes: 0.7588%; TOPMed: 1.2180%; UK10K: 1.8514%; gnomAD_G_AFR: 0.3331%; gnomAD_G_AMR: 1.0817%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.3440%; gnomAD_G_NFE: 1.4269%; gnomAD_G_OTH: 1.2270%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79555509G>A [0/1] rs193174527 (variation viewer)

Variant score: 0.184

Transcripts:: CTNNA2:ENST00000466387.5:c.-6+50327G>A:p.(=); CTNNA2:ENST00000496558.5:c.-6+42302G>A:p.(=); CTNNA2:ENST00000629316.2:c.-6+42302G>A:p.(=)

Pathogenicity Data:: Best Score: 0.19053143; CADD: 0.191 (0.918)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1354%; UK10K: 0.2116%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1403%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79851737CTT>C [1/1] rs11399192 (variation viewer)

Variant score: 0.182

Transcripts:: CTNNA2:ENST00000402739.8:c.299-6275_299-6274del:p.(=); CTNNA2:ENST00000466387.5:c.299-6275_299-6274del:p.(=); CTNNA2:ENST00000496558.5:c.299-6275_299-6274del:p.(=); CTNNA2:ENST00000629316.2:c.299-6275_299-6274del:p.(=)

Pathogenicity Data:: Best Score: 0.1822887; CADD: 0.182 (0.874)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79521107GATATATATAT>G [-/1] rs59797728 (variation viewer)

Variant score: 0.177

Transcripts:: CTNNA2:ENST00000466387.5:c.-6+15926_-6+15935del:p.(=); CTNNA2:ENST00000496558.5:c.-6+7901_-6+7910del:p.(=); CTNNA2:ENST00000629316.2:c.-6+7901_-6+7910del:p.(=)

Pathogenicity Data:: Best Score: 0.17699969; CADD: 0.177 (0.846)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79801992C>CA [0/1] rs57124311 (variation viewer)

Variant score: 0.172

Transcripts:: CTNNA2:ENST00000402739.8:c.299-56021_299-56020insA:p.(=); CTNNA2:ENST00000466387.5:c.299-56021_299-56020insA:p.(=); CTNNA2:ENST00000496558.5:c.299-56021_299-56020insA:p.(=); CTNNA2:ENST00000629316.2:c.299-56021_299-56020insA:p.(=)

Pathogenicity Data:: Best Score: 0.17186719; CADD: 0.172 (0.819)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80191361T>G [0/1]

Variant score: 0.159

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-201850T>G:p.(=); CTNNA2:ENST00000466387.5:c.1057-201850T>G:p.(=); CTNNA2:ENST00000496558.5:c.1057-201850T>G:p.(=); CTNNA2:ENST00000629316.2:c.1057-201850T>G:p.(=)

Pathogenicity Data:: Best Score: 0.15937948; CADD: 0.159 (0.754)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80596279GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT>G [1/1] rs60132060 (variation viewer)

Variant score: 0.149

Transcripts:: CTNNA2:ENST00000343114.7:c.1226+6795_1226+6825del:p.(=); CTNNA2:ENST00000361291.8:c.1037+6795_1037+6825del:p.(=); CTNNA2:ENST00000402739.8:c.2189+6795_2189+6825del:p.(=); CTNNA2:ENST00000466387.5:c.2189+6795_2189+6825del:p.(=); CTNNA2:ENST00000496558.5:c.2189+6795_2189+6825del:p.(=); CTNNA2:ENST00000540488.5:c.1037+6795_1037+6825del:p.(=); CTNNA2:ENST00000541047.5:c.1085+6795_1085+6825del:p.(=); CTNNA2:ENST00000629316.2:c.2189+6795_2189+6825del:p.(=)

Pathogenicity Data:: Best Score: 0.14925385; CADD: 0.149 (0.702)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80375562C>CTT [1/1] rs199662476 (variation viewer)

Variant score: 0.149

Transcripts:: CTNNA2:ENST00000343114.7:c.94-17649_94-17648insTT:p.(=); CTNNA2:ENST00000402739.8:c.1057-17649_1057-17648insTT:p.(=); CTNNA2:ENST00000466387.5:c.1057-17649_1057-17648insTT:p.(=); CTNNA2:ENST00000496558.5:c.1057-17649_1057-17648insTT:p.(=); CTNNA2:ENST00000629316.2:c.1057-17649_1057-17648insTT:p.(=); CTNNA2:ENST00000361291.8:c.-96-17649_-96-17648insTT:p.(=); CTNNA2:ENST00000540488.5:c.-96-17649_-96-17648insTT:p.(=); CTNNA2:ENST00000541047.5:c.-48-17649_-48-17648insTT:p.(=)

Pathogenicity Data:: Best Score: 0.14866596; CADD: 0.149 (0.699)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80364556A>ATTTT [1/1] rs57073635 (variation viewer)

Variant score: 0.146

Transcripts:: CTNNA2:ENST00000343114.7:c.94-28655_94-28654insTTTT:p.(=); CTNNA2:ENST00000402739.8:c.1057-28655_1057-28654insTTTT:p.(=); CTNNA2:ENST00000466387.5:c.1057-28655_1057-28654insTTTT:p.(=); CTNNA2:ENST00000496558.5:c.1057-28655_1057-28654insTTTT:p.(=); CTNNA2:ENST00000629316.2:c.1057-28655_1057-28654insTTTT:p.(=); CTNNA2:ENST00000361291.8:c.-96-28655_-96-28654insTTTT:p.(=); CTNNA2:ENST00000540488.5:c.-96-28655_-96-28654insTTTT:p.(=); CTNNA2:ENST00000541047.5:c.-48-28655_-48-28654insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14611381; CADD: 0.146 (0.686)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79956843G>GT [-/1] rs66471325 (variation viewer)

Variant score: 0.132

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+47046_1056+47047insT:p.(=); CTNNA2:ENST00000466387.5:c.1056+47046_1056+47047insT:p.(=); CTNNA2:ENST00000496558.5:c.1056+47046_1056+47047insT:p.(=); CTNNA2:ENST00000629316.2:c.1056+47046_1056+47047insT:p.(=)

Pathogenicity Data:: Best Score: 0.1316396; CADD: 0.132 (0.613)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79433624GAA>G [1/1] rs200656588 (variation viewer)

Variant score: 0.124

Transcripts:: CTNNA2:ENST00000466387.5:c.-135+59612_-135+59613del:p.(=)

Pathogenicity Data:: Best Score: 0.12441158; CADD: 0.124 (0.577)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79210088T>TTTTGTGTGTGTGTGTGTGTGTGTG [0/1] rs112984318 (variation viewer)

Variant score: 0.123

Transcripts:: CTNNA2:ENST00000466387.5:c.-406+12012_-406+12013insTTTGTGTGTGTGTGTGTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.12320107; CADD: 0.123 (0.571)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79338575A>ATCTTCTTCTTCT [-/1] rs1239699778 (variation viewer)

Variant score: 0.119

Transcripts:: CTNNA2:ENST00000466387.5:c.-318+25779_-318+25780insTCTTCTTCTTCT:p.(=)

Pathogenicity Data:: Best Score: 0.11874825; CADD: 0.119 (0.549)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79338575A>ATCTTCTTTTTCC [-/1] rs1239699778 (variation viewer)

Variant score: 0.119

Transcripts:: CTNNA2:ENST00000466387.5:c.-318+25779_-318+25780insTCTTCTTTTTCC:p.(=)

Pathogenicity Data:: Best Score: 0.11874825; CADD: 0.119 (0.549)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79888725A>G [0/1]

Variant score: 0.112

Transcripts:: CTNNA2:ENST00000402739.8:c.852+14383A>G:p.(=); CTNNA2:ENST00000466387.5:c.852+14383A>G:p.(=); CTNNA2:ENST00000496558.5:c.852+14383A>G:p.(=); CTNNA2:ENST00000629316.2:c.852+14383A>G:p.(=)

Pathogenicity Data:: Best Score: 0.11243534; CADD: 0.112 (0.518)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79682410C>CA [0/1] rs10674928 (variation viewer)

Variant score: 0.108

Transcripts:: CTNNA2:ENST00000402739.8:c.102+30752_102+30753insA:p.(=); CTNNA2:ENST00000409266.5:c.103-5154_103-5153insA:p.(=); CTNNA2:ENST00000466387.5:c.102+30752_102+30753insA:p.(=); CTNNA2:ENST00000496558.5:c.102+30752_102+30753insA:p.(=); CTNNA2:ENST00000629316.2:c.102+30752_102+30753insA:p.(=)

Pathogenicity Data:: Best Score: 0.107516885; CADD: 0.108 (0.494)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79847542C>CA [1/1] rs70940050 (variation viewer)

Variant score: 0.107

Transcripts:: CTNNA2:ENST00000402739.8:c.299-10471_299-10470insA:p.(=); CTNNA2:ENST00000466387.5:c.299-10471_299-10470insA:p.(=); CTNNA2:ENST00000496558.5:c.299-10471_299-10470insA:p.(=); CTNNA2:ENST00000629316.2:c.299-10471_299-10470insA:p.(=)

Pathogenicity Data:: Best Score: 0.106900156; CADD: 0.107 (0.491)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80279049C>CGTGTGTGTGTGTGT [0/1] rs3219982 (variation viewer)

Variant score: 0.107

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-114162_1057-114161insGTGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000466387.5:c.1057-114162_1057-114161insGTGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000496558.5:c.1057-114162_1057-114161insGTGTGTGTGTGTGT:p.(=); CTNNA2:ENST00000629316.2:c.1057-114162_1057-114161insGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.10669452; CADD: 0.107 (0.490)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79201924G>T [0/1] rs547232132 (variation viewer)

Variant score: 0.105

Transcripts:: CTNNA2:ENST00000466387.5:c.-406+3848G>T:p.(=)

Pathogenicity Data:: Best Score: 0.10710579; CADD: 0.107 (0.492)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0454%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0687%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1199%; gnomAD_G_OTH: 0.1022%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79508955GTATATATATA>G [0|1] rs530470576 (variation viewer)

Variant score: 0.105

Transcripts:: CTNNA2:ENST00000466387.5:c.-6+3774_-6+3783del:p.(=)

Pathogenicity Data:: Best Score: 0.10484135; CADD: 0.105 (0.481)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79396107C>A [0/1] rs144674977 (variation viewer)

Variant score: 0.103

Transcripts:: CTNNA2:ENST00000466387.5:c.-135+22094C>A:p.(=)

Pathogenicity Data:: Best Score: 0.10956955; CADD: 0.110 (0.504)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1378%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1067%; gnomAD_G_OTH: 0.1020%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79610564C>T [0/1] rs138569703 (variation viewer)

Variant score: 0.103

Transcripts:: CTNNA2:ENST00000466387.5:c.-5-40988C>T:p.(=); CTNNA2:ENST00000496558.5:c.-5-40988C>T:p.(=); CTNNA2:ENST00000629316.2:c.-5-40988C>T:p.(=)

Pathogenicity Data:: Best Score: 0.108338535; CADD: 0.108 (0.498)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1306%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1334%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80165231AT>A [0|1] rs573737593 (variation viewer)

Variant score: 0.102

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-227979del:p.(=); CTNNA2:ENST00000466387.5:c.1057-227979del:p.(=); CTNNA2:ENST00000496558.5:c.1057-227979del:p.(=); CTNNA2:ENST00000629316.2:c.1057-227979del:p.(=)

Pathogenicity Data:: Best Score: 0.108338535; CADD: 0.108 (0.498)

Frequency Data:: gnomAD_G_AFR: 0.2414%; gnomAD_G_AMR: 0.1479%; gnomAD_G_ASJ: 0.3597%; gnomAD_G_FIN: 0.0415%; gnomAD_G_NFE: 0.1048%; gnomAD_G_OTH: 0.1244%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79408086A>G [0/1] rs74611748 (variation viewer)

Variant score: 0.099

Transcripts:: CTNNA2:ENST00000466387.5:c.-135+34073A>G:p.(=)

Pathogenicity Data:: Best Score: 0.65246385; CADD: 0.652 (4.590)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 1.0850%; UK10K: 1.9836%; gnomAD_G_AFR: 0.3326%; gnomAD_G_AMR: 0.9615%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_FIN: 0.2865%; gnomAD_G_NFE: 1.4209%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80374680TGC>T [0/1] rs201668271 (variation viewer)

Variant score: 0.095

Transcripts:: CTNNA2:ENST00000343114.7:c.94-18530_94-18529del:p.(=); CTNNA2:ENST00000402739.8:c.1057-18530_1057-18529del:p.(=); CTNNA2:ENST00000466387.5:c.1057-18530_1057-18529del:p.(=); CTNNA2:ENST00000496558.5:c.1057-18530_1057-18529del:p.(=); CTNNA2:ENST00000629316.2:c.1057-18530_1057-18529del:p.(=); CTNNA2:ENST00000361291.8:c.-96-18530_-96-18529del:p.(=); CTNNA2:ENST00000540488.5:c.-96-18530_-96-18529del:p.(=); CTNNA2:ENST00000541047.5:c.-48-18530_-48-18529del:p.(=)

Pathogenicity Data:: Best Score: 0.21168464; CADD: 0.212 (1.033)

Frequency Data:: gnomAD_G_AFR: 1.6210%; gnomAD_G_AMR: 0.2584%; gnomAD_G_EAS: 0.0653%; gnomAD_G_FIN: 0.0307%; gnomAD_G_NFE: 0.1891%; gnomAD_G_OTH: 0.3275%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80512738G>A [0/1] rs56188522 (variation viewer)

Variant score: 0.089

Transcripts:: CTNNA2:ENST00000343114.7:c.328-32244G>A:p.(=); CTNNA2:ENST00000361291.8:c.139-32244G>A:p.(=); CTNNA2:ENST00000402739.8:c.1291-32244G>A:p.(=); CTNNA2:ENST00000466387.5:c.1291-32244G>A:p.(=); CTNNA2:ENST00000496558.5:c.1291-32244G>A:p.(=); CTNNA2:ENST00000540488.5:c.139-32244G>A:p.(=); CTNNA2:ENST00000541047.5:c.187-32244G>A:p.(=); CTNNA2:ENST00000629316.2:c.1291-32244G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12743056; CADD: 0.127 (0.592)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.9342%; UK10K: 1.1637%; gnomAD_G_AFR: 0.2645%; gnomAD_G_AMR: 0.4819%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4603%; gnomAD_G_NFE: 0.8242%; gnomAD_G_OTH: 0.5165%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80449287TTAAA>T [1/1] rs72400269 (variation viewer)

Variant score: 0.089

Transcripts:: CTNNA2:ENST00000343114.7:c.327+29687_327+29690del:p.(=); CTNNA2:ENST00000361291.8:c.138+29687_138+29690del:p.(=); CTNNA2:ENST00000402739.8:c.1290+29687_1290+29690del:p.(=); CTNNA2:ENST00000466387.5:c.1290+29687_1290+29690del:p.(=); CTNNA2:ENST00000496558.5:c.1290+29687_1290+29690del:p.(=); CTNNA2:ENST00000540488.5:c.138+29687_138+29690del:p.(=); CTNNA2:ENST00000541047.5:c.186+29687_186+29690del:p.(=); CTNNA2:ENST00000629316.2:c.1290+29687_1290+29690del:p.(=)

Pathogenicity Data:: Best Score: 0.1732009; CADD: 0.173 (0.826)

Frequency Data:: gnomAD_G_AFR: 1.5209%; gnomAD_G_AMR: 0.7538%; gnomAD_G_ASJ: 0.6944%; gnomAD_G_EAS: 0.0635%; gnomAD_G_FIN: 0.5882%; gnomAD_G_NFE: 1.3329%; gnomAD_G_OTH: 0.8658%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80567177C>G [0/1] rs138111350 (variation viewer)

Variant score: 0.088

Transcripts:: CTNNA2:ENST00000343114.7:c.779-6986C>G:p.(=); CTNNA2:ENST00000361291.8:c.590-6986C>G:p.(=); CTNNA2:ENST00000402739.8:c.1742-6986C>G:p.(=); CTNNA2:ENST00000466387.5:c.1742-6986C>G:p.(=); CTNNA2:ENST00000496558.5:c.1742-6986C>G:p.(=); CTNNA2:ENST00000540488.5:c.590-6986C>G:p.(=); CTNNA2:ENST00000541047.5:c.638-6986C>G:p.(=); CTNNA2:ENST00000629316.2:c.1742-6986C>G:p.(=)

Pathogenicity Data:: Best Score: 0.14375114; CADD: 0.144 (0.674)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.6634%; UK10K: 1.0976%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.3459%; gnomAD_G_NFE: 1.2602%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79977222G>GCACACACACACA [-/1] rs72018840 (variation viewer)

Variant score: 0.085

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+67425_1056+67426insCACACACACACA:p.(=); CTNNA2:ENST00000466387.5:c.1056+67425_1056+67426insCACACACACACA:p.(=); CTNNA2:ENST00000496558.5:c.1056+67425_1056+67426insCACACACACACA:p.(=); CTNNA2:ENST00000629316.2:c.1056+67425_1056+67426insCACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.08525509; CADD: 0.085 (0.387)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79699788TACACACACACAC>T [0|1] rs377095429 (variation viewer)

Variant score: 0.081

Transcripts:: CTNNA2:ENST00000402739.8:c.103-44598_103-44587del:p.(=); CTNNA2:ENST00000466387.5:c.103-44598_103-44587del:p.(=); CTNNA2:ENST00000496558.5:c.103-44598_103-44587del:p.(=); CTNNA2:ENST00000629316.2:c.103-44598_103-44587del:p.(=)

Pathogenicity Data:: Best Score: 0.081455946; CADD: 0.081 (0.369)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80434485C>CT [1|1] rs1169944635 (variation viewer)

Variant score: 0.080

Transcripts:: CTNNA2:ENST00000343114.7:c.327+14884_327+14885insT:p.(=); CTNNA2:ENST00000361291.8:c.138+14884_138+14885insT:p.(=); CTNNA2:ENST00000402739.8:c.1290+14884_1290+14885insT:p.(=); CTNNA2:ENST00000466387.5:c.1290+14884_1290+14885insT:p.(=); CTNNA2:ENST00000496558.5:c.1290+14884_1290+14885insT:p.(=); CTNNA2:ENST00000540488.5:c.138+14884_138+14885insT:p.(=); CTNNA2:ENST00000541047.5:c.186+14884_186+14885insT:p.(=); CTNNA2:ENST00000629316.2:c.1290+14884_1290+14885insT:p.(=)

Pathogenicity Data:: Best Score: 0.079550445; CADD: 0.080 (0.360)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79709045G>A [0/1] rs184356036 (variation viewer)

Variant score: 0.078

Transcripts:: CTNNA2:ENST00000402739.8:c.103-35342G>A:p.(=); CTNNA2:ENST00000466387.5:c.103-35342G>A:p.(=); CTNNA2:ENST00000496558.5:c.103-35342G>A:p.(=); CTNNA2:ENST00000629316.2:c.103-35342G>A:p.(=)

Pathogenicity Data:: Best Score: 0.08230156; CADD: 0.082 (0.373)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.1529%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.1867%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80075702ATAAATATTATAAAAATAATATTTATACT>A [0/1] rs1558783816 (variation viewer)

Variant score: 0.078

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+165906_1056+165933del:p.(=); CTNNA2:ENST00000466387.5:c.1056+165906_1056+165933del:p.(=); CTNNA2:ENST00000496558.5:c.1056+165906_1056+165933del:p.(=); CTNNA2:ENST00000629316.2:c.1056+165906_1056+165933del:p.(=)

Pathogenicity Data:: Best Score: 0.16727811; CADD: 0.167 (0.795)

Frequency Data:: gnomAD_G_AFR: 0.2136%; gnomAD_G_AMR: 1.0204%; gnomAD_G_ASJ: 1.5957%; gnomAD_G_EAS: 1.5251%; gnomAD_G_FIN: 0.7143%; gnomAD_G_NFE: 0.4035%; gnomAD_G_OTH: 0.5597%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80321730C>T [0/1] rs150793223 (variation viewer)

Variant score: 0.069

Transcripts:: CTNNA2:ENST00000343114.7:c.93+8076C>T:p.(=); CTNNA2:ENST00000402739.8:c.1057-71481C>T:p.(=); CTNNA2:ENST00000466387.5:c.1057-71481C>T:p.(=); CTNNA2:ENST00000496558.5:c.1057-71481C>T:p.(=); CTNNA2:ENST00000629316.2:c.1057-71481C>T:p.(=); CTNNA2:ENST00000361291.8:c.-97+8076C>T:p.(=); CTNNA2:ENST00000540488.5:c.-97+8076C>T:p.(=); CTNNA2:ENST00000541047.5:c.-49+16407C>T:p.(=)

Pathogenicity Data:: Best Score: 0.30385453; CADD: 0.304 (1.573)

Frequency Data:: 1000Genomes: 0.7788%; TOPMed: 1.2600%; UK10K: 1.9043%; gnomAD_G_AFR: 0.3436%; gnomAD_G_AMR: 1.1962%; gnomAD_G_FIN: 0.4296%; gnomAD_G_NFE: 1.4863%; gnomAD_G_OTH: 1.2220%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79416257CT>C [0/1] rs66830925 (variation viewer)

Variant score: 0.068

Transcripts:: CTNNA2:ENST00000466387.5:c.-135+42245del:p.(=)

Pathogenicity Data:: Best Score: 0.06846321; CADD: 0.068 (0.308)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80199182G>GA [0/1] rs70940076 (variation viewer)

Variant score: 0.061

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-194029_1057-194028insA:p.(=); CTNNA2:ENST00000466387.5:c.1057-194029_1057-194028insA:p.(=); CTNNA2:ENST00000496558.5:c.1057-194029_1057-194028insA:p.(=); CTNNA2:ENST00000629316.2:c.1057-194029_1057-194028insA:p.(=)

Pathogenicity Data:: Best Score: 0.060709357; CADD: 0.061 (0.272)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80368867G>GTATATATA [-/1] rs1553505682 (variation viewer)

Variant score: 0.060

Transcripts:: CTNNA2:ENST00000343114.7:c.94-24344_94-24343insTATATATA:p.(=); CTNNA2:ENST00000402739.8:c.1057-24344_1057-24343insTATATATA:p.(=); CTNNA2:ENST00000466387.5:c.1057-24344_1057-24343insTATATATA:p.(=); CTNNA2:ENST00000496558.5:c.1057-24344_1057-24343insTATATATA:p.(=); CTNNA2:ENST00000629316.2:c.1057-24344_1057-24343insTATATATA:p.(=); CTNNA2:ENST00000361291.8:c.-96-24344_-96-24343insTATATATA:p.(=); CTNNA2:ENST00000540488.5:c.-96-24344_-96-24343insTATATATA:p.(=); CTNNA2:ENST00000541047.5:c.-48-24344_-48-24343insTATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.05984384; CADD: 0.060 (0.268)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80565783G>A [0/1] rs147948015 (variation viewer)

Variant score: 0.059

Transcripts:: CTNNA2:ENST00000343114.7:c.779-8380G>A:p.(=); CTNNA2:ENST00000361291.8:c.590-8380G>A:p.(=); CTNNA2:ENST00000402739.8:c.1742-8380G>A:p.(=); CTNNA2:ENST00000466387.5:c.1742-8380G>A:p.(=); CTNNA2:ENST00000496558.5:c.1742-8380G>A:p.(=); CTNNA2:ENST00000540488.5:c.590-8380G>A:p.(=); CTNNA2:ENST00000541047.5:c.638-8380G>A:p.(=); CTNNA2:ENST00000629316.2:c.1742-8380G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09405881; CADD: 0.094 (0.429)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.6252%; UK10K: 1.0315%; gnomAD_G_AFR: 0.1030%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.3188%; gnomAD_G_NFE: 1.1875%; gnomAD_G_OTH: 0.9184%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80368867G>GTATATATATA [-/1] rs1553505682 (variation viewer)

Variant score: 0.058

Transcripts:: CTNNA2:ENST00000343114.7:c.94-24344_94-24343insTATATATATA:p.(=); CTNNA2:ENST00000402739.8:c.1057-24344_1057-24343insTATATATATA:p.(=); CTNNA2:ENST00000466387.5:c.1057-24344_1057-24343insTATATATATA:p.(=); CTNNA2:ENST00000496558.5:c.1057-24344_1057-24343insTATATATATA:p.(=); CTNNA2:ENST00000629316.2:c.1057-24344_1057-24343insTATATATATA:p.(=); CTNNA2:ENST00000361291.8:c.-96-24344_-96-24343insTATATATATA:p.(=); CTNNA2:ENST00000540488.5:c.-96-24344_-96-24343insTATATATATA:p.(=); CTNNA2:ENST00000541047.5:c.-48-24344_-48-24343insTATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.057676554; CADD: 0.058 (0.258)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79809545G>C [0|1] rs865904145 (variation viewer)

Variant score: 0.057

Transcripts:: CTNNA2:ENST00000402739.8:c.299-48468G>C:p.(=); CTNNA2:ENST00000466387.5:c.299-48468G>C:p.(=); CTNNA2:ENST00000496558.5:c.299-48468G>C:p.(=); CTNNA2:ENST00000629316.2:c.299-48468G>C:p.(=)

Pathogenicity Data:: Best Score: 0.05984384; CADD: 0.060 (0.268)

Frequency Data:: TOPMed: 0.0239%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0267%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79295885A>ACCTCAACAAAATTGTGGGGAAATTTTGTTTT [0/1] rs13411422 (variation viewer)

Variant score: 0.033

Transcripts:: CTNNA2:ENST00000466387.5:c.-405-16824_-405-16823insCCTCAACAAAATTGTGGGGAAATTTTGTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.033726633; CADD: 0.034 (0.149)

Frequency Data:: gnomAD_G_AFR: 0.2094%; gnomAD_G_NFE: 0.0090%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79982294TA>T [0/1] rs1298838226 (variation viewer)

Variant score: 0.033

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+72498del:p.(=); CTNNA2:ENST00000466387.5:c.1056+72498del:p.(=); CTNNA2:ENST00000496558.5:c.1056+72498del:p.(=); CTNNA2:ENST00000629316.2:c.1056+72498del:p.(=)

Pathogenicity Data:: Best Score: 0.03283626; CADD: 0.033 (0.145)

Frequency Data:: gnomAD_G_AFR: 0.0138%; gnomAD_G_NFE: 0.0428%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80281994C>T [0/1] rs139148626 (variation viewer)

Variant score: 0.032

Transcripts:: CTNNA2:ENST00000402739.8:c.1057-111217C>T:p.(=); CTNNA2:ENST00000466387.5:c.1057-111217C>T:p.(=); CTNNA2:ENST00000496558.5:c.1057-111217C>T:p.(=); CTNNA2:ENST00000629316.2:c.1057-111217C>T:p.(=)

Pathogenicity Data:: Best Score: 0.044127405; CADD: 0.044 (0.196)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.8211%; UK10K: 1.0050%; gnomAD_G_AFR: 0.3570%; gnomAD_G_AMR: 1.1002%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.7688%; gnomAD_G_NFE: 1.0724%; gnomAD_G_OTH: 0.9356%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79302099C>CAAAT [0/1] rs202007518 (variation viewer)

Variant score: 0.032

Transcripts:: CTNNA2:ENST00000466387.5:c.-405-10610_-405-10609insAAAT:p.(=)

Pathogenicity Data:: Best Score: 0.11671674; CADD: 0.117 (0.539)

Frequency Data:: 1000Genomes: 0.6989%; UK10K: 1.7059%; gnomAD_G_AFR: 0.2874%; gnomAD_G_AMR: 1.0843%; gnomAD_G_ASJ: 1.0000%; gnomAD_G_FIN: 0.5066%; gnomAD_G_NFE: 1.8519%; gnomAD_G_OTH: 1.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80409298TA>T [0/1] rs546092256 (variation viewer)

Variant score: 0.031

Transcripts:: CTNNA2:ENST00000343114.7:c.175-10150del:p.(=); CTNNA2:ENST00000402739.8:c.1138-10150del:p.(=); CTNNA2:ENST00000466387.5:c.1138-10150del:p.(=); CTNNA2:ENST00000496558.5:c.1138-10150del:p.(=); CTNNA2:ENST00000541047.5:c.34-10150del:p.(=); CTNNA2:ENST00000629316.2:c.1138-10150del:p.(=); CTNNA2:ENST00000361291.8:c.-15-10150del:p.(=); CTNNA2:ENST00000540488.5:c.-15-10150del:p.(=)

Pathogenicity Data:: Best Score: 0.06717539; CADD: 0.067 (0.302)

Frequency Data:: gnomAD_G_AFR: 0.7648%; gnomAD_G_AMR: 0.3436%; gnomAD_G_EAS: 0.0649%; gnomAD_G_FIN: 1.5988%; gnomAD_G_NFE: 0.1603%; gnomAD_G_OTH: 0.7485%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80084812G>A [0/1] rs528170436 (variation viewer)

Variant score: 0.025

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+175015G>A:p.(=); CTNNA2:ENST00000466387.5:c.1056+175015G>A:p.(=); CTNNA2:ENST00000496558.5:c.1056+175015G>A:p.(=); CTNNA2:ENST00000629316.2:c.1056+175015G>A:p.(=)

Pathogenicity Data:: Best Score: 0.025010347; CADD: 0.025 (0.110)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0422%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0334%; gnomAD_G_OTH: 0.1022%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79248887G>A [0|1] rs146367725 (variation viewer)

Variant score: 0.013

Transcripts:: CTNNA2:ENST00000466387.5:c.-406+50811G>A:p.(=)

Pathogenicity Data:: Best Score: 0.04720384; CADD: 0.047 (0.210)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 1.0900%; UK10K: 1.5737%; gnomAD_G_AFR: 0.8482%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.4891%; gnomAD_G_NFE: 1.8402%; gnomAD_G_OTH: 1.2220%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.79786357G>T [0/1] rs138483678 (variation viewer)

Variant score: 0.005

Transcripts:: CTNNA2:ENST00000402739.8:c.298+41775G>T:p.(=); CTNNA2:ENST00000466387.5:c.298+41775G>T:p.(=); CTNNA2:ENST00000496558.5:c.298+41775G>T:p.(=); CTNNA2:ENST00000629316.2:c.298+41775G>T:p.(=)

Pathogenicity Data:: Best Score: 0.0075697303; CADD: 0.008 (0.033)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1489%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.4796%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.1268%; gnomAD_G_OTH: 0.1022%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.79345110A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000466387.5:c.-317-28721A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80090150G>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+180353G>*:p.(=); CTNNA2:ENST00000466387.5:c.1056+180353G>*:p.(=); CTNNA2:ENST00000496558.5:c.1056+180353G>*:p.(=); CTNNA2:ENST00000629316.2:c.1056+180353G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80090152G>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000402739.8:c.1056+180355G>*:p.(=); CTNNA2:ENST00000466387.5:c.1056+180355G>*:p.(=); CTNNA2:ENST00000496558.5:c.1056+180355G>*:p.(=); CTNNA2:ENST00000629316.2:c.1056+180355G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80374682C>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000343114.7:c.94-18529C>*:p.(=); CTNNA2:ENST00000402739.8:c.1057-18529C>*:p.(=); CTNNA2:ENST00000466387.5:c.1057-18529C>*:p.(=); CTNNA2:ENST00000496558.5:c.1057-18529C>*:p.(=); CTNNA2:ENST00000629316.2:c.1057-18529C>*:p.(=); CTNNA2:ENST00000361291.8:c.-96-18529C>*:p.(=); CTNNA2:ENST00000540488.5:c.-96-18529C>*:p.(=); CTNNA2:ENST00000541047.5:c.-48-18529C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80558488A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000343114.7:c.778+2595A>*:p.(=); CTNNA2:ENST00000361291.8:c.589+2595A>*:p.(=); CTNNA2:ENST00000402739.8:c.1741+2595A>*:p.(=); CTNNA2:ENST00000466387.5:c.1741+2595A>*:p.(=); CTNNA2:ENST00000496558.5:c.1741+2595A>*:p.(=); CTNNA2:ENST00000540488.5:c.589+2595A>*:p.(=); CTNNA2:ENST00000541047.5:c.637+2595A>*:p.(=); CTNNA2:ENST00000629316.2:c.1741+2595A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80590433TG>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000343114.7:c.1226+948_1226+949delTGins*:p.(=); CTNNA2:ENST00000361291.8:c.1037+948_1037+949delTGins*:p.(=); CTNNA2:ENST00000402739.8:c.2189+948_2189+949delTGins*:p.(=); CTNNA2:ENST00000466387.5:c.2189+948_2189+949delTGins*:p.(=); CTNNA2:ENST00000496558.5:c.2189+948_2189+949delTGins*:p.(=); CTNNA2:ENST00000540488.5:c.1037+948_1037+949delTGins*:p.(=); CTNNA2:ENST00000541047.5:c.1085+948_1085+949delTGins*:p.(=); CTNNA2:ENST00000629316.2:c.2189+948_2189+949delTGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.80606412ACC>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA2:ENST00000343114.7:c.1333-1772_1333-1770delACCins*:p.(=); CTNNA2:ENST00000361291.8:c.1144-1772_1144-1770delACCins*:p.(=); CTNNA2:ENST00000402739.8:c.2296-1772_2296-1770delACCins*:p.(=); CTNNA2:ENST00000466387.5:c.2296-1772_2296-1770delACCins*:p.(=); CTNNA2:ENST00000496558.5:c.2296-1772_2296-1770delACCins*:p.(=); CTNNA2:ENST00000540488.5:c.1143+2233_1143+2235delACCins*:p.(=); CTNNA2:ENST00000541047.5:c.1192-1772_1192-1770delACCins*:p.(=); CTNNA2:ENST00000629316.2:c.2295+2233_2295+2235delACCins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CHRM1

Exomiser Score: 0.478

Phenotype Score: 0.501

Variant Score: 0.870

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.012

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.62919173G>C [0/1] rs1056077270 (variation viewer)

Variant score: 0.012 CONTRIBUTING VARIANT

Transcripts:: CHRM1:ENST00000306960.4:c.-79+2045C>G:p.(=)

Pathogenicity Data:: Best Score: 0.012129545; CADD: 0.012 (0.053)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.478

Phenotype Score: 0.501

Variant Score: 0.870

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.62924629G>GCTCTCTCTCT [1/1] rs1170059496 (variation viewer)

Variant score: 0.870 CONTRIBUTING VARIANT

Transcripts:: CHRM1:ENST00000306960.4::; CHRM1:ENST00000645905.1::

Pathogenicity Data:: Best Score: 0.870013; CADD: 0.870 (8.861)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr11:g.62905650T>C [0/1] rs137865609 (variation viewer)

Variant score: 0.230

Transcripts:: CHRM1:ENST00000306960.4::; CHRM1:ENST00000535296.5::

Pathogenicity Data:: Best Score: 0.53868246; CADD: 0.539 (3.360)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.9198%; UK10K: 1.4282%; gnomAD_G_AFR: 0.2634%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 1.5178%; gnomAD_G_NFE: 1.5063%; gnomAD_G_OTH: 1.3238%

AHCYL2

Exomiser Score: 0.477

Phenotype Score: 0.504

Variant Score: 0.866

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.477

Phenotype Score: 0.504

Variant Score: 0.866

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129352937C>CT [-/1] rs59762582 (variation viewer)

Variant score: 0.866 CONTRIBUTING VARIANT

Transcripts:: AHCYL2:ENST00000325006.7:c.364-26701_364-26700insT:p.(=); AHCYL2:ENST00000446544.6:c.364-26704_364-26703insT:p.(=)

Pathogenicity Data:: Best Score: 0.8660015; CADD: 0.866 (8.729)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.458

Phenotype Score: 0.504

Variant Score: 0.858

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129352937C>CT [-/1] rs59762582 (variation viewer)

Variant score: 0.866 CONTRIBUTING VARIANT

Transcripts:: AHCYL2:ENST00000325006.7:c.364-26701_364-26700insT:p.(=); AHCYL2:ENST00000446544.6:c.364-26704_364-26703insT:p.(=)

Pathogenicity Data:: Best Score: 0.8660015; CADD: 0.866 (8.729)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129352937CT>C [-/1] rs59762582 (variation viewer)

Variant score: 0.849 CONTRIBUTING VARIANT

Transcripts:: AHCYL2:ENST00000325006.7:c.364-26700del:p.(=); AHCYL2:ENST00000446544.6:c.364-26703del:p.(=)

Pathogenicity Data:: Best Score: 0.8493393; CADD: 0.849 (8.220)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129283495T>C [0/1]

Variant score: 0.796

Transcripts:: AHCYL2:ENST00000325006.7:c.363+58056T>C:p.(=); AHCYL2:ENST00000446544.6:c.363+58056T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7963427; CADD: 0.796 (6.911)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129273321C>CT [-/1] rs35236990 (variation viewer)

Variant score: 0.700

Transcripts:: AHCYL2:ENST00000325006.7:c.363+47882_363+47883insT:p.(=); AHCYL2:ENST00000446544.6:c.363+47882_363+47883insT:p.(=)

Pathogenicity Data:: Best Score: 0.69987655; CADD: 0.700 (5.227)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129263601A>G [0/1] rs116868236 (variation viewer)

Variant score: 0.466

Transcripts:: AHCYL2:ENST00000325006.7:c.363+38162A>G:p.(=); AHCYL2:ENST00000446544.6:c.363+38162A>G:p.(=)

Pathogenicity Data:: Best Score: 0.64868236; CADD: 0.649 (4.543)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.5240%; UK10K: 1.1240%; gnomAD_G_AFR: 0.2862%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.6661%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129387420C>T [0/1] rs116892104 (variation viewer)

Variant score: 0.288

Transcripts:: AHCYL2:ENST00000325006.7:c.476-1636C>T:p.(=); AHCYL2:ENST00000446544.6:c.473-1636C>T:p.(=); AHCYL2:ENST00000474594.5:c.167-1636C>T:p.(=); AHCYL2:ENST00000490911.5:c.167-1636C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5770393; CADD: 0.577 (3.737)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.8720%; UK10K: 1.5472%; gnomAD_G_AFR: 0.4467%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.6869%; gnomAD_G_NFE: 1.4459%; gnomAD_G_OTH: 1.1202%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129362597GT>G [0/1] rs769346623 (variation viewer)

Variant score: 0.131

Transcripts:: AHCYL2:ENST00000325006.7:c.364-17040del:p.(=); AHCYL2:ENST00000446544.6:c.364-17043del:p.(=)

Pathogenicity Data:: Best Score: 0.13143963; CADD: 0.131 (0.612)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129256547C>CCA [0|1] rs1554470553 (variation viewer)

Variant score: 0.082

Transcripts:: AHCYL2:ENST00000325006.7:c.363+31108_363+31109insCA:p.(=); AHCYL2:ENST00000446544.6:c.363+31108_363+31109insCA:p.(=)

Pathogenicity Data:: Best Score: 0.0820902; CADD: 0.082 (0.372)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129399749C>CA [0/1] rs532645447 (variation viewer)

Variant score: 0.068

Transcripts:: AHCYL2:ENST00000325006.7:c.824-541_824-540insA:p.(=); AHCYL2:ENST00000446544.6:c.821-541_821-540insA:p.(=); AHCYL2:ENST00000474594.5:c.515-541_515-540insA:p.(=); AHCYL2:ENST00000490911.5:c.515-541_515-540insA:p.(=)

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: UK10K: 1.4943%; gnomAD_G_AFR: 0.4549%; gnomAD_G_AMR: 0.3155%; gnomAD_G_FIN: 0.4660%; gnomAD_G_NFE: 1.4139%; gnomAD_G_OTH: 0.8824%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129239029A>* [-/1]

Variant score: 0.000

Transcripts:: AHCYL2:ENST00000325006.7:c.363+13590A>*:p.(=); AHCYL2:ENST00000446544.6:c.363+13590A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.129393403CAG>C [0/1]

Variant score: 0.000

Transcripts:: AHCYL2:ENST00000325006.7:c.720+3670_720+3671del:p.(=); AHCYL2:ENST00000446544.6:c.717+3670_717+3671del:p.(=); AHCYL2:ENST00000474594.5:c.411+3670_411+3671del:p.(=); AHCYL2:ENST00000490911.5:c.411+3670_411+3671del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TLE1

Exomiser Score: 0.465

Phenotype Score: 0.514

Variant Score: 0.850

Phenotype matches:

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.465

Phenotype Score: 0.514

Variant Score: 0.850

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81587907C>CGTGTGTGTGTGTGTGTGTGTCATCCCGCCTGTGTGT [0/1] rs1554716598 (variation viewer)

Variant score: 0.850 CONTRIBUTING VARIANT

Transcripts:: TLE1:ENST00000376499.8:c.1830-80_1830-79insACACACAGGCGGGATGACACACACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.8500315; CADD: 0.850 (8.240)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.033

Phenotype Score: 0.514

Variant Score: 0.497

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81587907C>CGTGTGTGTGTGTGTGTGTGTCATCCCGCCTGTGTGT [0/1] rs1554716598 (variation viewer)

Variant score: 0.850 CONTRIBUTING VARIANT

Transcripts:: TLE1:ENST00000376499.8:c.1830-80_1830-79insACACACAGGCGGGATGACACACACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.8500315; CADD: 0.850 (8.240)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81662361T>TTG [-/1] rs371936084 (variation viewer)

Variant score: 0.144 CONTRIBUTING VARIANT

Transcripts:: TLE1:ENST00000376499.8:c.235-8326_235-8325insCA:p.(=)

Pathogenicity Data:: Best Score: 0.14355397; CADD: 0.144 (0.673)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81675698G>GTTTTTTTTT [1/1] rs35060460 (variation viewer)

Variant score: 0.186

Transcripts:: TLE1:ENST00000376499.8:c.234+9977_234+9978insAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.18585831; CADD: 0.186 (0.893)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81662361T>TTGTGTGTG [-/1] rs371936084 (variation viewer)

Variant score: 0.128

Transcripts:: TLE1:ENST00000376499.8:c.235-8326_235-8325insCACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81625911TAA>T [1/1] rs35467275 (variation viewer)

Variant score: 0.038

Transcripts:: TLE1:ENST00000376499.8:c.595-5356_595-5355del:p.(=)

Pathogenicity Data:: Best Score: 0.037501633; CADD: 0.038 (0.166)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.81632474CCTTTT>* [-/1]

Variant score: 0.000

Transcripts:: TLE1:ENST00000376499.8:c.594+869_594+874delAAAAGGins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MEF2C

Exomiser Score: 0.464

Phenotype Score: 0.516

Variant Score: 0.847

Phenotype matches:

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases:: OMIM:613443 Chromosome 5q14.3 deletion syndrome (CNV); OMIM:613443 Mental retardation, stereotypic movements, epilepsy, and/or cerebral malformations - autosomal dominant; ORPHA:228384 5q14.3 microdeletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.464

Phenotype Score: 0.516

Variant Score: 0.847

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.88723200A>G [0/1] rs776359544 (variation viewer)

Variant score: 0.847 CONTRIBUTING VARIANT

Transcripts:: MEF2C:ENST00000340208.9:c.1131-275T>C:p.(=); MEF2C:ENST00000424173.6:c.1071-275T>C:p.(=); MEF2C:ENST00000437473.6:c.1101-275T>C:p.(=); MEF2C:ENST00000503554.4:c.723-335T>C:p.(=); MEF2C:ENST00000504921.6:c.1101-275T>C:p.(=); MEF2C:ENST00000506554.5:c.1101-348T>C:p.(=); MEF2C:ENST00000508569.5:c.1077-275T>C:p.(=); MEF2C:ENST00000510942.5:c.1077-371T>C:p.(=); MEF2C:ENST00000514015.5:c.1101-371T>C:p.(=); MEF2C:ENST00000514028.5:c.1101-371T>C:p.(=); MEF2C:ENST00000625585.2:c.1095-275T>C:p.(=); MEF2C:ENST00000625674.2:c.1071-275T>C:p.(=); MEF2C:ENST00000626391.2:c.957-371T>C:p.(=); MEF2C:ENST00000627659.2:c.1071-371T>C:p.(=); MEF2C:ENST00000628656.2:c.933-275T>C:p.(=); MEF2C:ENST00000629612.2:c.1077-275T>C:p.(=); MEF2C:ENST00000636294.1:c.1101-275T>C:p.(=); MEF2C:ENST00000636998.1:c.1101-371T>C:p.(=); MEF2C:ENST00000637481.1:c.1068-275T>C:p.(=); MEF2C:ENST00000637732.1:c.1101-371T>C:p.(=)

Pathogenicity Data:: Best Score: 0.84853923; CADD: 0.849 (8.197)

Frequency Data:: TOPMed: 0.0088%; UK10K: 0.0132%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.028

Phenotype Score: 0.258

Variant Score: 0.770

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.88723200A>G [0/1] rs776359544 (variation viewer)

Variant score: 0.847 CONTRIBUTING VARIANT

Transcripts:: MEF2C:ENST00000340208.9:c.1131-275T>C:p.(=); MEF2C:ENST00000424173.6:c.1071-275T>C:p.(=); MEF2C:ENST00000437473.6:c.1101-275T>C:p.(=); MEF2C:ENST00000503554.4:c.723-335T>C:p.(=); MEF2C:ENST00000504921.6:c.1101-275T>C:p.(=); MEF2C:ENST00000506554.5:c.1101-348T>C:p.(=); MEF2C:ENST00000508569.5:c.1077-275T>C:p.(=); MEF2C:ENST00000510942.5:c.1077-371T>C:p.(=); MEF2C:ENST00000514015.5:c.1101-371T>C:p.(=); MEF2C:ENST00000514028.5:c.1101-371T>C:p.(=); MEF2C:ENST00000625585.2:c.1095-275T>C:p.(=); MEF2C:ENST00000625674.2:c.1071-275T>C:p.(=); MEF2C:ENST00000626391.2:c.957-371T>C:p.(=); MEF2C:ENST00000627659.2:c.1071-371T>C:p.(=); MEF2C:ENST00000628656.2:c.933-275T>C:p.(=); MEF2C:ENST00000629612.2:c.1077-275T>C:p.(=); MEF2C:ENST00000636294.1:c.1101-275T>C:p.(=); MEF2C:ENST00000636998.1:c.1101-371T>C:p.(=); MEF2C:ENST00000637481.1:c.1068-275T>C:p.(=); MEF2C:ENST00000637732.1:c.1101-371T>C:p.(=)

Pathogenicity Data:: Best Score: 0.84853923; CADD: 0.849 (8.197)

Frequency Data:: TOPMed: 0.0088%; UK10K: 0.0132%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.88805974A>G [0/1] rs180905506 (variation viewer)

Variant score: 0.692 CONTRIBUTING VARIANT

Transcripts:: MEF2C:ENST00000340208.9:c.55-1173T>C:p.(=); MEF2C:ENST00000424173.6:c.55-1173T>C:p.(=); MEF2C:ENST00000437473.6:c.55-1173T>C:p.(=); MEF2C:ENST00000504921.6:c.55-1173T>C:p.(=); MEF2C:ENST00000506554.5:c.55-1173T>C:p.(=); MEF2C:ENST00000508569.5:c.55-1173T>C:p.(=); MEF2C:ENST00000510942.5:c.55-1173T>C:p.(=); MEF2C:ENST00000514015.5:c.55-1173T>C:p.(=); MEF2C:ENST00000514028.5:c.55-1173T>C:p.(=); MEF2C:ENST00000625585.2:c.55-1173T>C:p.(=); MEF2C:ENST00000625674.2:c.55-1173T>C:p.(=); MEF2C:ENST00000626391.2:c.55-1173T>C:p.(=); MEF2C:ENST00000627659.2:c.55-1173T>C:p.(=); MEF2C:ENST00000628656.2:c.55-1173T>C:p.(=); MEF2C:ENST00000629612.2:c.55-1173T>C:p.(=); MEF2C:ENST00000636294.1:c.55-1173T>C:p.(=); MEF2C:ENST00000636998.1:c.55-1173T>C:p.(=); MEF2C:ENST00000637481.1:c.55-1173T>C:p.(=); MEF2C:ENST00000637732.1:c.55-1173T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8175264; CADD: 0.818 (7.388)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.4316%; UK10K: 0.4232%; gnomAD_G_AFR: 0.1044%; gnomAD_G_AMR: 0.1247%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.7576%; gnomAD_G_NFE: 0.7214%; gnomAD_G_OTH: 0.4228%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.88754614G>T [0/1] rs542969448 (variation viewer)

Variant score: 0.352

Transcripts:: MEF2C:ENST00000340208.9:c.457-2571C>A:p.(=); MEF2C:ENST00000424173.6:c.397-2571C>A:p.(=); MEF2C:ENST00000437473.6:c.403-2571C>A:p.(=); MEF2C:ENST00000503554.4:c.25-2571C>A:p.(=); MEF2C:ENST00000504921.6:c.403-2571C>A:p.(=); MEF2C:ENST00000506554.5:c.403-2571C>A:p.(=); MEF2C:ENST00000508569.5:c.403-2571C>A:p.(=); MEF2C:ENST00000510942.5:c.403-2571C>A:p.(=); MEF2C:ENST00000514015.5:c.403-2571C>A:p.(=); MEF2C:ENST00000514028.5:c.403-2571C>A:p.(=); MEF2C:ENST00000625585.2:c.397-2571C>A:p.(=); MEF2C:ENST00000625674.2:c.397-2571C>A:p.(=); MEF2C:ENST00000626391.2:c.259-2571C>A:p.(=); MEF2C:ENST00000627659.2:c.397-2571C>A:p.(=); MEF2C:ENST00000628656.2:c.259-2571C>A:p.(=); MEF2C:ENST00000629612.2:c.403-2571C>A:p.(=); MEF2C:ENST00000636294.1:c.403-2571C>A:p.(=); MEF2C:ENST00000636998.1:c.403-2571C>A:p.(=); MEF2C:ENST00000637481.1:c.403-2571C>A:p.(=); MEF2C:ENST00000637732.1:c.403-2571C>A:p.(=)

Pathogenicity Data:: Best Score: 0.3662762; CADD: 0.366 (1.981)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1362%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0573%; gnomAD_G_NFE: 0.2600%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.88736525A>T [0/1] rs113320204 (variation viewer)

Variant score: 0.327

Transcripts:: MEF2C:ENST00000340208.9:c.692-4624T>A:p.(=); MEF2C:ENST00000424173.6:c.632-4624T>A:p.(=); MEF2C:ENST00000437473.6:c.638-4624T>A:p.(=); MEF2C:ENST00000503554.4:c.260-4624T>A:p.(=); MEF2C:ENST00000504921.6:c.638-4624T>A:p.(=); MEF2C:ENST00000506554.5:c.638-4624T>A:p.(=); MEF2C:ENST00000508569.5:c.638-4624T>A:p.(=); MEF2C:ENST00000510942.5:c.638-4624T>A:p.(=); MEF2C:ENST00000514015.5:c.638-4624T>A:p.(=); MEF2C:ENST00000514028.5:c.638-4624T>A:p.(=); MEF2C:ENST00000625585.2:c.632-4624T>A:p.(=); MEF2C:ENST00000625674.2:c.632-4624T>A:p.(=); MEF2C:ENST00000626391.2:c.494-4624T>A:p.(=); MEF2C:ENST00000627659.2:c.632-4624T>A:p.(=); MEF2C:ENST00000628656.2:c.494-4624T>A:p.(=); MEF2C:ENST00000629612.2:c.638-4624T>A:p.(=); MEF2C:ENST00000636294.1:c.638-4624T>A:p.(=); MEF2C:ENST00000636998.1:c.638-4624T>A:p.(=); MEF2C:ENST00000637481.1:c.629-4624T>A:p.(=); MEF2C:ENST00000637732.1:c.638-4624T>A:p.(=)

Pathogenicity Data:: Best Score: 0.38538945; CADD: 0.385 (2.114)

Frequency Data:: gnomAD_G_AFR: 0.3099%; gnomAD_G_AMR: 0.7519%; gnomAD_G_FIN: 0.6410%; gnomAD_G_NFE: 0.1807%; gnomAD_G_OTH: 0.4587%

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.88856517C>A [0/1] rs547307867 (variation viewer)

Variant score: 0.266

Transcripts:: MEF2C:ENST00000340208.9:c.-143+30985G>T:p.(=); MEF2C:ENST00000424173.6:c.-143+30985G>T:p.(=); MEF2C:ENST00000437473.6:c.-140+26438G>T:p.(=); MEF2C:ENST00000504921.6:c.-143+26438G>T:p.(=); MEF2C:ENST00000506554.5:c.-143+26438G>T:p.(=); MEF2C:ENST00000508569.5:c.-143+26438G>T:p.(=); MEF2C:ENST00000510942.5:c.-140+26438G>T:p.(=); MEF2C:ENST00000514015.5:c.-143+26438G>T:p.(=); MEF2C:ENST00000625674.2:c.-140+30985G>T:p.(=); MEF2C:ENST00000627659.2:c.-140+30985G>T:p.(=); MEF2C:ENST00000629612.2:c.-140+30985G>T:p.(=); MEF2C:ENST00000636294.1:c.-140+21425G>T:p.(=); MEF2C:ENST00000636998.1:c.-140+26438G>T:p.(=); MEF2C:ENST00000637481.1:c.-140+26438G>T:p.(=); MEF2C:ENST00000637732.1:c.-140+26532G>T:p.(=)

Pathogenicity Data:: Best Score: 0.27355957; CADD: 0.274 (1.388)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1163%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.1932%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.88734565GTTTTTT>G [0/1] rs66505441 (variation viewer)

Variant score: 0.185

Transcripts:: MEF2C:ENST00000340208.9:c.692-2670_692-2665del:p.(=); MEF2C:ENST00000424173.6:c.632-2670_632-2665del:p.(=); MEF2C:ENST00000437473.6:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000503554.4:c.260-2670_260-2665del:p.(=); MEF2C:ENST00000504921.6:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000506554.5:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000508569.5:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000510942.5:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000514015.5:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000514028.5:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000625585.2:c.632-2670_632-2665del:p.(=); MEF2C:ENST00000625674.2:c.632-2670_632-2665del:p.(=); MEF2C:ENST00000626391.2:c.494-2670_494-2665del:p.(=); MEF2C:ENST00000627659.2:c.632-2670_632-2665del:p.(=); MEF2C:ENST00000628656.2:c.494-2670_494-2665del:p.(=); MEF2C:ENST00000629612.2:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000636294.1:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000636998.1:c.638-2670_638-2665del:p.(=); MEF2C:ENST00000637481.1:c.629-2670_629-2665del:p.(=); MEF2C:ENST00000637732.1:c.638-2670_638-2665del:p.(=)

Pathogenicity Data:: Best Score: 0.18492043; CADD: 0.185 (0.888)

Frequency Data:: No frequency data

TRDN

Exomiser Score: 0.453

Phenotype Score: 0.501

Variant Score: 0.859

Phenotype matches:

Proximity score 0.501 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615441 Ventricular tachycardia, catecholaminergic polymorphic, 5, with or without muscle weakness - autosomal recessive; ORPHA:101016 Romano-Ward syndrome; ORPHA:3286 Catecholaminergic polymorphic ventricular tachycardia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.453

Phenotype Score: 0.501

Variant Score: 0.859

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123233105C>G [0/1] rs750246653 (variation viewer)

Variant score: 0.859 CONTRIBUTING VARIANT

Transcripts:: TRDN:ENST00000334268.9:c.1976-8974G>C:p.(=)

Pathogenicity Data:: Best Score: 0.8605881; CADD: 0.861 (8.557)

Frequency Data:: UK10K: 0.0132%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.169

Phenotype Score: 0.501

Variant Score: 0.707

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123551203G>GATATATATATATATATATATATATATATATATATAT [1/1]

Variant score: 0.707 CONTRIBUTING VARIANT

Transcripts:: TRDN:ENST00000334268.9:c.233-2592_233-2591insATATATATATATATATATATATATATATATATATAT:p.(=); TRDN:ENST00000542443.5:c.233-2592_233-2591insATATATATATATATATATATATATATATATATATAT:p.(=); TRDN:ENST00000546248.5:c.233-2592_233-2591insATATATATATATATATATATATATATATATATATAT:p.(=); TRDN:ENST00000628709.2:c.233-2592_233-2591insATATATATATATATATATATATATATATATATATAT:p.(=); TRDN:ENST00000662930.1:c.233-2592_233-2591insATATATATATATATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.7065055; CADD: 0.707 (5.324)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123559335A>G [0/1] rs902768668 (variation viewer)

Variant score: 0.315

Transcripts:: TRDN:ENST00000334268.9:c.233-10723T>C:p.(=); TRDN:ENST00000542443.5:c.233-10723T>C:p.(=); TRDN:ENST00000546248.5:c.233-10723T>C:p.(=); TRDN:ENST00000628709.2:c.233-10723T>C:p.(=); TRDN:ENST00000662930.1:c.233-10723T>C:p.(=)

Pathogenicity Data:: Best Score: 0.32204634; CADD: 0.322 (1.688)

Frequency Data:: TOPMed: 0.0629%; gnomAD_G_AFR: 0.0115%; gnomAD_G_FIN: 0.0860%; gnomAD_G_NFE: 0.1467%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123465582CA>C [0/1] rs1223948612 (variation viewer)

Variant score: 0.194

Transcripts:: TRDN:ENST00000334268.9:c.854-600del:p.(=); TRDN:ENST00000628709.2:c.794-600del:p.(=); TRDN:ENST00000662930.1:c.854-600del:p.(=)

Pathogenicity Data:: Best Score: 0.19350815; CADD: 0.194 (0.934)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123421805C>CAAAAAAA [0/1] rs56022131 (variation viewer)

Variant score: 0.185

Transcripts:: TRDN:ENST00000334268.9:c.1051+16257_1051+16258insTTTTTTT:p.(=); TRDN:ENST00000662930.1:c.1054+16257_1054+16258insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.18548328; CADD: 0.185 (0.891)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123433162A>AAT [-/1] rs1554236915 (variation viewer)

Variant score: 0.174

Transcripts:: TRDN:ENST00000334268.9:c.1051+4900_1051+4901insAT:p.(=); TRDN:ENST00000662930.1:c.1054+4900_1054+4901insAT:p.(=)

Pathogenicity Data:: Best Score: 0.1743424; CADD: 0.174 (0.832)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123551342T>TACACACAC [-/1] rs10638140 (variation viewer)

Variant score: 0.170

Transcripts:: TRDN:ENST00000334268.9:c.233-2731_233-2730insGTGTGTGT:p.(=); TRDN:ENST00000542443.5:c.233-2731_233-2730insGTGTGTGT:p.(=); TRDN:ENST00000546248.5:c.233-2731_233-2730insGTGTGTGT:p.(=); TRDN:ENST00000628709.2:c.233-2731_233-2730insGTGTGTGT:p.(=); TRDN:ENST00000662930.1:c.233-2731_233-2730insGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.16976696; CADD: 0.170 (0.808)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123433162A>ATAAT [-/1] rs796874348 (variation viewer)

Variant score: 0.168

Transcripts:: TRDN:ENST00000334268.9:c.1051+4900_1051+4901insATTA:p.(=); TRDN:ENST00000662930.1:c.1054+4900_1054+4901insATTA:p.(=)

Pathogenicity Data:: Best Score: 0.16804469; CADD: 0.168 (0.799)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123614300C>CA [1/1] rs1199509406 (variation viewer)

Variant score: 0.158

Transcripts:: TRDN:ENST00000334268.9:c.22+22453_22+22454insT:p.(=); TRDN:ENST00000542443.5:c.22+22453_22+22454insT:p.(=); TRDN:ENST00000546248.5:c.22+22453_22+22454insT:p.(=); TRDN:ENST00000628709.2:c.22+22453_22+22454insT:p.(=); TRDN:ENST00000662930.1:c.22+22453_22+22454insT:p.(=)

Pathogenicity Data:: Best Score: 0.15763563; CADD: 0.158 (0.745)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123410946A>G [0/1] rs575746195 (variation viewer)

Variant score: 0.138

Transcripts:: TRDN:ENST00000334268.9:c.1052-17269T>C:p.(=); TRDN:ENST00000662930.1:c.1055-17269T>C:p.(=)

Pathogenicity Data:: Best Score: 0.14019495; CADD: 0.140 (0.656)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0342%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.1027%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123267101C>CAAAAAAAAAAAAAA [1/1] rs768727745 (variation viewer)

Variant score: 0.105

Transcripts:: TRDN:ENST00000334268.9:c.1783+605_1783+606insTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.10545951; CADD: 0.105 (0.484)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123301772TATATATATATATATAC>T [0|1]

Variant score: 0.103

Transcripts:: TRDN:ENST00000334268.9:c.1510+14669_1510+14684del:p.(=)

Pathogenicity Data:: Best Score: 0.10298437; CADD: 0.103 (0.472)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123301768TAC>T [0|1] rs36076877 (variation viewer)

Variant score: 0.084

Transcripts:: TRDN:ENST00000334268.9:c.1510+14687_1510+14688del:p.(=)

Pathogenicity Data:: Best Score: 0.08356851; CADD: 0.084 (0.379)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123522517C>CT [1|1] rs375665403 (variation viewer)

Variant score: 0.040

Transcripts:: TRDN:ENST00000334268.9:c.485-6312_485-6311insA:p.(=); TRDN:ENST00000546248.5:c.485-6312_485-6311insA:p.(=); TRDN:ENST00000628709.2:c.485-6312_485-6311insA:p.(=); TRDN:ENST00000662930.1:c.485-6312_485-6311insA:p.(=)

Pathogenicity Data:: Best Score: 0.03971535; CADD: 0.040 (0.176)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123400167G>GTATATATATATATATATA [0/1] rs374126829 (variation viewer)

Variant score: 0.037

Transcripts:: TRDN:ENST00000334268.9:c.1052-6491_1052-6490insTATATATATATATATATA:p.(=); TRDN:ENST00000662930.1:c.1055-6491_1055-6490insTATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.036836565; CADD: 0.037 (0.163)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123520791A>G [0/1] rs555989659 (variation viewer)

Variant score: 0.003

Transcripts:: TRDN:ENST00000334268.9:c.485-4585T>C:p.(=); TRDN:ENST00000546248.5:c.485-4585T>C:p.(=); TRDN:ENST00000628709.2:c.485-4585T>C:p.(=); TRDN:ENST00000662930.1:c.485-4585T>C:p.(=)

Pathogenicity Data:: Best Score: 0.0034478903; CADD: 0.003 (0.015)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1258%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1133%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123519491TA>* [-/1]

Variant score: 0.000

Transcripts:: TRDN:ENST00000334268.9:c.485-3286_485-3285delTAins:p.(=); TRDN:ENST00000546248.5:c.485-3286_485-3285delTAins:p.(=); TRDN:ENST00000628709.2:c.485-3286_485-3285delTAins:p.(=); TRDN:ENST00000662930.1:c.485-3286_485-3285delTAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.123622342CACACAG>* [-/1]

Variant score: 0.000

Transcripts:: TRDN:ENST00000334268.9:c.22+14406_22+14412delCTGTGTGins:p.(=); TRDN:ENST00000542443.5:c.22+14406_22+14412delCTGTGTGins:p.(=); TRDN:ENST00000546248.5:c.22+14406_22+14412delCTGTGTGins:p.(=); TRDN:ENST00000628709.2:c.22+14406_22+14412delCTGTGTGins:p.(=); TRDN:ENST00000662930.1:c.22+14406_22+14412delCTGTGTGins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SEC24D

Exomiser Score: 0.452

Phenotype Score: 0.506

Variant Score: 0.854

Phenotype matches:

Proximity score 0.506 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616294 Cole-Carpenter syndrome 2 - autosomal recessive; ORPHA:2050 Cole-Carpenter syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.098

Phenotype Score: 0.253

Variant Score: 0.919

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.118727561T>A [0/1] rs946687946 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: SEC24D:ENST00000280551.11:c.2958+1000A>T:p.(=); SEC24D:ENST00000511481.5:c.1851+1000A>T:p.(=)

Pathogenicity Data:: Best Score: 0.9189039; CADD: 0.919 (10.910)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.452

Phenotype Score: 0.506

Variant Score: 0.854

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.118727561T>A [0/1] rs946687946 (variation viewer)

Variant score: 0.919 CONTRIBUTING VARIANT

Transcripts:: SEC24D:ENST00000280551.11:c.2958+1000A>T:p.(=); SEC24D:ENST00000511481.5:c.1851+1000A>T:p.(=)

Pathogenicity Data:: Best Score: 0.9189039; CADD: 0.919 (10.910)

Frequency Data:: TOPMed: 0.0016%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.118764664G>A [0/1] rs887768558 (variation viewer)

Variant score: 0.788 CONTRIBUTING VARIANT

Transcripts:: SEC24D:ENST00000280551.11:c.1296+138C>T:p.(=); SEC24D:ENST00000511481.5:c.189+138C>T:p.(=); SEC24D:ENST00000419654.6:c.-37+138C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7886511; CADD: 0.789 (6.750)

Frequency Data:: TOPMed: 0.0024%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.118759063T>C [0/1] rs539235013 (variation viewer)

Variant score: 0.719

Transcripts:: SEC24D:ENST00000280551.11:c.1297-1218A>G:p.(=); SEC24D:ENST00000511481.5:c.190-1218A>G:p.(=); SEC24D:ENST00000419654.6:c.-36-1218A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7636803; CADD: 0.764 (6.265)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0558%; UK10K: 0.0926%; gnomAD_G_AMR: 0.3580%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.118822925T>C [0/1] rs545586847 (variation viewer)

Variant score: 0.500

Transcripts:: SEC24D:ENST00000280551.11:c.248+1695A>G:p.(=); SEC24D:ENST00000419654.6:c.-1085+1695A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5013452; CADD: 0.501 (3.022)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0040%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.118735941G>A [0/1] rs184775802 (variation viewer)

Variant score: 0.271

Transcripts:: SEC24D:ENST00000280551.11:c.2496+2320C>T:p.(=); SEC24D:ENST00000511481.5:c.1389+2320C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2725553; CADD: 0.273 (1.382)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0200%; UK10K: 0.0529%; gnomAD_G_NFE: 0.0270%

PIK3R5

Exomiser Score: 0.449

Phenotype Score: 0.507

Variant Score: 0.851

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615217 Ataxia-oculomotor apraxia 3 - autosomal recessive; ORPHA:64753 Spinocerebellar ataxia with axonal neuropathy type 2

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.090

Phenotype Score: 0.253

Variant Score: 0.908

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.8928309G>A [0/1] rs567706014 (variation viewer)

Variant score: 0.908 CONTRIBUTING VARIANT

Transcripts:: PIK3R5:ENST00000447110.5:c.-13-16802C>T:p.(=); PIK3R5:ENST00000611902.4:c.-1017-16802C>T:p.(=); PIK3R5:ENST00000616147.4:c.-1055-19135C>T:p.(=); PIK3R5:ENST00000623421.3:c.-996-16802C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9154721; CADD: 0.915 (10.730)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.449

Phenotype Score: 0.507

Variant Score: 0.851

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.8928309G>A [0/1] rs567706014 (variation viewer)

Variant score: 0.908 CONTRIBUTING VARIANT

Transcripts:: PIK3R5:ENST00000447110.5:c.-13-16802C>T:p.(=); PIK3R5:ENST00000611902.4:c.-1017-16802C>T:p.(=); PIK3R5:ENST00000616147.4:c.-1055-19135C>T:p.(=); PIK3R5:ENST00000623421.3:c.-996-16802C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9154721; CADD: 0.915 (10.730)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0016%

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.8965001CCA>C [-/1] rs10680170 (variation viewer)

Variant score: 0.794 CONTRIBUTING VARIANT

Transcripts:: PIK3R5:ENST00000447110.5:c.-14+593_-14+594del:p.(=); PIK3R5:ENST00000611902.4:c.-1018+593_-1018+594del:p.(=); PIK3R5:ENST00000616147.4:c.-1056+593_-1056+594del:p.(=); PIK3R5:ENST00000623421.3:c.-997+593_-997+594del:p.(=)

Pathogenicity Data:: Best Score: 0.79431623; CADD: 0.794 (6.868)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.8905216T>TGTATAATGGTCTTCAATGCCTAAACCACCTTTACTTAAATAGCCTCATTACAGGTAAATGTTTATTTTTTGAGGGCGGATTCAATGGTCTTCAGTGTTATGTTAC [0/1]

Variant score: 0.000

Transcripts:: PIK3R5:ENST00000447110.5:c.274-302_274-301insGTAACATAACACTGAAGACCATTGAATCCGCCCTCAAAAAATAAACATTTACCTGTAATGAGGCTATTTAAGTAAAGGTGGTTTAGGCATTGAAGACCATTATAC:p.(=); PIK3R5:ENST00000581552.5:c.274-302_274-301insGTAACATAACACTGAAGACCATTGAATCCGCCCTCAAAAAATAAACATTTACCTGTAATGAGGCTATTTAAGTAAAGGTGGTTTAGGCATTGAAGACCATTATAC:p.(=); PIK3R5:ENST00000584803.1:c.274-302_274-301insGTAACATAACACTGAAGACCATTGAATCCGCCCTCAAAAAATAAACATTTACCTGTAATGAGGCTATTTAAGTAAAGGTGGTTTAGGCATTGAAGACCATTATAC:p.(=); PIK3R5:ENST00000611902.4:c.-731-302_-731-301insGTAACATAACACTGAAGACCATTGAATCCGCCCTCAAAAAATAAACATTTACCTGTAATGAGGCTATTTAAGTAAAGGTGGTTTAGGCATTGAAGACCATTATAC:p.(=); PIK3R5:ENST00000616147.4:c.-885-302_-885-301insGTAACATAACACTGAAGACCATTGAATCCGCCCTCAAAAAATAAACATTTACCTGTAATGAGGCTATTTAAGTAAAGGTGGTTTAGGCATTGAAGACCATTATAC:p.(=); PIK3R5:ENST00000623421.3:c.-710-302_-710-301insGTAACATAACACTGAAGACCATTGAATCCGCCCTCAAAAAATAAACATTTACCTGTAATGAGGCTATTTAAGTAAAGGTGGTTTAGGCATTGAAGACCATTATAC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MAPK10

Exomiser Score: 0.449

Phenotype Score: 0.502

Variant Score: 0.857

Phenotype matches:

Phenotypic similarity 0.479 to Lennox-Gastaut syndrome associated with MAPK10.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0012075, Personality disorder

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:2382 Lennox-Gastaut syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.449

Phenotype Score: 0.502

Variant Score: 0.857

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86517269CT>C [0/1] rs1176457005 (variation viewer)

Variant score: 0.857 CONTRIBUTING VARIANT

Transcripts:: MAPK10:ENST00000513186.7:c.-122+76640del:p.(=); MAPK10:ENST00000515400.3:c.-158-64089del:p.(=); MAPK10:ENST00000641050.1:c.-273-64089del:p.(=); MAPK10:ENST00000641051.1:c.-273-64089del:p.(=); MAPK10:ENST00000641157.1:c.-182+76640del:p.(=); MAPK10:ENST00000641391.1:c.-299-64089del:p.(=); MAPK10:ENST00000641737.1:c.-414-64089del:p.(=); MAPK10:ENST00000641831.1:c.-427-64089del:p.(=)

Pathogenicity Data:: Best Score: 0.856946; CADD: 0.857 (8.445)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.055

Phenotype Score: 0.251

Variant Score: 0.852

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86517269CT>C [0/1] rs1176457005 (variation viewer)

Variant score: 0.857 CONTRIBUTING VARIANT

Transcripts:: MAPK10:ENST00000513186.7:c.-122+76640del:p.(=); MAPK10:ENST00000515400.3:c.-158-64089del:p.(=); MAPK10:ENST00000641050.1:c.-273-64089del:p.(=); MAPK10:ENST00000641051.1:c.-273-64089del:p.(=); MAPK10:ENST00000641157.1:c.-182+76640del:p.(=); MAPK10:ENST00000641391.1:c.-299-64089del:p.(=); MAPK10:ENST00000641737.1:c.-414-64089del:p.(=); MAPK10:ENST00000641831.1:c.-427-64089del:p.(=)

Pathogenicity Data:: Best Score: 0.856946; CADD: 0.857 (8.445)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86506241C>T [0/1] rs528917315 (variation viewer)

Variant score: 0.848 CONTRIBUTING VARIANT

Transcripts:: MAPK10:ENST00000513186.7:c.-122+87669G>A:p.(=); MAPK10:ENST00000515400.3:c.-158-53060G>A:p.(=); MAPK10:ENST00000641050.1:c.-273-53060G>A:p.(=); MAPK10:ENST00000641051.1:c.-273-53060G>A:p.(=); MAPK10:ENST00000641157.1:c.-182+87669G>A:p.(=); MAPK10:ENST00000641391.1:c.-299-53060G>A:p.(=); MAPK10:ENST00000641737.1:c.-414-53060G>A:p.(=); MAPK10:ENST00000641831.1:c.-427-53060G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8522934; CADD: 0.852 (8.306)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0199%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0333%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86342148C>T [0/1] rs943783998 (variation viewer)

Variant score: 0.805

Transcripts:: MAPK10:ENST00000641020.1:c.59+12382G>A:p.(=); MAPK10:ENST00000641459.1:c.3+17510G>A:p.(=); MAPK10:ENST00000641677.1:c.3+17510G>A:p.(=); MAPK10:ENST00000359221.8:c.-148+12382G>A:p.(=); MAPK10:ENST00000361569.8:c.-7+12382G>A:p.(=); MAPK10:ENST00000395157.9:c.-7+12382G>A:p.(=); MAPK10:ENST00000395160.9:c.-7+12382G>A:p.(=); MAPK10:ENST00000395166.6:c.-148+12382G>A:p.(=); MAPK10:ENST00000395169.9:c.-7+12382G>A:p.(=); MAPK10:ENST00000511167.6:c.-7+12382G>A:p.(=); MAPK10:ENST00000512689.6:c.-148+12382G>A:p.(=); MAPK10:ENST00000513186.7:c.-7+12382G>A:p.(=); MAPK10:ENST00000515400.3:c.-7+110882G>A:p.(=); MAPK10:ENST00000515650.2:c.-7+12382G>A:p.(=); MAPK10:ENST00000638225.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000638313.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000639175.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000639234.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000639242.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000639972.2:c.-148+12382G>A:p.(=); MAPK10:ENST00000640490.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000640858.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000640970.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641010.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641047.1:c.-179+12382G>A:p.(=); MAPK10:ENST00000641050.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641051.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641052.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641066.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641102.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641110.1:c.-148+10017G>A:p.(=); MAPK10:ENST00000641120.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641157.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641166.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641170.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641207.1:c.-91-1725G>A:p.(=); MAPK10:ENST00000641208.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641217.1:c.-206+12382G>A:p.(=); MAPK10:ENST00000641274.1:c.-7+87530G>A:p.(=); MAPK10:ENST00000641283.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641287.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641297.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641313.1:c.-49+12382G>A:p.(=); MAPK10:ENST00000641324.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641341.1:c.-193+12382G>A:p.(=); MAPK10:ENST00000641384.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641391.1:c.-148+110882G>A:p.(=); MAPK10:ENST00000641405.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641462.2:c.-7+12382G>A:p.(=); MAPK10:ENST00000641485.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641493.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641537.1:c.-49+12382G>A:p.(=); MAPK10:ENST00000641553.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641555.1:c.-334+12382G>A:p.(=); MAPK10:ENST00000641607.1:c.-179+12382G>A:p.(=); MAPK10:ENST00000641647.1:c.-193+12382G>A:p.(=); MAPK10:ENST00000641657.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641718.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641724.1:c.-334+12382G>A:p.(=); MAPK10:ENST00000641737.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641762.1:c.-193+12382G>A:p.(=); MAPK10:ENST00000641767.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641777.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641803.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641823.1:c.-87-6992G>A:p.(=); MAPK10:ENST00000641831.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641862.1:c.-180-64925G>A:p.(=); MAPK10:ENST00000641864.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641902.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641903.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000641911.1:c.-148+17510G>A:p.(=); MAPK10:ENST00000641943.1:c.-322+12382G>A:p.(=); MAPK10:ENST00000641952.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641954.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641983.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000641989.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000642006.1:c.-206+12382G>A:p.(=); MAPK10:ENST00000642009.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000642013.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000642015.1:c.-49+12382G>A:p.(=); MAPK10:ENST00000642023.1:c.-148+12382G>A:p.(=); MAPK10:ENST00000642032.1:c.-322+12382G>A:p.(=); MAPK10:ENST00000642038.1:c.-7+12382G>A:p.(=); MAPK10:ENST00000642103.1:c.-76+12382G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8073363; CADD: 0.807 (7.152)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86417329A>G [0/1] rs559078195 (variation viewer)

Variant score: 0.766

Transcripts:: MAPK10:ENST00000361569.8:c.-122+35701T>C:p.(=); MAPK10:ENST00000395160.9:c.-122+35701T>C:p.(=); MAPK10:ENST00000513186.7:c.-121-62685T>C:p.(=); MAPK10:ENST00000515400.3:c.-7+35701T>C:p.(=); MAPK10:ENST00000639972.2:c.-263+35701T>C:p.(=); MAPK10:ENST00000641050.1:c.-122+35701T>C:p.(=); MAPK10:ENST00000641051.1:c.-122+35701T>C:p.(=); MAPK10:ENST00000641120.1:c.-263+35701T>C:p.(=); MAPK10:ENST00000641157.1:c.-181-17523T>C:p.(=); MAPK10:ENST00000641170.1:c.-122+35701T>C:p.(=); MAPK10:ENST00000641274.1:c.-7+12349T>C:p.(=); MAPK10:ENST00000641297.1:c.-322-17523T>C:p.(=); MAPK10:ENST00000641313.1:c.-164+35701T>C:p.(=); MAPK10:ENST00000641384.1:c.-263+35701T>C:p.(=); MAPK10:ENST00000641391.1:c.-148+35701T>C:p.(=); MAPK10:ENST00000641657.1:c.-263+35701T>C:p.(=); MAPK10:ENST00000641718.1:c.-122+35701T>C:p.(=); MAPK10:ENST00000641737.1:c.-263+35701T>C:p.(=); MAPK10:ENST00000641831.1:c.-276+35701T>C:p.(=); MAPK10:ENST00000641862.1:c.-181+35701T>C:p.(=); MAPK10:ENST00000641902.1:c.-181-17523T>C:p.(=); MAPK10:ENST00000641952.1:c.-122+35701T>C:p.(=); MAPK10:ENST00000642009.1:c.-417+35701T>C:p.(=); MAPK10:ENST00000642023.1:c.-263+35701T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7699618; CADD: 0.770 (6.382)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0263%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0333%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86508178T>C [0/1] rs577433686 (variation viewer)

Variant score: 0.664

Transcripts:: MAPK10:ENST00000513186.7:c.-122+85732A>G:p.(=); MAPK10:ENST00000515400.3:c.-158-54997A>G:p.(=); MAPK10:ENST00000641050.1:c.-273-54997A>G:p.(=); MAPK10:ENST00000641051.1:c.-273-54997A>G:p.(=); MAPK10:ENST00000641157.1:c.-182+85732A>G:p.(=); MAPK10:ENST00000641391.1:c.-299-54997A>G:p.(=); MAPK10:ENST00000641737.1:c.-414-54997A>G:p.(=); MAPK10:ENST00000641831.1:c.-427-54997A>G:p.(=)

Pathogenicity Data:: Best Score: 0.66818196; CADD: 0.668 (4.791)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0199%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0333%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86192641T>G [0/1] rs187165183 (variation viewer)

Variant score: 0.588

Transcripts:: MAPK10:ENST00000361569.8:c.66+1695A>C:p.(=); MAPK10:ENST00000395157.9:c.66+1695A>C:p.(=); MAPK10:ENST00000395160.9:c.66+1695A>C:p.(=); MAPK10:ENST00000395169.9:c.66+1695A>C:p.(=); MAPK10:ENST00000449047.8:c.66+1695A>C:p.(=); MAPK10:ENST00000511167.6:c.66+1695A>C:p.(=); MAPK10:ENST00000513186.7:c.66+1695A>C:p.(=); MAPK10:ENST00000515400.3:c.66+1695A>C:p.(=); MAPK10:ENST00000515650.2:c.66+1695A>C:p.(=); MAPK10:ENST00000638313.1:c.66+1695A>C:p.(=); MAPK10:ENST00000639234.1:c.66+1695A>C:p.(=); MAPK10:ENST00000640858.1:c.66+1695A>C:p.(=); MAPK10:ENST00000640970.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641010.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641020.1:c.60-85289A>C:p.(=); MAPK10:ENST00000641050.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641051.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641066.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641102.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641157.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641170.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641207.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641274.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641341.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641405.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641459.1:c.75+1695A>C:p.(=); MAPK10:ENST00000641462.2:c.66+1695A>C:p.(=); MAPK10:ENST00000641485.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641493.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641553.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641647.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641677.1:c.75+1695A>C:p.(=); MAPK10:ENST00000641718.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641762.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641777.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641823.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641831.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641862.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641902.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641952.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641954.1:c.66+1695A>C:p.(=); MAPK10:ENST00000641983.1:c.66+1695A>C:p.(=); MAPK10:ENST00000642013.1:c.66+1695A>C:p.(=); MAPK10:ENST00000642038.1:c.66+1695A>C:p.(=); MAPK10:ENST00000359221.8:c.-49+1668A>C:p.(=); MAPK10:ENST00000395166.6:c.-49+1668A>C:p.(=); MAPK10:ENST00000512689.6:c.-49+1668A>C:p.(=); MAPK10:ENST00000638225.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000639175.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000639242.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000639972.2:c.-49+1668A>C:p.(=); MAPK10:ENST00000640490.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641047.1:c.-107+1695A>C:p.(=); MAPK10:ENST00000641052.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641110.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641120.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641166.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641208.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641217.1:c.-107+1668A>C:p.(=); MAPK10:ENST00000641237.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641283.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641287.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641297.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641313.1:c.-48-33174A>C:p.(=); MAPK10:ENST00000641324.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641384.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641391.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641430.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641537.1:c.-48-33174A>C:p.(=); MAPK10:ENST00000641555.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641607.1:c.-107+1695A>C:p.(=); MAPK10:ENST00000641657.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641724.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641737.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641767.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641803.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641864.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641903.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641911.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641943.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000641989.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000642006.1:c.-107+1668A>C:p.(=); MAPK10:ENST00000642009.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000642015.1:c.-48-33174A>C:p.(=); MAPK10:ENST00000642023.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000642032.1:c.-49+1668A>C:p.(=); MAPK10:ENST00000642103.1:c.-49+1668A>C:p.(=)

Pathogenicity Data:: Best Score: 0.86707705; CADD: 0.867 (8.764)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.6650%; UK10K: 1.2166%; gnomAD_G_AFR: 0.2749%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 1.1162%; gnomAD_G_NFE: 1.1927%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86138511A>C [0/1] rs1196050903 (variation viewer)

Variant score: 0.556

Transcripts:: MAPK10:ENST00000359221.8:c.122+20787T>G:p.(=); MAPK10:ENST00000361569.8:c.236+20787T>G:p.(=); MAPK10:ENST00000395157.9:c.236+20787T>G:p.(=); MAPK10:ENST00000395160.9:c.236+20787T>G:p.(=); MAPK10:ENST00000395166.6:c.122+20787T>G:p.(=); MAPK10:ENST00000395169.9:c.236+20787T>G:p.(=); MAPK10:ENST00000449047.8:c.236+20787T>G:p.(=); MAPK10:ENST00000511167.6:c.236+20787T>G:p.(=); MAPK10:ENST00000512689.6:c.122+20787T>G:p.(=); MAPK10:ENST00000513186.7:c.236+20787T>G:p.(=); MAPK10:ENST00000515400.3:c.236+20787T>G:p.(=); MAPK10:ENST00000515650.2:c.236+20787T>G:p.(=); MAPK10:ENST00000638225.1:c.122+20787T>G:p.(=); MAPK10:ENST00000638313.1:c.236+20787T>G:p.(=); MAPK10:ENST00000639175.1:c.122+20787T>G:p.(=); MAPK10:ENST00000639234.1:c.236+20787T>G:p.(=); MAPK10:ENST00000639242.1:c.122+20787T>G:p.(=); MAPK10:ENST00000639972.2:c.122+20787T>G:p.(=); MAPK10:ENST00000640490.1:c.122+20787T>G:p.(=); MAPK10:ENST00000640858.1:c.236+20787T>G:p.(=); MAPK10:ENST00000640970.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641010.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641020.1:c.60-31159T>G:p.(=); MAPK10:ENST00000641050.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641051.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641052.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641066.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641102.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641110.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641120.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641157.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641166.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641170.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641207.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641208.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641237.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641274.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641283.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641287.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641297.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641313.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641324.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641341.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641384.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641391.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641405.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641430.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641459.1:c.245+20787T>G:p.(=); MAPK10:ENST00000641462.2:c.236+20787T>G:p.(=); MAPK10:ENST00000641485.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641493.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641537.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641553.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641555.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641647.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641657.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641677.1:c.245+20787T>G:p.(=); MAPK10:ENST00000641718.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641724.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641737.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641762.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641767.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641803.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641823.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641831.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641862.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641864.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641902.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641903.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641911.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641943.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641952.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641954.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641983.1:c.236+20787T>G:p.(=); MAPK10:ENST00000641989.1:c.122+20787T>G:p.(=); MAPK10:ENST00000642009.1:c.122+20787T>G:p.(=); MAPK10:ENST00000642013.1:c.236+20787T>G:p.(=); MAPK10:ENST00000642015.1:c.122+20787T>G:p.(=); MAPK10:ENST00000642023.1:c.122+20787T>G:p.(=); MAPK10:ENST00000642032.1:c.122+20787T>G:p.(=); MAPK10:ENST00000642038.1:c.236+20787T>G:p.(=); MAPK10:ENST00000642103.1:c.122+20787T>G:p.(=); MAPK10:ENST00000641047.1:c.-106-31159T>G:p.(=); MAPK10:ENST00000641217.1:c.-106-31159T>G:p.(=); MAPK10:ENST00000641607.1:c.-106-31159T>G:p.(=); MAPK10:ENST00000642006.1:c.-106-31159T>G:p.(=)

Pathogenicity Data:: Best Score: 0.5604584; CADD: 0.560 (3.570)

Frequency Data:: gnomAD_G_AFR: 0.0125%; gnomAD_G_NFE: 0.0559%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86465924A>G [0/1] rs974269442 (variation viewer)

Variant score: 0.502

Transcripts:: MAPK10:ENST00000513186.7:c.-121-111280T>C:p.(=); MAPK10:ENST00000515400.3:c.-158-12743T>C:p.(=); MAPK10:ENST00000641050.1:c.-273-12743T>C:p.(=); MAPK10:ENST00000641051.1:c.-273-12743T>C:p.(=); MAPK10:ENST00000641157.1:c.-181-66118T>C:p.(=); MAPK10:ENST00000641391.1:c.-299-12743T>C:p.(=); MAPK10:ENST00000641737.1:c.-414-12743T>C:p.(=); MAPK10:ENST00000641831.1:c.-427-12743T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5023775; CADD: 0.502 (3.031)

Frequency Data:: TOPMed: 0.0016%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86063669A>G [0/1] rs114752552 (variation viewer)

Variant score: 0.499

Transcripts:: MAPK10:ENST00000359221.8:c.996+597T>C:p.(=); MAPK10:ENST00000361569.8:c.1110+597T>C:p.(=); MAPK10:ENST00000395157.9:c.1110+597T>C:p.(=); MAPK10:ENST00000395160.9:c.1110+597T>C:p.(=); MAPK10:ENST00000395166.6:c.996+597T>C:p.(=); MAPK10:ENST00000395169.9:c.1110+597T>C:p.(=); MAPK10:ENST00000449047.8:c.1110+597T>C:p.(=); MAPK10:ENST00000512689.6:c.996+597T>C:p.(=); MAPK10:ENST00000513186.7:c.367-32238T>C:p.(=); MAPK10:ENST00000515400.3:c.1110+597T>C:p.(=); MAPK10:ENST00000515650.2:c.1110+597T>C:p.(=); MAPK10:ENST00000638225.1:c.996+597T>C:p.(=); MAPK10:ENST00000638313.1:c.1110+597T>C:p.(=); MAPK10:ENST00000639175.1:c.996+597T>C:p.(=); MAPK10:ENST00000639234.1:c.1110+597T>C:p.(=); MAPK10:ENST00000639242.1:c.996+597T>C:p.(=); MAPK10:ENST00000639972.2:c.996+597T>C:p.(=); MAPK10:ENST00000640490.1:c.996+597T>C:p.(=); MAPK10:ENST00000640858.1:c.1110+597T>C:p.(=); MAPK10:ENST00000640970.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641010.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641020.1:c.933+597T>C:p.(=); MAPK10:ENST00000641047.1:c.768+597T>C:p.(=); MAPK10:ENST00000641050.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641051.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641052.1:c.996+597T>C:p.(=); MAPK10:ENST00000641066.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641102.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641110.1:c.996+597T>C:p.(=); MAPK10:ENST00000641120.1:c.996+597T>C:p.(=); MAPK10:ENST00000641157.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641166.1:c.996+597T>C:p.(=); MAPK10:ENST00000641170.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641207.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641208.1:c.996+597T>C:p.(=); MAPK10:ENST00000641217.1:c.768+597T>C:p.(=); MAPK10:ENST00000641237.1:c.996+597T>C:p.(=); MAPK10:ENST00000641274.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641283.1:c.996+597T>C:p.(=); MAPK10:ENST00000641287.1:c.996+597T>C:p.(=); MAPK10:ENST00000641297.1:c.996+597T>C:p.(=); MAPK10:ENST00000641313.1:c.996+597T>C:p.(=); MAPK10:ENST00000641324.1:c.996+597T>C:p.(=); MAPK10:ENST00000641341.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641384.1:c.924+597T>C:p.(=); MAPK10:ENST00000641391.1:c.996+597T>C:p.(=); MAPK10:ENST00000641405.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641430.1:c.996+597T>C:p.(=); MAPK10:ENST00000641459.1:c.1119+597T>C:p.(=); MAPK10:ENST00000641462.2:c.1110+597T>C:p.(=); MAPK10:ENST00000641485.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641493.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641537.1:c.996+597T>C:p.(=); MAPK10:ENST00000641553.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641555.1:c.996+597T>C:p.(=); MAPK10:ENST00000641607.1:c.768+597T>C:p.(=); MAPK10:ENST00000641647.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641657.1:c.996+597T>C:p.(=); MAPK10:ENST00000641677.1:c.1119+597T>C:p.(=); MAPK10:ENST00000641718.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641724.1:c.996+597T>C:p.(=); MAPK10:ENST00000641737.1:c.996+597T>C:p.(=); MAPK10:ENST00000641762.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641767.1:c.996+597T>C:p.(=); MAPK10:ENST00000641803.1:c.996+597T>C:p.(=); MAPK10:ENST00000641823.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641831.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641862.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641864.1:c.996+597T>C:p.(=); MAPK10:ENST00000641902.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641903.1:c.996+597T>C:p.(=); MAPK10:ENST00000641911.1:c.996+597T>C:p.(=); MAPK10:ENST00000641943.1:c.996+597T>C:p.(=); MAPK10:ENST00000641952.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641954.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641983.1:c.1110+597T>C:p.(=); MAPK10:ENST00000641989.1:c.996+597T>C:p.(=); MAPK10:ENST00000642006.1:c.768+597T>C:p.(=); MAPK10:ENST00000642009.1:c.996+597T>C:p.(=); MAPK10:ENST00000642013.1:c.1110+597T>C:p.(=); MAPK10:ENST00000642015.1:c.996+597T>C:p.(=); MAPK10:ENST00000642023.1:c.924+597T>C:p.(=); MAPK10:ENST00000642032.1:c.996+597T>C:p.(=); MAPK10:ENST00000642038.1:c.1110+597T>C:p.(=); MAPK10:ENST00000642103.1:c.996+597T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6736377; CADD: 0.674 (4.863)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.6180%; UK10K: 1.0711%; gnomAD_G_AFR: 0.2636%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 1.0046%; gnomAD_G_NFE: 1.0472%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86001870G>A [0|1] rs114726604 (variation viewer)

Variant score: 0.467

Transcripts:: MAPK10:ENST00000641010.1:c.1392-9707C>T:p.(=); MAPK10:ENST00000641102.1:c.1392-393C>T:p.(=); MAPK10:ENST00000641324.1:c.1278-9707C>T:p.(=); MAPK10:ENST00000264343.4:c.*1148G>A:p.(=); MAPK10:ENST00000395184.6:c.*1148G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4844153; CADD: 0.484 (2.877)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0645%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.0466%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86173925C>T [0/1] rs187052375 (variation viewer)

Variant score: 0.433

Transcripts:: MAPK10:ENST00000361569.8:c.67-14458G>A:p.(=); MAPK10:ENST00000395157.9:c.67-14458G>A:p.(=); MAPK10:ENST00000395160.9:c.67-14458G>A:p.(=); MAPK10:ENST00000395169.9:c.67-14458G>A:p.(=); MAPK10:ENST00000449047.8:c.67-14458G>A:p.(=); MAPK10:ENST00000511167.6:c.67-14458G>A:p.(=); MAPK10:ENST00000513186.7:c.67-14458G>A:p.(=); MAPK10:ENST00000515400.3:c.67-14458G>A:p.(=); MAPK10:ENST00000515650.2:c.67-14458G>A:p.(=); MAPK10:ENST00000638313.1:c.67-14458G>A:p.(=); MAPK10:ENST00000639234.1:c.67-14458G>A:p.(=); MAPK10:ENST00000640858.1:c.67-14458G>A:p.(=); MAPK10:ENST00000640970.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641010.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641020.1:c.60-66573G>A:p.(=); MAPK10:ENST00000641050.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641051.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641066.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641102.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641157.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641170.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641207.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641274.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641341.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641405.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641459.1:c.76-14458G>A:p.(=); MAPK10:ENST00000641462.2:c.67-14458G>A:p.(=); MAPK10:ENST00000641485.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641493.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641553.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641647.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641677.1:c.76-14458G>A:p.(=); MAPK10:ENST00000641718.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641762.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641777.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641823.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641831.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641862.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641902.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641952.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641954.1:c.67-14458G>A:p.(=); MAPK10:ENST00000641983.1:c.67-14458G>A:p.(=); MAPK10:ENST00000642013.1:c.67-14458G>A:p.(=); MAPK10:ENST00000642038.1:c.67-14458G>A:p.(=); MAPK10:ENST00000359221.8:c.-48-14458G>A:p.(=); MAPK10:ENST00000395166.6:c.-48-14458G>A:p.(=); MAPK10:ENST00000512689.6:c.-48-14458G>A:p.(=); MAPK10:ENST00000638225.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000639175.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000639242.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000639972.2:c.-48-14458G>A:p.(=); MAPK10:ENST00000640490.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641047.1:c.-107+20411G>A:p.(=); MAPK10:ENST00000641052.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641110.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641120.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641166.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641208.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641217.1:c.-107+20384G>A:p.(=); MAPK10:ENST00000641237.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641283.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641287.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641297.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641313.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641324.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641384.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641391.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641430.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641537.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641555.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641607.1:c.-107+20411G>A:p.(=); MAPK10:ENST00000641657.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641724.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641737.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641767.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641803.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641864.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641903.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641911.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641943.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000641989.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000642006.1:c.-107+20384G>A:p.(=); MAPK10:ENST00000642009.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000642015.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000642023.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000642032.1:c.-48-14458G>A:p.(=); MAPK10:ENST00000642103.1:c.-48-14458G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6850802; CADD: 0.685 (5.018)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.6626%; UK10K: 1.1902%; gnomAD_G_AFR: 0.3706%; gnomAD_G_AMR: 0.1323%; gnomAD_G_FIN: 1.1963%; gnomAD_G_NFE: 1.3135%; gnomAD_G_OTH: 0.6881%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86001875A>G [0|1] rs145127332 (variation viewer)

Variant score: 0.433

Transcripts:: MAPK10:ENST00000641010.1:c.1392-9712T>C:p.(=); MAPK10:ENST00000641102.1:c.1392-398T>C:p.(=); MAPK10:ENST00000641324.1:c.1278-9712T>C:p.(=); MAPK10:ENST00000264343.4:c.*1153A>G:p.(=); MAPK10:ENST00000395184.6:c.*1153A>G:p.(=)

Pathogenicity Data:: Best Score: 0.44931912; CADD: 0.449 (2.591)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0645%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.0466%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86105264G>A [0/1] rs538043259 (variation viewer)

Variant score: 0.427

Transcripts:: MAPK10:ENST00000359221.8:c.252+1959C>T:p.(=); MAPK10:ENST00000361569.8:c.366+1959C>T:p.(=); MAPK10:ENST00000395157.9:c.366+1959C>T:p.(=); MAPK10:ENST00000395160.9:c.366+1959C>T:p.(=); MAPK10:ENST00000395166.6:c.252+1959C>T:p.(=); MAPK10:ENST00000395169.9:c.366+1959C>T:p.(=); MAPK10:ENST00000449047.8:c.366+1959C>T:p.(=); MAPK10:ENST00000511167.6:c.366+1959C>T:p.(=); MAPK10:ENST00000512689.6:c.252+1959C>T:p.(=); MAPK10:ENST00000513186.7:c.366+1959C>T:p.(=); MAPK10:ENST00000515400.3:c.366+1959C>T:p.(=); MAPK10:ENST00000515650.2:c.366+1959C>T:p.(=); MAPK10:ENST00000638225.1:c.252+1959C>T:p.(=); MAPK10:ENST00000638313.1:c.366+1959C>T:p.(=); MAPK10:ENST00000639175.1:c.252+1959C>T:p.(=); MAPK10:ENST00000639234.1:c.366+1959C>T:p.(=); MAPK10:ENST00000639242.1:c.252+1959C>T:p.(=); MAPK10:ENST00000639972.2:c.252+1959C>T:p.(=); MAPK10:ENST00000640490.1:c.252+1959C>T:p.(=); MAPK10:ENST00000640858.1:c.366+1959C>T:p.(=); MAPK10:ENST00000640970.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641010.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641020.1:c.189+1959C>T:p.(=); MAPK10:ENST00000641047.1:c.24+1959C>T:p.(=); MAPK10:ENST00000641050.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641051.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641052.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641066.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641102.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641110.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641120.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641157.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641166.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641170.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641207.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641208.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641217.1:c.24+1959C>T:p.(=); MAPK10:ENST00000641237.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641274.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641283.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641287.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641297.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641313.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641324.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641341.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641384.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641391.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641405.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641430.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641459.1:c.375+1959C>T:p.(=); MAPK10:ENST00000641462.2:c.366+1959C>T:p.(=); MAPK10:ENST00000641485.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641493.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641537.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641553.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641555.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641607.1:c.24+1959C>T:p.(=); MAPK10:ENST00000641647.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641657.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641677.1:c.375+1959C>T:p.(=); MAPK10:ENST00000641718.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641724.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641737.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641762.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641767.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641803.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641823.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641831.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641862.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641864.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641902.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641903.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641911.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641943.1:c.252+1959C>T:p.(=); MAPK10:ENST00000641952.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641954.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641983.1:c.366+1959C>T:p.(=); MAPK10:ENST00000641989.1:c.252+1959C>T:p.(=); MAPK10:ENST00000642006.1:c.24+1959C>T:p.(=); MAPK10:ENST00000642009.1:c.252+1959C>T:p.(=); MAPK10:ENST00000642013.1:c.366+1959C>T:p.(=); MAPK10:ENST00000642015.1:c.252+1959C>T:p.(=); MAPK10:ENST00000642023.1:c.252+1959C>T:p.(=); MAPK10:ENST00000642032.1:c.252+1959C>T:p.(=); MAPK10:ENST00000642038.1:c.366+1959C>T:p.(=); MAPK10:ENST00000642103.1:c.252+1959C>T:p.(=)

Pathogenicity Data:: Best Score: 0.43271667; CADD: 0.433 (2.462)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0279%; UK10K: 0.0926%; gnomAD_G_NFE: 0.0534%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86390391CT>C [0/1] rs566409689 (variation viewer)

Variant score: 0.424

Transcripts:: MAPK10:ENST00000361569.8:c.-121-35748del:p.(=); MAPK10:ENST00000395160.9:c.-121-35748del:p.(=); MAPK10:ENST00000513186.7:c.-121-35748del:p.(=); MAPK10:ENST00000515400.3:c.-7+62638del:p.(=); MAPK10:ENST00000639972.2:c.-262-35748del:p.(=); MAPK10:ENST00000641050.1:c.-121-35748del:p.(=); MAPK10:ENST00000641051.1:c.-121-35748del:p.(=); MAPK10:ENST00000641120.1:c.-262-35748del:p.(=); MAPK10:ENST00000641157.1:c.-122+9355del:p.(=); MAPK10:ENST00000641170.1:c.-121-35748del:p.(=); MAPK10:ENST00000641274.1:c.-7+39286del:p.(=); MAPK10:ENST00000641297.1:c.-263+9355del:p.(=); MAPK10:ENST00000641313.1:c.-163-35748del:p.(=); MAPK10:ENST00000641384.1:c.-262-35748del:p.(=); MAPK10:ENST00000641391.1:c.-148+62638del:p.(=); MAPK10:ENST00000641657.1:c.-262-35748del:p.(=); MAPK10:ENST00000641718.1:c.-121-35748del:p.(=); MAPK10:ENST00000641737.1:c.-262-35748del:p.(=); MAPK10:ENST00000641831.1:c.-275-19525del:p.(=); MAPK10:ENST00000641862.1:c.-181+62638del:p.(=); MAPK10:ENST00000641902.1:c.-122+9355del:p.(=); MAPK10:ENST00000641952.1:c.-121-35748del:p.(=); MAPK10:ENST00000642009.1:c.-416-19525del:p.(=); MAPK10:ENST00000642023.1:c.-262-35748del:p.(=)

Pathogenicity Data:: Best Score: 0.4264121; CADD: 0.426 (2.414)

Frequency Data:: TOPMed: 0.0191%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0333%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86251145T>TTTTTA [0/1] rs71657510 (variation viewer)

Variant score: 0.364

Transcripts:: MAPK10:ENST00000641020.1:c.59+103384_59+103385insTAAAA:p.(=); MAPK10:ENST00000641459.1:c.4-56739_4-56738insTAAAA:p.(=); MAPK10:ENST00000641677.1:c.4-56739_4-56738insTAAAA:p.(=); MAPK10:ENST00000359221.8:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000361569.8:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000395157.9:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000395160.9:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000395166.6:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000395169.9:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000511167.6:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000512689.6:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000513186.7:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000515400.3:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000515650.2:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000638225.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000638313.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000639175.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000639234.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000639242.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000639972.2:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000640490.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000640858.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000640970.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641010.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641047.1:c.-178-56739_-178-56738insTAAAA:p.(=); MAPK10:ENST00000641050.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641051.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641052.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641066.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641102.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641110.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641120.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641157.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641166.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641170.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641207.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641208.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641217.1:c.-205-56739_-205-56738insTAAAA:p.(=); MAPK10:ENST00000641237.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641274.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641283.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641287.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641297.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641313.1:c.-48-91679_-48-91678insTAAAA:p.(=); MAPK10:ENST00000641324.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641341.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641384.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641391.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641405.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641430.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641462.2:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641485.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641493.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641537.1:c.-48-91679_-48-91678insTAAAA:p.(=); MAPK10:ENST00000641553.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641555.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641607.1:c.-178-56739_-178-56738insTAAAA:p.(=); MAPK10:ENST00000641647.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641657.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641718.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641724.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641737.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641762.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641767.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641777.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641803.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641823.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641831.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641862.1:c.-7+25904_-7+25905insTAAAA:p.(=); MAPK10:ENST00000641864.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641902.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641903.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641911.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000641943.1:c.-148+25904_-148+25905insTAAAA:p.(=); MAPK10:ENST00000641952.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641954.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641983.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000641989.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000642006.1:c.-205-56739_-205-56738insTAAAA:p.(=); MAPK10:ENST00000642009.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000642013.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000642015.1:c.-48-91679_-48-91678insTAAAA:p.(=); MAPK10:ENST00000642023.1:c.-147-56739_-147-56738insTAAAA:p.(=); MAPK10:ENST00000642032.1:c.-148+25904_-148+25905insTAAAA:p.(=); MAPK10:ENST00000642038.1:c.-6-56739_-6-56738insTAAAA:p.(=); MAPK10:ENST00000642103.1:c.-75-56811_-75-56810insTAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.516162; CADD: 0.516 (3.153)

Frequency Data:: UK10K: 0.8728%; gnomAD_G_AFR: 0.3376%; gnomAD_G_AMR: 0.8557%; gnomAD_G_EAS: 1.0533%; gnomAD_G_FIN: 1.1559%; gnomAD_G_NFE: 1.0969%; gnomAD_G_OTH: 0.8264%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86002786C>G [0/1] rs555016927 (variation viewer)

Variant score: 0.354

Transcripts:: MAPK10:ENST00000641010.1:c.1392-10623G>C:p.(=); MAPK10:ENST00000641102.1:c.1392-1309G>C:p.(=); MAPK10:ENST00000641324.1:c.1278-10623G>C:p.(=)

Pathogenicity Data:: Best Score: 0.36758816; CADD: 0.368 (1.990)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0645%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.2451%; gnomAD_G_NFE: 0.0474%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86182509C>G [0/1] rs538746791 (variation viewer)

Variant score: 0.295

Transcripts:: MAPK10:ENST00000361569.8:c.66+11827G>C:p.(=); MAPK10:ENST00000395157.9:c.66+11827G>C:p.(=); MAPK10:ENST00000395160.9:c.66+11827G>C:p.(=); MAPK10:ENST00000395169.9:c.66+11827G>C:p.(=); MAPK10:ENST00000449047.8:c.66+11827G>C:p.(=); MAPK10:ENST00000511167.6:c.66+11827G>C:p.(=); MAPK10:ENST00000513186.7:c.66+11827G>C:p.(=); MAPK10:ENST00000515400.3:c.66+11827G>C:p.(=); MAPK10:ENST00000515650.2:c.66+11827G>C:p.(=); MAPK10:ENST00000638313.1:c.66+11827G>C:p.(=); MAPK10:ENST00000639234.1:c.66+11827G>C:p.(=); MAPK10:ENST00000640858.1:c.66+11827G>C:p.(=); MAPK10:ENST00000640970.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641010.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641020.1:c.60-75157G>C:p.(=); MAPK10:ENST00000641050.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641051.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641066.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641102.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641157.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641170.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641207.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641274.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641341.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641405.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641459.1:c.75+11827G>C:p.(=); MAPK10:ENST00000641462.2:c.66+11827G>C:p.(=); MAPK10:ENST00000641485.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641493.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641553.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641647.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641677.1:c.75+11827G>C:p.(=); MAPK10:ENST00000641718.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641762.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641777.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641823.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641831.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641862.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641902.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641952.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641954.1:c.66+11827G>C:p.(=); MAPK10:ENST00000641983.1:c.66+11827G>C:p.(=); MAPK10:ENST00000642013.1:c.66+11827G>C:p.(=); MAPK10:ENST00000642038.1:c.66+11827G>C:p.(=); MAPK10:ENST00000359221.8:c.-49+11800G>C:p.(=); MAPK10:ENST00000395166.6:c.-49+11800G>C:p.(=); MAPK10:ENST00000512689.6:c.-49+11800G>C:p.(=); MAPK10:ENST00000638225.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000639175.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000639242.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000639972.2:c.-49+11800G>C:p.(=); MAPK10:ENST00000640490.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641047.1:c.-107+11827G>C:p.(=); MAPK10:ENST00000641052.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641110.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641120.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641166.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641208.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641217.1:c.-107+11800G>C:p.(=); MAPK10:ENST00000641237.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641283.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641287.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641297.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641313.1:c.-48-23042G>C:p.(=); MAPK10:ENST00000641324.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641384.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641391.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641430.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641537.1:c.-48-23042G>C:p.(=); MAPK10:ENST00000641555.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641607.1:c.-107+11827G>C:p.(=); MAPK10:ENST00000641657.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641724.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641737.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641767.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641803.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641864.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641903.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641911.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641943.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000641989.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000642006.1:c.-107+11800G>C:p.(=); MAPK10:ENST00000642009.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000642015.1:c.-48-23042G>C:p.(=); MAPK10:ENST00000642023.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000642032.1:c.-49+11800G>C:p.(=); MAPK10:ENST00000642103.1:c.-49+11800G>C:p.(=)

Pathogenicity Data:: Best Score: 0.50625813; CADD: 0.506 (3.065)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.3369%; UK10K: 0.7141%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.4785%; gnomAD_G_FIN: 1.4080%; gnomAD_G_NFE: 0.6287%; gnomAD_G_OTH: 0.3080%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.85998831C>T [0/1] rs190131723 (variation viewer)

Variant score: 0.268

Transcripts:: MAPK10:ENST00000641010.1:c.1392-6668G>A:p.(=); MAPK10:ENST00000641324.1:c.1278-6668G>A:p.(=); MAPK10:ENST00000264343.4:c.1725-1648C>T:p.(=); MAPK10:ENST00000395183.6:c.1719-1648C>T:p.(=); MAPK10:ENST00000395184.6:c.2004-1648C>T:p.(=)

Pathogenicity Data:: Best Score: 0.27839422; CADD: 0.278 (1.417)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0669%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.0467%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86579516TACAC>T [-/1] rs35878270 (variation viewer)

Variant score: 0.260

Transcripts:: MAPK10:ENST00000513186.7:c.-122+14390_-122+14393del:p.(=); MAPK10:ENST00000515400.3:c.-159+14390_-159+14393del:p.(=); MAPK10:ENST00000641050.1:c.-274+14390_-274+14393del:p.(=); MAPK10:ENST00000641051.1:c.-274+14390_-274+14393del:p.(=); MAPK10:ENST00000641157.1:c.-182+14390_-182+14393del:p.(=); MAPK10:ENST00000641391.1:c.-300+14390_-300+14393del:p.(=); MAPK10:ENST00000641737.1:c.-415+14390_-415+14393del:p.(=); MAPK10:ENST00000641831.1:c.-428+14213_-428+14216del:p.(=)

Pathogenicity Data:: Best Score: 0.25971323; CADD: 0.260 (1.306)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86365431C>CA [-/1] rs70948789 (variation viewer)

Variant score: 0.242

Transcripts:: MAPK10:ENST00000361569.8:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000395160.9:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000513186.7:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000515400.3:c.-7+87598_-7+87599insT:p.(=); MAPK10:ENST00000639972.2:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641050.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000641051.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000641120.1:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641157.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000641170.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000641274.1:c.-7+64246_-7+64247insT:p.(=); MAPK10:ENST00000641283.1:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641297.1:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641313.1:c.-163-10788_-163-10787insT:p.(=); MAPK10:ENST00000641384.1:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641391.1:c.-148+87598_-148+87599insT:p.(=); MAPK10:ENST00000641657.1:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641718.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000641737.1:c.-262-10788_-262-10787insT:p.(=); MAPK10:ENST00000641831.1:c.-122+5282_-122+5283insT:p.(=); MAPK10:ENST00000641862.1:c.-181+87598_-181+87599insT:p.(=); MAPK10:ENST00000641902.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000641952.1:c.-121-10788_-121-10787insT:p.(=); MAPK10:ENST00000642009.1:c.-263+5282_-263+5283insT:p.(=); MAPK10:ENST00000642023.1:c.-262-10788_-262-10787insT:p.(=)

Pathogenicity Data:: Best Score: 0.24229527; CADD: 0.242 (1.205)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86365431C>CAAA [-/1] rs70948789 (variation viewer)

Variant score: 0.234

Transcripts:: MAPK10:ENST00000361569.8:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000395160.9:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000513186.7:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000515400.3:c.-7+87598_-7+87599insTTT:p.(=); MAPK10:ENST00000639972.2:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641050.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000641051.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000641120.1:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641157.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000641170.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000641274.1:c.-7+64246_-7+64247insTTT:p.(=); MAPK10:ENST00000641283.1:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641297.1:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641313.1:c.-163-10788_-163-10787insTTT:p.(=); MAPK10:ENST00000641384.1:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641391.1:c.-148+87598_-148+87599insTTT:p.(=); MAPK10:ENST00000641657.1:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641718.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000641737.1:c.-262-10788_-262-10787insTTT:p.(=); MAPK10:ENST00000641831.1:c.-122+5282_-122+5283insTTT:p.(=); MAPK10:ENST00000641862.1:c.-181+87598_-181+87599insTTT:p.(=); MAPK10:ENST00000641902.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000641952.1:c.-121-10788_-121-10787insTTT:p.(=); MAPK10:ENST00000642009.1:c.-263+5282_-263+5283insTTT:p.(=); MAPK10:ENST00000642023.1:c.-262-10788_-262-10787insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.23405075; CADD: 0.234 (1.158)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86471275C>CA [0/1] rs60423060 (variation viewer)

Variant score: 0.169

Transcripts:: MAPK10:ENST00000513186.7:c.-121-116632_-121-116631insT:p.(=); MAPK10:ENST00000515400.3:c.-158-18095_-158-18094insT:p.(=); MAPK10:ENST00000641050.1:c.-273-18095_-273-18094insT:p.(=); MAPK10:ENST00000641051.1:c.-273-18095_-273-18094insT:p.(=); MAPK10:ENST00000641157.1:c.-181-71470_-181-71469insT:p.(=); MAPK10:ENST00000641391.1:c.-299-18095_-299-18094insT:p.(=); MAPK10:ENST00000641737.1:c.-414-18095_-414-18094insT:p.(=); MAPK10:ENST00000641831.1:c.-427-18095_-427-18094insT:p.(=)

Pathogenicity Data:: Best Score: 0.16861916; CADD: 0.169 (0.802)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86459610C>T [0/1] rs574961585 (variation viewer)

Variant score: 0.166

Transcripts:: MAPK10:ENST00000513186.7:c.-121-104966G>A:p.(=); MAPK10:ENST00000515400.3:c.-158-6429G>A:p.(=); MAPK10:ENST00000641050.1:c.-273-6429G>A:p.(=); MAPK10:ENST00000641051.1:c.-273-6429G>A:p.(=); MAPK10:ENST00000641157.1:c.-181-59804G>A:p.(=); MAPK10:ENST00000641391.1:c.-299-6429G>A:p.(=); MAPK10:ENST00000641737.1:c.-414-6429G>A:p.(=); MAPK10:ENST00000641831.1:c.-427-6429G>A:p.(=)

Pathogenicity Data:: Best Score: 0.16670263; CADD: 0.167 (0.792)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0200%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86174936C>T [0/1] rs188352236 (variation viewer)

Variant score: 0.116

Transcripts:: MAPK10:ENST00000361569.8:c.67-15469G>A:p.(=); MAPK10:ENST00000395157.9:c.67-15469G>A:p.(=); MAPK10:ENST00000395160.9:c.67-15469G>A:p.(=); MAPK10:ENST00000395169.9:c.67-15469G>A:p.(=); MAPK10:ENST00000449047.8:c.67-15469G>A:p.(=); MAPK10:ENST00000511167.6:c.67-15469G>A:p.(=); MAPK10:ENST00000513186.7:c.67-15469G>A:p.(=); MAPK10:ENST00000515400.3:c.67-15469G>A:p.(=); MAPK10:ENST00000515650.2:c.67-15469G>A:p.(=); MAPK10:ENST00000638313.1:c.67-15469G>A:p.(=); MAPK10:ENST00000639234.1:c.67-15469G>A:p.(=); MAPK10:ENST00000640858.1:c.67-15469G>A:p.(=); MAPK10:ENST00000640970.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641010.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641020.1:c.60-67584G>A:p.(=); MAPK10:ENST00000641050.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641051.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641066.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641102.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641157.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641170.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641207.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641274.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641341.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641405.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641459.1:c.76-15469G>A:p.(=); MAPK10:ENST00000641462.2:c.67-15469G>A:p.(=); MAPK10:ENST00000641485.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641493.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641553.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641647.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641677.1:c.76-15469G>A:p.(=); MAPK10:ENST00000641718.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641762.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641777.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641823.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641831.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641862.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641902.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641952.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641954.1:c.67-15469G>A:p.(=); MAPK10:ENST00000641983.1:c.67-15469G>A:p.(=); MAPK10:ENST00000642013.1:c.67-15469G>A:p.(=); MAPK10:ENST00000642038.1:c.67-15469G>A:p.(=); MAPK10:ENST00000359221.8:c.-48-15469G>A:p.(=); MAPK10:ENST00000395166.6:c.-48-15469G>A:p.(=); MAPK10:ENST00000512689.6:c.-48-15469G>A:p.(=); MAPK10:ENST00000638225.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000639175.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000639242.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000639972.2:c.-48-15469G>A:p.(=); MAPK10:ENST00000640490.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641047.1:c.-107+19400G>A:p.(=); MAPK10:ENST00000641052.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641110.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641120.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641166.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641208.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641217.1:c.-107+19373G>A:p.(=); MAPK10:ENST00000641237.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641283.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641287.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641297.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641313.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641324.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641384.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641391.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641430.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641537.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641555.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641607.1:c.-107+19400G>A:p.(=); MAPK10:ENST00000641657.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641724.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641737.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641767.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641803.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641864.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641903.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641911.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641943.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000641989.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000642006.1:c.-107+19373G>A:p.(=); MAPK10:ENST00000642009.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000642015.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000642023.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000642032.1:c.-48-15469G>A:p.(=); MAPK10:ENST00000642103.1:c.-48-15469G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11610639; CADD: 0.116 (0.536)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0199%; gnomAD_G_NFE: 0.0333%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.86454434C>T [0/1] rs536920294 (variation viewer)

Variant score: 0.111

Transcripts:: MAPK10:ENST00000513186.7:c.-121-99790G>A:p.(=); MAPK10:ENST00000515400.3:c.-158-1253G>A:p.(=); MAPK10:ENST00000641050.1:c.-273-1253G>A:p.(=); MAPK10:ENST00000641051.1:c.-273-1253G>A:p.(=); MAPK10:ENST00000641157.1:c.-181-54628G>A:p.(=); MAPK10:ENST00000641391.1:c.-299-1253G>A:p.(=); MAPK10:ENST00000641737.1:c.-414-1253G>A:p.(=); MAPK10:ENST00000641831.1:c.-427-1253G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11120826; CADD: 0.111 (0.512)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0239%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0334%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86336784C>CT [0/1] rs70948788 (variation viewer)

Variant score: 0.101

Transcripts:: MAPK10:ENST00000641020.1:c.59+17745_59+17746insA:p.(=); MAPK10:ENST00000641459.1:c.3+22873_3+22874insA:p.(=); MAPK10:ENST00000641677.1:c.3+22873_3+22874insA:p.(=); MAPK10:ENST00000359221.8:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000361569.8:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000395157.9:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000395160.9:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000395166.6:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000395169.9:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000511167.6:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000512689.6:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000513186.7:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000515400.3:c.-7+116245_-7+116246insA:p.(=); MAPK10:ENST00000515650.2:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000638225.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000638313.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000639175.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000639234.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000639242.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000639972.2:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000640490.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000640858.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000640970.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641010.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641047.1:c.-179+17745_-179+17746insA:p.(=); MAPK10:ENST00000641050.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641051.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641052.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641066.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641102.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641110.1:c.-148+15380_-148+15381insA:p.(=); MAPK10:ENST00000641120.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641157.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641166.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641170.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641207.1:c.-7+3554_-7+3555insA:p.(=); MAPK10:ENST00000641208.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641217.1:c.-206+17745_-206+17746insA:p.(=); MAPK10:ENST00000641274.1:c.-7+92893_-7+92894insA:p.(=); MAPK10:ENST00000641283.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641287.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641297.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641313.1:c.-49+17745_-49+17746insA:p.(=); MAPK10:ENST00000641324.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641341.1:c.-192-14756_-192-14755insA:p.(=); MAPK10:ENST00000641384.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641391.1:c.-148+116245_-148+116246insA:p.(=); MAPK10:ENST00000641405.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641430.1:c.-148+3554_-148+3555insA:p.(=); MAPK10:ENST00000641462.2:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641485.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641493.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641537.1:c.-49+17745_-49+17746insA:p.(=); MAPK10:ENST00000641553.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641555.1:c.-333-14756_-333-14755insA:p.(=); MAPK10:ENST00000641607.1:c.-179+17745_-179+17746insA:p.(=); MAPK10:ENST00000641647.1:c.-192-14756_-192-14755insA:p.(=); MAPK10:ENST00000641657.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641718.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641724.1:c.-333-14756_-333-14755insA:p.(=); MAPK10:ENST00000641737.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641762.1:c.-192-14756_-192-14755insA:p.(=); MAPK10:ENST00000641767.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641777.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641803.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641823.1:c.-87-1629_-87-1628insA:p.(=); MAPK10:ENST00000641831.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641862.1:c.-180-59562_-180-59561insA:p.(=); MAPK10:ENST00000641864.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641902.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641903.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000641911.1:c.-148+22873_-148+22874insA:p.(=); MAPK10:ENST00000641943.1:c.-322+17745_-322+17746insA:p.(=); MAPK10:ENST00000641952.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641954.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641983.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000641989.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000642006.1:c.-206+17745_-206+17746insA:p.(=); MAPK10:ENST00000642009.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000642013.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000642015.1:c.-49+17745_-49+17746insA:p.(=); MAPK10:ENST00000642023.1:c.-148+17745_-148+17746insA:p.(=); MAPK10:ENST00000642032.1:c.-322+17745_-322+17746insA:p.(=); MAPK10:ENST00000642038.1:c.-7+17745_-7+17746insA:p.(=); MAPK10:ENST00000642103.1:c.-76+17745_-76+17746insA:p.(=)

Pathogenicity Data:: Best Score: 0.10133052; CADD: 0.101 (0.464)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86117843G>A [0/1] rs116124723 (variation viewer)

Variant score: 0.094

Transcripts:: MAPK10:ENST00000359221.8:c.123-10491C>T:p.(=); MAPK10:ENST00000361569.8:c.237-10491C>T:p.(=); MAPK10:ENST00000395157.9:c.237-10491C>T:p.(=); MAPK10:ENST00000395160.9:c.237-10491C>T:p.(=); MAPK10:ENST00000395166.6:c.123-10491C>T:p.(=); MAPK10:ENST00000395169.9:c.237-10491C>T:p.(=); MAPK10:ENST00000449047.8:c.237-10491C>T:p.(=); MAPK10:ENST00000511167.6:c.237-10491C>T:p.(=); MAPK10:ENST00000512689.6:c.123-10491C>T:p.(=); MAPK10:ENST00000513186.7:c.237-10491C>T:p.(=); MAPK10:ENST00000515400.3:c.237-10491C>T:p.(=); MAPK10:ENST00000515650.2:c.237-10491C>T:p.(=); MAPK10:ENST00000638225.1:c.123-10491C>T:p.(=); MAPK10:ENST00000638313.1:c.237-10491C>T:p.(=); MAPK10:ENST00000639175.1:c.123-10491C>T:p.(=); MAPK10:ENST00000639234.1:c.237-10491C>T:p.(=); MAPK10:ENST00000639242.1:c.123-10491C>T:p.(=); MAPK10:ENST00000639972.2:c.123-10491C>T:p.(=); MAPK10:ENST00000640490.1:c.123-10491C>T:p.(=); MAPK10:ENST00000640858.1:c.237-10491C>T:p.(=); MAPK10:ENST00000640970.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641010.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641020.1:c.60-10491C>T:p.(=); MAPK10:ENST00000641050.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641051.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641052.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641066.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641102.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641110.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641120.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641157.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641166.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641170.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641207.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641208.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641237.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641274.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641283.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641287.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641297.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641313.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641324.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641341.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641384.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641391.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641405.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641430.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641459.1:c.246-10491C>T:p.(=); MAPK10:ENST00000641462.2:c.237-10491C>T:p.(=); MAPK10:ENST00000641485.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641493.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641537.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641553.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641555.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641647.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641657.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641677.1:c.246-10491C>T:p.(=); MAPK10:ENST00000641718.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641724.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641737.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641762.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641767.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641803.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641823.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641831.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641862.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641864.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641902.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641903.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641911.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641943.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641952.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641954.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641983.1:c.237-10491C>T:p.(=); MAPK10:ENST00000641989.1:c.123-10491C>T:p.(=); MAPK10:ENST00000642009.1:c.123-10491C>T:p.(=); MAPK10:ENST00000642013.1:c.237-10491C>T:p.(=); MAPK10:ENST00000642015.1:c.123-10491C>T:p.(=); MAPK10:ENST00000642023.1:c.123-10491C>T:p.(=); MAPK10:ENST00000642032.1:c.123-10491C>T:p.(=); MAPK10:ENST00000642038.1:c.237-10491C>T:p.(=); MAPK10:ENST00000642103.1:c.123-10491C>T:p.(=); MAPK10:ENST00000641047.1:c.-106-10491C>T:p.(=); MAPK10:ENST00000641217.1:c.-106-10491C>T:p.(=); MAPK10:ENST00000641607.1:c.-106-10491C>T:p.(=); MAPK10:ENST00000642006.1:c.-106-10491C>T:p.(=)

Pathogenicity Data:: Best Score: 0.13702142; CADD: 0.137 (0.640)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.6491%; UK10K: 1.2034%; gnomAD_G_AFR: 0.2750%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 1.0309%; gnomAD_G_NFE: 1.0926%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86359263C>CCTCTCTCTCTCTCTCT [-/1] rs367595812 (variation viewer)

Variant score: 0.079

Transcripts:: MAPK10:ENST00000641459.1:c.3+394_3+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641677.1:c.3+394_3+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000359221.8:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000361569.8:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000395157.9:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000395160.9:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000395169.9:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000513186.7:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000515400.3:c.-7+93766_-7+93767insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000515650.2:c.-567+394_-567+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000638225.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000639175.1:c.-321+394_-321+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000639234.1:c.-567+394_-567+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000639972.2:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000640490.1:c.-321+394_-321+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641010.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641020.1:c.-57+394_-57+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641047.1:c.-294+394_-294+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641050.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641051.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641052.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641102.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641110.1:c.-323+394_-323+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641120.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641157.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641166.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641170.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641207.1:c.-207+394_-207+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641208.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641217.1:c.-321+394_-321+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641274.1:c.-7+70414_-7+70415insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641283.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641287.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641297.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641313.1:c.-163-4620_-163-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641324.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641384.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641391.1:c.-148+93766_-148+93767insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641405.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641462.2:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641485.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641493.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641537.1:c.-164+394_-164+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641553.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641555.1:c.-449+394_-449+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641607.1:c.-294+394_-294+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641647.1:c.-308+394_-308+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641657.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641718.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641724.1:c.-449+394_-449+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641737.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641762.1:c.-308+394_-308+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641777.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641823.1:c.-203+394_-203+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641831.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641862.1:c.-180-82041_-180-82040insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641864.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641902.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641903.1:c.-263+394_-263+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641911.1:c.-148+394_-148+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641943.1:c.-437+394_-437+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641952.1:c.-121-4620_-121-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000641954.1:c.-122+394_-122+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000642006.1:c.-321+394_-321+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000642009.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000642015.1:c.-164+394_-164+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000642023.1:c.-262-4620_-262-4619insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000642032.1:c.-437+394_-437+395insAGAGAGAGAGAGAGAG:p.(=); MAPK10:ENST00000642103.1:c.-191+394_-191+395insAGAGAGAGAGAGAGAG:p.(=)

Pathogenicity Data:: Best Score: 0.07870227; CADD: 0.079 (0.356)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86327785C>CAAAAAAAAA [0/1] rs5860023 (variation viewer)

Variant score: 0.052

Transcripts:: MAPK10:ENST00000641020.1:c.59+26744_59+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641459.1:c.3+31872_3+31873insTTTTTTTTT:p.(=); MAPK10:ENST00000641677.1:c.3+31872_3+31873insTTTTTTTTT:p.(=); MAPK10:ENST00000359221.8:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000361569.8:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000395157.9:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000395160.9:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000395166.6:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000395169.9:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000511167.6:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000512689.6:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000513186.7:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000515400.3:c.-7+125244_-7+125245insTTTTTTTTT:p.(=); MAPK10:ENST00000515650.2:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000638225.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000638313.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000639175.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000639234.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000639242.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000639972.2:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000640490.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000640858.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000640970.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641010.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641047.1:c.-179+26744_-179+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641050.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641051.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641052.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641066.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641102.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641110.1:c.-148+24379_-148+24380insTTTTTTTTT:p.(=); MAPK10:ENST00000641120.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641157.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641166.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641170.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641207.1:c.-7+12553_-7+12554insTTTTTTTTT:p.(=); MAPK10:ENST00000641208.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641217.1:c.-206+26744_-206+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641274.1:c.-7+101892_-7+101893insTTTTTTTTT:p.(=); MAPK10:ENST00000641283.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641287.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641297.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641313.1:c.-49+26744_-49+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641324.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641341.1:c.-192-5757_-192-5756insTTTTTTTTT:p.(=); MAPK10:ENST00000641384.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641391.1:c.-148+125244_-148+125245insTTTTTTTTT:p.(=); MAPK10:ENST00000641405.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641430.1:c.-148+12553_-148+12554insTTTTTTTTT:p.(=); MAPK10:ENST00000641462.2:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641485.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641493.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641537.1:c.-49+26744_-49+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641553.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641555.1:c.-333-5757_-333-5756insTTTTTTTTT:p.(=); MAPK10:ENST00000641607.1:c.-179+26744_-179+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641647.1:c.-192-5757_-192-5756insTTTTTTTTT:p.(=); MAPK10:ENST00000641657.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641718.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641724.1:c.-333-5757_-333-5756insTTTTTTTTT:p.(=); MAPK10:ENST00000641737.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641762.1:c.-192-5757_-192-5756insTTTTTTTTT:p.(=); MAPK10:ENST00000641767.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641777.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641803.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641823.1:c.-7+7290_-7+7291insTTTTTTTTT:p.(=); MAPK10:ENST00000641831.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641862.1:c.-180-50563_-180-50562insTTTTTTTTT:p.(=); MAPK10:ENST00000641864.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641902.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641903.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641911.1:c.-148+31872_-148+31873insTTTTTTTTT:p.(=); MAPK10:ENST00000641943.1:c.-322+26744_-322+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641952.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641954.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641983.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000641989.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642006.1:c.-206+26744_-206+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642009.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642013.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642015.1:c.-49+26744_-49+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642023.1:c.-148+26744_-148+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642032.1:c.-322+26744_-322+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642038.1:c.-7+26744_-7+26745insTTTTTTTTT:p.(=); MAPK10:ENST00000642103.1:c.-76+26744_-76+26745insTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.052236438; CADD: 0.052 (0.233)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86006126A>G [0/1] rs543027814 (variation viewer)

Variant score: 0.047

Transcripts:: MAPK10:ENST00000641010.1:c.1391+11106T>C:p.(=); MAPK10:ENST00000641102.1:c.1392-4649T>C:p.(=); MAPK10:ENST00000641324.1:c.1277+11106T>C:p.(=)

Pathogenicity Data:: Best Score: 0.04764253; CADD: 0.048 (0.212)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0605%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0400%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86133357C>T [0/1] rs115057059 (variation viewer)

Variant score: 0.008

Transcripts:: MAPK10:ENST00000359221.8:c.122+25941G>A:p.(=); MAPK10:ENST00000361569.8:c.236+25941G>A:p.(=); MAPK10:ENST00000395157.9:c.236+25941G>A:p.(=); MAPK10:ENST00000395160.9:c.236+25941G>A:p.(=); MAPK10:ENST00000395166.6:c.122+25941G>A:p.(=); MAPK10:ENST00000395169.9:c.236+25941G>A:p.(=); MAPK10:ENST00000449047.8:c.236+25941G>A:p.(=); MAPK10:ENST00000511167.6:c.236+25941G>A:p.(=); MAPK10:ENST00000512689.6:c.122+25941G>A:p.(=); MAPK10:ENST00000513186.7:c.236+25941G>A:p.(=); MAPK10:ENST00000515400.3:c.236+25941G>A:p.(=); MAPK10:ENST00000515650.2:c.236+25941G>A:p.(=); MAPK10:ENST00000638225.1:c.122+25941G>A:p.(=); MAPK10:ENST00000638313.1:c.236+25941G>A:p.(=); MAPK10:ENST00000639175.1:c.122+25941G>A:p.(=); MAPK10:ENST00000639234.1:c.236+25941G>A:p.(=); MAPK10:ENST00000639242.1:c.122+25941G>A:p.(=); MAPK10:ENST00000639972.2:c.122+25941G>A:p.(=); MAPK10:ENST00000640490.1:c.122+25941G>A:p.(=); MAPK10:ENST00000640858.1:c.236+25941G>A:p.(=); MAPK10:ENST00000640970.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641010.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641020.1:c.60-26005G>A:p.(=); MAPK10:ENST00000641050.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641051.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641052.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641066.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641102.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641110.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641120.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641157.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641166.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641170.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641207.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641208.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641237.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641274.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641283.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641287.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641297.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641313.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641324.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641341.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641384.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641391.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641405.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641430.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641459.1:c.245+25941G>A:p.(=); MAPK10:ENST00000641462.2:c.236+25941G>A:p.(=); MAPK10:ENST00000641485.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641493.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641537.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641553.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641555.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641647.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641657.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641677.1:c.245+25941G>A:p.(=); MAPK10:ENST00000641718.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641724.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641737.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641762.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641767.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641803.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641823.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641831.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641862.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641864.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641902.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641903.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641911.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641943.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641952.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641954.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641983.1:c.236+25941G>A:p.(=); MAPK10:ENST00000641989.1:c.122+25941G>A:p.(=); MAPK10:ENST00000642009.1:c.122+25941G>A:p.(=); MAPK10:ENST00000642013.1:c.236+25941G>A:p.(=); MAPK10:ENST00000642015.1:c.122+25941G>A:p.(=); MAPK10:ENST00000642023.1:c.122+25941G>A:p.(=); MAPK10:ENST00000642032.1:c.122+25941G>A:p.(=); MAPK10:ENST00000642038.1:c.236+25941G>A:p.(=); MAPK10:ENST00000642103.1:c.122+25941G>A:p.(=); MAPK10:ENST00000641047.1:c.-106-26005G>A:p.(=); MAPK10:ENST00000641217.1:c.-106-26005G>A:p.(=); MAPK10:ENST00000641607.1:c.-106-26005G>A:p.(=); MAPK10:ENST00000642006.1:c.-106-26005G>A:p.(=)

Pathogenicity Data:: Best Score: 0.014855385; CADD: 0.015 (0.065)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3576%; UK10K: 0.7141%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.4785%; gnomAD_G_FIN: 1.4343%; gnomAD_G_NFE: 0.7209%; gnomAD_G_OTH: 0.3067%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.86359263CCTCT>C [-/1] rs367595812 (variation viewer)

Variant score: 0.008

Transcripts:: MAPK10:ENST00000641459.1:c.3+391_3+394del:p.(=); MAPK10:ENST00000641677.1:c.3+391_3+394del:p.(=); MAPK10:ENST00000359221.8:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000361569.8:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000395157.9:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000395160.9:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000395169.9:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000513186.7:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000515400.3:c.-7+93763_-7+93766del:p.(=); MAPK10:ENST00000515650.2:c.-567+391_-567+394del:p.(=); MAPK10:ENST00000638225.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000639175.1:c.-321+391_-321+394del:p.(=); MAPK10:ENST00000639234.1:c.-567+391_-567+394del:p.(=); MAPK10:ENST00000639972.2:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000640490.1:c.-321+391_-321+394del:p.(=); MAPK10:ENST00000641010.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641020.1:c.-57+391_-57+394del:p.(=); MAPK10:ENST00000641047.1:c.-294+391_-294+394del:p.(=); MAPK10:ENST00000641050.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641051.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641052.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641102.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641110.1:c.-323+391_-323+394del:p.(=); MAPK10:ENST00000641120.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000641157.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641166.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641170.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641207.1:c.-207+391_-207+394del:p.(=); MAPK10:ENST00000641208.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641217.1:c.-321+391_-321+394del:p.(=); MAPK10:ENST00000641274.1:c.-7+70411_-7+70414del:p.(=); MAPK10:ENST00000641283.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000641287.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641297.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000641313.1:c.-163-4623_-163-4620del:p.(=); MAPK10:ENST00000641324.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641384.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000641391.1:c.-148+93763_-148+93766del:p.(=); MAPK10:ENST00000641405.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641462.2:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641485.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641493.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641537.1:c.-164+391_-164+394del:p.(=); MAPK10:ENST00000641553.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641555.1:c.-449+391_-449+394del:p.(=); MAPK10:ENST00000641607.1:c.-294+391_-294+394del:p.(=); MAPK10:ENST00000641647.1:c.-308+391_-308+394del:p.(=); MAPK10:ENST00000641657.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000641718.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641724.1:c.-449+391_-449+394del:p.(=); MAPK10:ENST00000641737.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000641762.1:c.-308+391_-308+394del:p.(=); MAPK10:ENST00000641777.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000641823.1:c.-203+391_-203+394del:p.(=); MAPK10:ENST00000641831.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641862.1:c.-180-82044_-180-82041del:p.(=); MAPK10:ENST00000641864.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641902.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641903.1:c.-263+391_-263+394del:p.(=); MAPK10:ENST00000641911.1:c.-148+391_-148+394del:p.(=); MAPK10:ENST00000641943.1:c.-437+391_-437+394del:p.(=); MAPK10:ENST00000641952.1:c.-121-4623_-121-4620del:p.(=); MAPK10:ENST00000641954.1:c.-122+391_-122+394del:p.(=); MAPK10:ENST00000642006.1:c.-321+391_-321+394del:p.(=); MAPK10:ENST00000642009.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000642015.1:c.-164+391_-164+394del:p.(=); MAPK10:ENST00000642023.1:c.-262-4623_-262-4620del:p.(=); MAPK10:ENST00000642032.1:c.-437+391_-437+394del:p.(=); MAPK10:ENST00000642103.1:c.-191+391_-191+394del:p.(=)

Pathogenicity Data:: Best Score: 0.0075697303; CADD: 0.008 (0.033)

Frequency Data:: No frequency data

SUZ12

Exomiser Score: 0.447

Phenotype Score: 0.505

Variant Score: 0.852

Phenotype matches:

Proximity score 0.505 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618786 Imagawa-Matsumoto syndrome - autosomal dominant; ORPHA:3447 Weaver syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.447

Phenotype Score: 0.505

Variant Score: 0.852

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.31921747C>CTTT [0/1] rs1232639558 (variation viewer)

Variant score: 0.852 CONTRIBUTING VARIANT

Transcripts:: SUZ12:ENST00000322652.10::

Pathogenicity Data:: Best Score: 0.8524973; CADD: 0.852 (8.312)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.053

Phenotype Score: 0.252

Variant Score: 0.848

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.31921747C>CTTT [0/1] rs1232639558 (variation viewer)

Variant score: 0.852 CONTRIBUTING VARIANT

Transcripts:: SUZ12:ENST00000322652.10::

Pathogenicity Data:: Best Score: 0.8524973; CADD: 0.852 (8.312)

Frequency Data:: No frequency data

MISSENSE_VARIANT chr17:g.31998960G>A [0/1] rs140801412 (variation viewer)

Variant score: 0.843 CONTRIBUTING VARIANT

Transcripts:: SUZ12:ENST00000322652.10:c.2177G>A:p.(Ser726Asn); SUZ12:ENST00000580398.1:c.2108G>A:p.(Ser703Asn)

Pathogenicity Data:: Best Score: 0.9823803; SIFT: 0.056 (D); CADD: 0.982 (17.540)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0948%; UK10K: 0.1455%; ESP EA: 0.1640%; ESP All: 0.1090%; ExAC AFR: 0.0353%; ExAC AMR: 0.0268%; ExAC FIN: 0.0456%; ExAC NFE: 0.1642%; ExAC OTH: 0.1229%; ExAC SAS: 0.1443%; gnomAD_E_AFR: 0.0354%; gnomAD_E_AMR: 0.0235%; gnomAD_E_ASJ: 0.7159%; gnomAD_E_FIN: 0.0320%; gnomAD_E_NFE: 0.1345%; gnomAD_E_OTH: 0.2628%; gnomAD_E_SAS: 0.1070%; gnomAD_G_AFR: 0.0687%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.1334%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.31971421C>CTT [0/1] rs11383306 (variation viewer)

Variant score: 0.435

Transcripts:: SUZ12:ENST00000322652.10:c.506-1725_506-1724insTT:p.(=); SUZ12:ENST00000580398.1:c.437-1725_437-1724insTT:p.(=)

Pathogenicity Data:: Best Score: 0.43454248; CADD: 0.435 (2.476)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr17:g.32001818C>G [0/1] rs1031837960 (variation viewer)

Variant score: 0.380

Transcripts:: SUZ12:ENST00000322652.10::; SUZ12:ENST00000582184.1::

Pathogenicity Data:: Best Score: 0.3801309; CADD: 0.380 (2.077)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr17:g.31926943T>C [0/1] rs1404224069 (variation viewer)

Variant score: 0.356

Transcripts:: SUZ12:ENST00000322652.10::

Pathogenicity Data:: Best Score: 0.35627556; CADD: 0.356 (1.913)

Frequency Data:: TOPMed: 0.0008%

INTERGENIC_VARIANT chr17:g.31926654AT>A [0/1] rs760267243 (variation viewer)

Variant score: 0.271

Transcripts:: SUZ12:ENST00000322652.10::

Pathogenicity Data:: Best Score: 0.271214; CADD: 0.271 (1.374)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr17:g.31919690T>C [0/1] rs184107024 (variation viewer)

Variant score: 0.186

Transcripts:: SUZ12:ENST00000322652.10::

Pathogenicity Data:: Best Score: 0.45184928; CADD: 0.452 (2.611)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 1.0270%; UK10K: 1.4414%; gnomAD_G_AFR: 0.2431%; gnomAD_G_AMR: 0.3641%; gnomAD_G_ASJ: 1.6779%; gnomAD_G_FIN: 0.5039%; gnomAD_G_NFE: 1.6601%; gnomAD_G_OTH: 1.5991%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.31979103C>CAAAAA [0/1] rs61307349 (variation viewer)

Variant score: 0.157

Transcripts:: SUZ12:ENST00000322652.10:c.917+2489_917+2490insAAAAA:p.(=); SUZ12:ENST00000580398.1:c.848+2489_848+2490insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.1572476; CADD: 0.157 (0.743)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.31951889C>T [0/1] rs1027104296 (variation viewer)

Variant score: 0.152

Transcripts:: SUZ12:ENST00000322652.10:c.455+4204C>T:p.(=); SUZ12:ENST00000580398.1:c.386+11403C>T:p.(=)

Pathogenicity Data:: Best Score: 0.15296763; CADD: 0.153 (0.721)

Frequency Data:: TOPMed: 0.0111%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0269%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.31972400T>TAA [0/1] rs768108129 (variation viewer)

Variant score: 0.049

Transcripts:: SUZ12:ENST00000322652.10:c.506-746_506-745insAA:p.(=); SUZ12:ENST00000580398.1:c.437-746_437-745insAA:p.(=)

Pathogenicity Data:: Best Score: 0.12501621; CADD: 0.125 (0.580)

Frequency Data:: gnomAD_G_AFR: 0.2262%; gnomAD_G_AMR: 0.1767%; gnomAD_G_ASJ: 1.7007%; gnomAD_G_FIN: 0.3338%; gnomAD_G_NFE: 1.5403%; gnomAD_G_OTH: 1.3100%

DOWNSTREAM_GENE_VARIANT chr17:g.32003013ATTTT>A [0/1] rs201248045 (variation viewer)

Variant score: 0.048

Transcripts:: SUZ12:ENST00000322652.10::; SUZ12:ENST00000582184.1::

Pathogenicity Data:: Best Score: 0.049176276; CADD: 0.049 (0.219)

Frequency Data:: gnomAD_G_AFR: 0.2017%; gnomAD_G_NFE: 0.0414%

REGULATORY_REGION_VARIANT chr17:g.32397939G>A [0/1] rs116887675 (variation viewer)

Variant score: 0.044

Transcripts:

Pathogenicity Data:: Best Score: 0.10236454; CADD: 0.102 (0.469)

Frequency Data:: 1000Genomes: 0.9984%; TOPMed: 0.7032%; UK10K: 0.8860%; gnomAD_G_AFR: 0.2068%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.2577%; gnomAD_G_NFE: 0.9810%; gnomAD_G_OTH: 0.8264%

IL2

Exomiser Score: 0.441

Phenotype Score: 0.504

Variant Score: 0.851

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.441

Phenotype Score: 0.504

Variant Score: 0.851

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.122441467C>T [0/1] rs747853230 (variation viewer)

Variant score: 0.851 CONTRIBUTING VARIANT

Transcripts:: IL2:ENST00000226730.4::; IL2:ENST00000388724.6::

Pathogenicity Data:: Best Score: 0.8507893; CADD: 0.851 (8.262)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.067

Phenotype Score: 0.504

Variant Score: 0.590

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.122441467C>T [0/1] rs747853230 (variation viewer)

Variant score: 0.851 CONTRIBUTING VARIANT

Transcripts:: IL2:ENST00000226730.4::; IL2:ENST00000388724.6::

Pathogenicity Data:: Best Score: 0.8507893; CADD: 0.851 (8.262)

Frequency Data:: TOPMed: 0.0016%

INTERGENIC_VARIANT chr4:g.122464777G>A [0/1] rs199497494 (variation viewer)

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: IL2:ENST00000226730.4::; IL2:ENST00000648588.1::

Pathogenicity Data:: Best Score: 0.3316561; CADD: 0.332 (1.750)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0223%; gnomAD_G_AFR: 0.0345%; gnomAD_G_EAS: 0.0621%; gnomAD_G_NFE: 0.0200%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr4:g.122448712CT>C [1/1] rs35002064 (variation viewer)

Variant score: 0.085

Transcripts:: IL2:ENST00000226730.4::; IL2:ENST00000388724.6::

Pathogenicity Data:: Best Score: 0.08462298; CADD: 0.085 (0.384)

Frequency Data:: No frequency data

EHMT1

Exomiser Score: 0.439

Phenotype Score: 0.503

Variant Score: 0.850

Phenotype matches:

Phenotypic similarity 0.471 to Kleefstra syndrome due to 9q34 microdeletion associated with EHMT1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Phenotypic similarity 0.436 to mouse mutant involving EHMT1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:610253 Kleefstra syndrome 1 - autosomal dominant; ORPHA:261652 Kleefstra syndrome due to a point mutation; ORPHA:96147 Kleefstra syndrome due to 9q34 microdeletion

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.439

Phenotype Score: 0.503

Variant Score: 0.850

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137645887T>C [0/1]

Variant score: 0.850 CONTRIBUTING VARIANT

Transcripts:: EHMT1:ENST00000460843.6:c.21+26838T>C:p.(=); EHMT1:ENST00000462484.5:c.21+26838T>C:p.(=); EHMT1:ENST00000629335.2:c.21+26838T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8504798; CADD: 0.850 (8.253)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.018

Phenotype Score: 0.252

Variant Score: 0.726

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137645887T>C [0/1]

Variant score: 0.850 CONTRIBUTING VARIANT

Transcripts:: EHMT1:ENST00000460843.6:c.21+26838T>C:p.(=); EHMT1:ENST00000462484.5:c.21+26838T>C:p.(=); EHMT1:ENST00000629335.2:c.21+26838T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8504798; CADD: 0.850 (8.253)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137697557GTAGAAGGACACTTT>G [0/1] rs573218198 (variation viewer)

Variant score: 0.602 CONTRIBUTING VARIANT

Transcripts:: EHMT1:ENST00000460843.6:c.22-13409_22-13396del:p.(=); EHMT1:ENST00000462484.5:c.22-13409_22-13396del:p.(=); EHMT1:ENST00000629335.2:c.22-13409_22-13396del:p.(=); EHMT1:ENST00000637161.1:c.-72-13409_-72-13396del:p.(=)

Pathogenicity Data:: Best Score: 0.7301018; CADD: 0.730 (5.688)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.4993%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.5444%; gnomAD_G_NFE: 0.8330%; gnomAD_G_OTH: 0.3055%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137795401G>GCACACACA [0|1] rs554055210 (variation viewer)

Variant score: 0.439

Transcripts:: EHMT1:ENST00000460843.6:c.2506-3412_2506-3411insCACACACA:p.(=); EHMT1:ENST00000482340.5:c.76-3412_76-3411insCACACACA:p.(=); EHMT1:ENST00000493484.5:c.76-3412_76-3411insCACACACA:p.(=); EHMT1:ENST00000637161.1:c.2413-3412_2413-3411insCACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.4394685; CADD: 0.439 (2.514)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137641979A>C [0/1] rs189482621 (variation viewer)

Variant score: 0.424

Transcripts:: EHMT1:ENST00000460843.6:c.21+22930A>C:p.(=); EHMT1:ENST00000462484.5:c.21+22930A>C:p.(=); EHMT1:ENST00000629335.2:c.21+22930A>C:p.(=)

Pathogenicity Data:: Best Score: 0.53708637; CADD: 0.537 (3.345)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.5208%; UK10K: 0.9389%; gnomAD_G_AFR: 0.1061%; gnomAD_G_AMR: 0.2439%; gnomAD_G_FIN: 0.5479%; gnomAD_G_NFE: 0.8958%; gnomAD_G_OTH: 0.3099%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137669820T>A [0/1] rs117597986 (variation viewer)

Variant score: 0.266

Transcripts:: EHMT1:ENST00000460843.6:c.22-41147T>A:p.(=); EHMT1:ENST00000462484.5:c.22-41147T>A:p.(=); EHMT1:ENST00000629335.2:c.22-41147T>A:p.(=)

Pathogenicity Data:: Best Score: 0.46543568; CADD: 0.465 (2.720)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.8513%; UK10K: 1.4282%; gnomAD_G_AFR: 0.1832%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.5438%; gnomAD_G_NFE: 1.2207%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137680230C>G [0/1] rs139748939 (variation viewer)

Variant score: 0.121

Transcripts:: EHMT1:ENST00000460843.6:c.22-30737C>G:p.(=); EHMT1:ENST00000462484.5:c.22-30737C>G:p.(=); EHMT1:ENST00000629335.2:c.22-30737C>G:p.(=); EHMT1:ENST00000637161.1:c.-73+5019C>G:p.(=)

Pathogenicity Data:: Best Score: 0.1527726; CADD: 0.153 (0.720)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4993%; UK10K: 0.9257%; gnomAD_G_AFR: 0.1146%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.5438%; gnomAD_G_NFE: 0.8198%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137811343C>T [0|1] rs141138372 (variation viewer)

Variant score: 0.098

Transcripts:: EHMT1:ENST00000460843.6:c.2713-118C>T:p.(=); EHMT1:ENST00000637161.1:c.2620-118C>T:p.(=)

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.5065%; UK10K: 0.9918%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.4009%; gnomAD_G_NFE: 0.8329%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137810194T>TGTGGACCGTCGGTGATGGGTCCGGAGGCGGTTCCGATGCCGCCCCGC [0/1] rs56220863 (variation viewer)

Variant score: 0.079

Transcripts:: EHMT1:ENST00000460843.6:c.2713-1267_2713-1266insGTGGACCGTCGGTGATGGGTCCGGAGGCGGTTCCGATGCCGCCCCGC:p.(=); EHMT1:ENST00000637161.1:c.2620-1267_2620-1266insGTGGACCGTCGGTGATGGGTCCGGAGGCGGTTCCGATGCCGCCCCGC:p.(=)

Pathogenicity Data:: Best Score: 0.20913929; CADD: 0.209 (1.019)

Frequency Data:: gnomAD_G_AFR: 1.3761%; gnomAD_G_AMR: 0.3205%; gnomAD_G_ASJ: 1.7241%; gnomAD_G_EAS: 1.5306%; gnomAD_G_FIN: 0.2517%; gnomAD_G_NFE: 0.9924%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137747693G>A [0/1] rs117714395 (variation viewer)

Variant score: 0.016

Transcripts:: EHMT1:ENST00000460843.6:c.1170+3603G>A:p.(=); EHMT1:ENST00000462484.5:c.1170+3603G>A:p.(=); EHMT1:ENST00000629335.2:c.1170+3603G>A:p.(=); EHMT1:ENST00000637161.1:c.1077+3603G>A:p.(=); EHMT1:ENST00000637318.1:c.*2134G>A:p.(=)

Pathogenicity Data:: Best Score: 0.026356459; CADD: 0.026 (0.116)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.8537%; UK10K: 1.3753%; gnomAD_G_AFR: 0.1718%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4007%; gnomAD_G_NFE: 1.2190%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.137814059C>* [-/1]

Variant score: 0.000

Transcripts:: EHMT1:ENST00000460843.6:c.3181-372C>*:p.(=); EHMT1:ENST00000637161.1:c.3088-372C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SEC24A

Exomiser Score: 0.436

Phenotype Score: 0.505

Variant Score: 0.847

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.436

Phenotype Score: 0.505

Variant Score: 0.847

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134699301C>CTTTTTTTTT [0/1] rs1208203003 (variation viewer)

Variant score: 0.847 CONTRIBUTING VARIANT

Transcripts:: SEC24A:ENST00000398844.7:c.2266+1244_2266+1245insTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.84741914; CADD: 0.847 (8.165)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.203

Phenotype Score: 0.505

Variant Score: 0.727

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134699301C>CTTTTTTTTT [0/1] rs1208203003 (variation viewer)

Variant score: 0.847 CONTRIBUTING VARIANT

Transcripts:: SEC24A:ENST00000398844.7:c.2266+1244_2266+1245insTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.84741914; CADD: 0.847 (8.165)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134650894C>T [0/1] rs546139430 (variation viewer)

Variant score: 0.606 CONTRIBUTING VARIANT

Transcripts:: SEC24A:ENST00000322887.8:c.97+1721C>T:p.(=); SEC24A:ENST00000398844.7:c.97+1721C>T:p.(=)

Pathogenicity Data:: Best Score: 0.60726464; CADD: 0.607 (4.059)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0200%; gnomAD_G_NFE: 0.0201%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134723741A>G [0/1] rs182587652 (variation viewer)

Variant score: 0.534

Transcripts:: SEC24A:ENST00000398844.7:c.3167+71A>G:p.(=)

Pathogenicity Data:: Best Score: 0.56708765; CADD: 0.567 (3.636)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0350%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.0576%; gnomAD_G_NFE: 0.0200%

INTERGENIC_VARIANT chr5:g.134733187G>C [0/1] rs797004490 (variation viewer)

Variant score: 0.393

Transcripts:: SEC24A:ENST00000398844.7::; SEC24A:ENST00000297156.4::

Pathogenicity Data:: Best Score: 0.627351; CADD: 0.627 (4.287)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1728%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1399%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134664796T>TTC [0/1] rs1393709690 (variation viewer)

Variant score: 0.250

Transcripts:: SEC24A:ENST00000322887.8:c.566-2027_566-2026insTC:p.(=); SEC24A:ENST00000398844.7:c.566-2027_566-2026insTC:p.(=)

Pathogenicity Data:: Best Score: 0.25148588; CADD: 0.251 (1.258)

Frequency Data:: gnomAD_G_AFR: 0.0343%; gnomAD_G_NFE: 0.0086%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134718402A>AT [0/1] rs200655017 (variation viewer)

Variant score: 0.126

Transcripts:: SEC24A:ENST00000398844.7:c.2970+229_2970+230insT:p.(=)

Pathogenicity Data:: Best Score: 0.20384067; CADD: 0.204 (0.990)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.4792%; gnomAD_G_AFR: 0.0922%; gnomAD_G_AMR: 1.3415%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 0.1195%; gnomAD_G_NFE: 0.6372%; gnomAD_G_OTH: 0.2053%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134705090A>AT [0/1] rs58181904 (variation viewer)

Variant score: 0.121

Transcripts:: SEC24A:ENST00000398844.7:c.2441-237_2441-236insT:p.(=)

Pathogenicity Data:: Best Score: 0.120775044; CADD: 0.121 (0.559)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134712399C>T [0/1] rs183049502 (variation viewer)

Variant score: 0.119

Transcripts:: SEC24A:ENST00000398844.7:c.2728-2625C>T:p.(=)

Pathogenicity Data:: Best Score: 0.19071782; CADD: 0.191 (0.919)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.1760%; gnomAD_G_AFR: 0.0233%; gnomAD_G_AMR: 0.6024%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0581%; gnomAD_G_NFE: 0.1425%; gnomAD_G_OTH: 0.1044%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134699155C>T [0/1] rs78476338 (variation viewer)

Variant score: 0.060

Transcripts:: SEC24A:ENST00000398844.7:c.2266+1098C>T:p.(=)

Pathogenicity Data:: Best Score: 0.105665445; CADD: 0.106 (0.485)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.5495%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1377%; gnomAD_G_AMR: 1.4354%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.1152%; gnomAD_G_NFE: 0.6350%; gnomAD_G_OTH: 0.2058%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134668314C>T [0/1] rs114161966 (variation viewer)

Variant score: 0.030

Transcripts:: SEC24A:ENST00000322887.8:c.739+1318C>T:p.(=); SEC24A:ENST00000398844.7:c.739+1318C>T:p.(=)

Pathogenicity Data:: Best Score: 0.048519254; CADD: 0.049 (0.216)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.5344%; UK10K: 0.8067%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.1146%; gnomAD_G_NFE: 0.6329%; gnomAD_G_OTH: 0.2041%

UQCRC2

Exomiser Score: 0.424

Phenotype Score: 0.506

Variant Score: 0.841

Phenotype matches:

Proximity score 0.506 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615160 Mitochondrial complex III deficiency, nuclear type 5 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.246

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.21961626T>TTATATATATATA [-/1] rs67999727 (variation viewer)

Variant score: 0.246 CONTRIBUTING VARIANT

Transcripts:: UQCRC2:ENST00000268379.9:c.333-834_333-833insTATATATATATA:p.(=); UQCRC2:ENST00000561553.5:c.333-834_333-833insTATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.24595022; CADD: 0.246 (1.226)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.424

Phenotype Score: 0.506

Variant Score: 0.841

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.21968873A>G [0/1] rs1032728197 (variation viewer)

Variant score: 0.939 CONTRIBUTING VARIANT

Transcripts:: UQCRC2:ENST00000268379.9:c.670+188A>G:p.(=); UQCRC2:ENST00000561553.5:c.670+188A>G:p.(=)

Pathogenicity Data:: Best Score: 0.95301056; CADD: 0.953 (13.280)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0133%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.21976789A>C [0/1] rs189727018 (variation viewer)

Variant score: 0.743 CONTRIBUTING VARIANT

Transcripts:: UQCRC2:ENST00000268379.9:c.1124+546A>C:p.(=); UQCRC2:ENST00000561553.5:c.1124+546A>C:p.(=)

Pathogenicity Data:: Best Score: 0.82457155; CADD: 0.825 (7.559)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.5240%; UK10K: 0.5025%; gnomAD_G_AFR: 0.1832%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.5463%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.21956946G>A [0/1] rs985406369 (variation viewer)

Variant score: 0.567

Transcripts:: UQCRC2:ENST00000268379.9:c.34-289G>A:p.(=); UQCRC2:ENST00000561553.5:c.34-289G>A:p.(=); UQCRC2:ENST00000630839.2:c.34-289G>A:p.(=)

Pathogenicity Data:: Best Score: 0.57577133; CADD: 0.576 (3.724)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0134%; gnomAD_G_OTH: 0.1020%

UBE3A

Exomiser Score: 0.418

Phenotype Score: 0.505

Variant Score: 0.839

Phenotype matches:

Phenotypic similarity 0.443 to Angelman syndrome associated with UBE3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000749, Paroxysmal bursts of laughter

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:105830 Angelman syndrome - autosomal dominant; ORPHA:238446 15q11q13 microduplication syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.418

Phenotype Score: 0.505

Variant Score: 0.839

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25362519T>C [0/1] rs955067035 (variation viewer)

Variant score: 0.839 CONTRIBUTING VARIANT

Transcripts:: UBE3A:ENST00000428984.6:c.1549-1992A>G:p.(=); UBE3A:ENST00000438097.6:c.1549-1992A>G:p.(=); UBE3A:ENST00000566215.5:c.1549-1992A>G:p.(=); UBE3A:ENST00000625778.2:c.1549-1992A>G:p.(=); UBE3A:ENST00000630424.2:c.1549-1992A>G:p.(=); UBE3A:ENST00000635914.1:c.1549-1992A>G:p.(=); UBE3A:ENST00000637886.1:c.1609-1992A>G:p.(=); UBE3A:ENST00000638011.1:c.1549-1992A>G:p.(=); UBE3A:ENST00000638155.1:c.1549-1992A>G:p.(=); UBE3A:ENST00000648336.1:c.1609-1992A>G:p.(=); UBE3A:ENST00000649550.1:c.1549-1992A>G:p.(=); UBE3A:ENST00000650110.1:c.1618-1992A>G:p.(=)

Pathogenicity Data:: Best Score: 0.84022826; CADD: 0.840 (7.965)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.035

Phenotype Score: 0.252

Variant Score: 0.800

Variants contributing to score:

SPLICE_REGION_VARIANT chr15:g.25415849G>GA [1/1] rs57736236 (variation viewer)

Variant score: 0.800 CONTRIBUTING VARIANT

Transcripts:: UBE3A:ENST00000638155.1:c.-568-8_-568-7insT:p.(=); UBE3A:ENST00000428984.6:c.-360-3879_-360-3878insT:p.(=); UBE3A:ENST00000438097.6:c.-451-3879_-451-3878insT:p.(=); UBE3A:ENST00000566215.5:c.-533-3879_-533-3878insT:p.(=); UBE3A:ENST00000625778.2:c.-40-10348_-40-10347insT:p.(=); UBE3A:ENST00000630424.2:c.-420-3879_-420-3878insT:p.(=); UBE3A:ENST00000635914.1:c.-40-10348_-40-10347insT:p.(=); UBE3A:ENST00000637886.1:c.-164-3879_-164-3878insT:p.(=); UBE3A:ENST00000638011.1:c.-337-3879_-337-3878insT:p.(=); UBE3A:ENST00000648336.1:c.-164-3879_-164-3878insT:p.(=); UBE3A:ENST00000649550.1:c.-40-10348_-40-10347insT:p.(=); UBE3A:ENST00000650110.1:c.-220-3879_-220-3878insT:p.(=)

Pathogenicity Data:: Best Score: 0.4130515; CADD: 0.413 (2.314)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25398190A>C [1/1] rs12910781 (variation viewer)

Variant score: 0.352

Transcripts:: UBE3A:ENST00000428984.6:c.2+7271T>G:p.(=); UBE3A:ENST00000438097.6:c.2+7271T>G:p.(=); UBE3A:ENST00000566215.5:c.2+7271T>G:p.(=); UBE3A:ENST00000625778.2:c.2+7271T>G:p.(=); UBE3A:ENST00000630424.2:c.2+7271T>G:p.(=); UBE3A:ENST00000635914.1:c.2+7271T>G:p.(=); UBE3A:ENST00000637886.1:c.62+7271T>G:p.(=); UBE3A:ENST00000638155.1:c.2+7271T>G:p.(=); UBE3A:ENST00000648336.1:c.62+7271T>G:p.(=); UBE3A:ENST00000649550.1:c.2+7271T>G:p.(=); UBE3A:ENST00000650110.1:c.71+7271T>G:p.(=); UBE3A:ENST00000638011.1:c.-111-4332T>G:p.(=)

Pathogenicity Data:: Best Score: 0.35226107; CADD: 0.352 (1.886)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25346419C>T [0/1] rs375363778 (variation viewer)

Variant score: 0.351

Transcripts:: UBE3A:ENST00000428984.6:c.2295-6191G>A:p.(=); UBE3A:ENST00000438097.6:c.2295-6191G>A:p.(=); UBE3A:ENST00000566215.5:c.2295-6191G>A:p.(=); UBE3A:ENST00000630424.2:c.2295-6191G>A:p.(=); UBE3A:ENST00000635914.1:c.2295-6191G>A:p.(=); UBE3A:ENST00000637886.1:c.2355-6191G>A:p.(=); UBE3A:ENST00000638011.1:c.2295-6191G>A:p.(=); UBE3A:ENST00000638155.1:c.2295-6191G>A:p.(=); UBE3A:ENST00000648336.1:c.2355-6191G>A:p.(=); UBE3A:ENST00000649550.1:c.2295-6191G>A:p.(=); UBE3A:ENST00000650110.1:c.2364-6191G>A:p.(=)

Pathogenicity Data:: Best Score: 0.37194163; CADD: 0.372 (2.020)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.2254%; UK10K: 0.3438%; gnomAD_G_AFR: 0.0691%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.3068%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25367223A>ACATATTTGTAAATATGTAAATATTTG [0/1] rs148089259 (variation viewer)

Variant score: 0.092

Transcripts:: UBE3A:ENST00000428984.6:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000438097.6:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000566215.5:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000625778.2:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000630424.2:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000635914.1:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000637886.1:c.1608+3342_1608+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000638011.1:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000638155.1:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000648336.1:c.1608+3342_1608+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000649550.1:c.1548+3342_1548+3343insCAAATATTTACATATTTACAAATATG:p.(=); UBE3A:ENST00000650110.1:c.1617+3342_1617+3343insCAAATATTTACATATTTACAAATATG:p.(=)

Pathogenicity Data:: Best Score: 0.11813927; CADD: 0.118 (0.546)

Frequency Data:: gnomAD_G_AFR: 0.0951%; gnomAD_G_AMR: 0.9804%; gnomAD_G_EAS: 0.8065%; gnomAD_G_FIN: 0.1214%; gnomAD_G_NFE: 0.3676%; gnomAD_G_OTH: 0.7184%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25399724G>A [0|1] rs539486575 (variation viewer)

Variant score: 0.088

Transcripts:: UBE3A:ENST00000428984.6:c.2+5737C>T:p.(=); UBE3A:ENST00000438097.6:c.2+5737C>T:p.(=); UBE3A:ENST00000566215.5:c.2+5737C>T:p.(=); UBE3A:ENST00000625778.2:c.2+5737C>T:p.(=); UBE3A:ENST00000630424.2:c.2+5737C>T:p.(=); UBE3A:ENST00000635914.1:c.2+5737C>T:p.(=); UBE3A:ENST00000637886.1:c.62+5737C>T:p.(=); UBE3A:ENST00000638155.1:c.2+5737C>T:p.(=); UBE3A:ENST00000648336.1:c.62+5737C>T:p.(=); UBE3A:ENST00000649550.1:c.2+5737C>T:p.(=); UBE3A:ENST00000650110.1:c.71+5737C>T:p.(=); UBE3A:ENST00000638011.1:c.-112+5737C>T:p.(=)

Pathogenicity Data:: Best Score: 0.08987719; CADD: 0.090 (0.409)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.0669%; UK10K: 0.0132%; gnomAD_G_EAS: 0.0627%; gnomAD_G_NFE: 0.0669%; gnomAD_G_OTH: 0.1029%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25398770T>TA [0/1] rs1567066949 (variation viewer)

Variant score: 0.075

Transcripts:: UBE3A:ENST00000428984.6:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000438097.6:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000566215.5:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000625778.2:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000630424.2:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000635914.1:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000637886.1:c.62+6690_62+6691insT:p.(=); UBE3A:ENST00000638155.1:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000648336.1:c.62+6690_62+6691insT:p.(=); UBE3A:ENST00000649550.1:c.2+6690_2+6691insT:p.(=); UBE3A:ENST00000650110.1:c.71+6690_71+6691insT:p.(=); UBE3A:ENST00000638011.1:c.-111-4913_-111-4912insT:p.(=)

Pathogenicity Data:: Best Score: 0.07636583; CADD: 0.076 (0.345)

Frequency Data:: gnomAD_G_AFR: 0.1455%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.25398771T>TATATATA [0/1]

Variant score: 0.062

Transcripts:: UBE3A:ENST00000428984.6:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000438097.6:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000566215.5:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000625778.2:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000630424.2:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000635914.1:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000637886.1:c.62+6689_62+6690insTATATAT:p.(=); UBE3A:ENST00000638155.1:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000648336.1:c.62+6689_62+6690insTATATAT:p.(=); UBE3A:ENST00000649550.1:c.2+6689_2+6690insTATATAT:p.(=); UBE3A:ENST00000650110.1:c.71+6689_71+6690insTATATAT:p.(=); UBE3A:ENST00000638011.1:c.-111-4914_-111-4913insTATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.06179011; CADD: 0.062 (0.277)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.25434975C>* [-/1]

Variant score: 0.000

Transcripts:: UBE3A:ENST00000428984.6:c.-361+3514G>:p.(=); UBE3A:ENST00000438097.6:c.-452+3514G>:p.(=); UBE3A:ENST00000566215.5:c.-534+3514G>:p.(=); UBE3A:ENST00000625778.2:c.-41+3514G>:p.(=); UBE3A:ENST00000630424.2:c.-421+3514G>:p.(=); UBE3A:ENST00000635914.1:c.-41+3514G>:p.(=); UBE3A:ENST00000637886.1:c.-201+3514G>:p.(=); UBE3A:ENST00000638011.1:c.-338+3514G>:p.(=); UBE3A:ENST00000638155.1:c.-666+3514G>:p.(=); UBE3A:ENST00000648336.1:c.-165+3514G>:p.(=); UBE3A:ENST00000649550.1:c.-41+3514G>:p.(=); UBE3A:ENST00000650110.1:c.-221+3514G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ATXN10

Exomiser Score: 0.411

Phenotype Score: 0.511

Variant Score: 0.829

Phenotype matches:

Phenotypic similarity 0.479 to Spinocerebellar ataxia type 10 associated with ATXN10.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.511 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:603516 Spinocerebellar ataxia 10 - autosomal dominant; ORPHA:98761 Spinocerebellar ataxia type 10

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.411

Phenotype Score: 0.511

Variant Score: 0.829

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45684397G>A [0/1]

Variant score: 0.829 CONTRIBUTING VARIANT

Transcripts:: ATXN10:ENST00000252934.10:c.117-5315G>A:p.(=); ATXN10:ENST00000381061.8:c.117-8599G>A:p.(=); ATXN10:ENST00000640901.1:c.117-5315G>A:p.(=)

Pathogenicity Data:: Best Score: 0.82923454; CADD: 0.829 (7.676)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.053

Phenotype Score: 0.256

Variant Score: 0.843

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45702901T>G [0/1] rs140990591 (variation viewer)

Variant score: 0.857 CONTRIBUTING VARIANT

Transcripts:: ATXN10:ENST00000252934.10:c.647+54T>G:p.(=); ATXN10:ENST00000381061.8:c.455+54T>G:p.(=); ATXN10:ENST00000640901.1:c.647+54T>G:p.(=)

Pathogenicity Data:: Best Score: 0.90472037; CADD: 0.905 (10.210)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0358%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0400%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45684397G>A [0/1]

Variant score: 0.829 CONTRIBUTING VARIANT

Transcripts:: ATXN10:ENST00000252934.10:c.117-5315G>A:p.(=); ATXN10:ENST00000381061.8:c.117-8599G>A:p.(=); ATXN10:ENST00000640901.1:c.117-5315G>A:p.(=)

Pathogenicity Data:: Best Score: 0.82923454; CADD: 0.829 (7.676)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45735812CT>C [-/1] rs746222703 (variation viewer)

Variant score: 0.300

Transcripts:: ATXN10:ENST00000252934.10:c.895-2918del:p.(=); ATXN10:ENST00000381061.8:c.703-2918del:p.(=); ATXN10:ENST00000640901.1:c.923+1396del:p.(=)

Pathogenicity Data:: Best Score: 0.2996744; CADD: 0.300 (1.547)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.45850549A>G [0/1] rs142585609 (variation viewer)

Variant score: 0.133

Transcripts:: ATXN10:ENST00000252934.10::; ATXN10:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.31134772; CADD: 0.311 (1.620)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1218%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45740679T>TACAC [-/1] rs74268525 (variation viewer)

Variant score: 0.113

Transcripts:: ATXN10:ENST00000252934.10:c.1173+141_1173+142insACAC:p.(=); ATXN10:ENST00000381061.8:c.981+141_981+142insACAC:p.(=)

Pathogenicity Data:: Best Score: 0.11284399; CADD: 0.113 (0.520)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45751740G>GA [0/1] rs200364242 (variation viewer)

Variant score: 0.109

Transcripts:: ATXN10:ENST00000252934.10:c.1173+11202_1173+11203insA:p.(=); ATXN10:ENST00000381061.8:c.981+11202_981+11203insA:p.(=)

Pathogenicity Data:: Best Score: 0.10915941; CADD: 0.109 (0.502)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.45805712G>A [0/1] rs930252084 (variation viewer)

Variant score: 0.062

Transcripts:: ATXN10:ENST00000252934.10:c.1174-1247G>A:p.(=); ATXN10:ENST00000381061.8:c.982-1247G>A:p.(=); ATXN10:ENST00000402380.3:c.127-1247G>A:p.(=)

Pathogenicity Data:: Best Score: 0.063301146; CADD: 0.063 (0.284)

Frequency Data:: TOPMed: 0.0088%; gnomAD_G_OTH: 0.1018%

NAA20

Exomiser Score: 0.410

Phenotype Score: 0.502

Variant Score: 0.839

Phenotype matches:

Proximity score 0.502 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.410

Phenotype Score: 0.502

Variant Score: 0.839

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.20028818G>GA [0/1] rs1346582870 (variation viewer)

Variant score: 0.839 CONTRIBUTING VARIANT

Transcripts:: NAA20:ENST00000310450.8:c.305+1899_305+1900insA:p.(=); NAA20:ENST00000334982.9:c.305+1899_305+1900insA:p.(=); NAA20:ENST00000398602.2:c.269+1899_269+1900insA:p.(=)

Pathogenicity Data:: Best Score: 0.8388983; CADD: 0.839 (7.929)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.283

Phenotype Score: 0.502

Variant Score: 0.777

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.20028818G>GA [0/1] rs1346582870 (variation viewer)

Variant score: 0.839 CONTRIBUTING VARIANT

Transcripts:: NAA20:ENST00000310450.8:c.305+1899_305+1900insA:p.(=); NAA20:ENST00000334982.9:c.305+1899_305+1900insA:p.(=); NAA20:ENST00000398602.2:c.269+1899_269+1900insA:p.(=)

Pathogenicity Data:: Best Score: 0.8388983; CADD: 0.839 (7.929)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.20028221T>C [0/1]

Variant score: 0.716 CONTRIBUTING VARIANT

Transcripts:: NAA20:ENST00000310450.8:c.305+1302T>C:p.(=); NAA20:ENST00000334982.9:c.305+1302T>C:p.(=); NAA20:ENST00000398602.2:c.269+1302T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7158812; CADD: 0.716 (5.465)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr20:g.20012115C>CA [1/1] rs10693396 (variation viewer)

Variant score: 0.257

Transcripts:: NAA20:ENST00000310450.8::

Pathogenicity Data:: Best Score: 0.25732297; CADD: 0.257 (1.292)

Frequency Data:: No frequency data

KLC1

Exomiser Score: 0.409

Phenotype Score: 0.507

Variant Score: 0.833

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.409

Phenotype Score: 0.507

Variant Score: 0.833

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103680557A>G [0/1] rs970246730 (variation viewer)

Variant score: 0.833 CONTRIBUTING VARIANT

Transcripts:: KLC1:ENST00000246489.11:c.1650+1012A>G:p.(=); KLC1:ENST00000334553.10:c.1650+1012A>G:p.(=); KLC1:ENST00000347839.10:c.1623+1039A>G:p.(=); KLC1:ENST00000348520.10:c.1650+1012A>G:p.(=); KLC1:ENST00000380038.7:c.1698+1039A>G:p.(=); KLC1:ENST00000389744.8:c.1650+1012A>G:p.(=); KLC1:ENST00000445352.8:c.1617+1039A>G:p.(=); KLC1:ENST00000452929.6:c.1650+1012A>G:p.(=); KLC1:ENST00000553286.5:c.1650+1012A>G:p.(=); KLC1:ENST00000554280.5:c.1623+1039A>G:p.(=); KLC1:ENST00000555836.5:c.1623+1039A>G:p.(=); KLC1:ENST00000557450.5:c.1623+1039A>G:p.(=); KLC1:ENST00000557575.5:c.1650+1012A>G:p.(=); KLC1:ENST00000634686.1:c.1623+1039A>G:p.(=); KLC1:ENST00000472726.2:c.2166+1012A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8329679; CADD: 0.833 (7.772)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.031

Phenotype Score: 0.507

Variant Score: 0.499

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103680557A>G [0/1] rs970246730 (variation viewer)

Variant score: 0.833 CONTRIBUTING VARIANT

Transcripts:: KLC1:ENST00000246489.11:c.1650+1012A>G:p.(=); KLC1:ENST00000334553.10:c.1650+1012A>G:p.(=); KLC1:ENST00000347839.10:c.1623+1039A>G:p.(=); KLC1:ENST00000348520.10:c.1650+1012A>G:p.(=); KLC1:ENST00000380038.7:c.1698+1039A>G:p.(=); KLC1:ENST00000389744.8:c.1650+1012A>G:p.(=); KLC1:ENST00000445352.8:c.1617+1039A>G:p.(=); KLC1:ENST00000452929.6:c.1650+1012A>G:p.(=); KLC1:ENST00000553286.5:c.1650+1012A>G:p.(=); KLC1:ENST00000554280.5:c.1623+1039A>G:p.(=); KLC1:ENST00000555836.5:c.1623+1039A>G:p.(=); KLC1:ENST00000557450.5:c.1623+1039A>G:p.(=); KLC1:ENST00000557575.5:c.1650+1012A>G:p.(=); KLC1:ENST00000634686.1:c.1623+1039A>G:p.(=); KLC1:ENST00000472726.2:c.2166+1012A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8329679; CADD: 0.833 (7.772)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr14:g.103712773C>T [0/1] rs3212035 (variation viewer)

Variant score: 0.166 CONTRIBUTING VARIANT

Transcripts:: KLC1:ENST00000348520.10:c.*11574C>T:p.(=); KLC1:ENST00000352127.11:c.-260-1206G>A:p.(=); KLC1:ENST00000554913.5:c.-196+102G>A:p.(=); KLC1:ENST00000554974.5:c.-55+2651G>A:p.(=); KLC1:ENST00000555055.6:c.-261+102G>A:p.(=)

Pathogenicity Data:: Best Score: 0.39854932; CADD: 0.399 (2.208)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 1.0230%; UK10K: 1.3885%; gnomAD_G_AFR: 0.3097%; gnomAD_G_AMR: 1.6706%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.3150%; gnomAD_G_NFE: 1.4676%; gnomAD_G_OTH: 1.1224%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103693805C>T [0|1] rs147672245 (variation viewer)

Variant score: 0.073

Transcripts:: KLC1:ENST00000334553.10:c.1848+1380C>T:p.(=); KLC1:ENST00000348520.10:c.1651-6850C>T:p.(=); KLC1:ENST00000452929.6:c.1781+6594C>T:p.(=); KLC1:ENST00000554280.5:c.1754+6594C>T:p.(=); KLC1:ENST00000555836.5:c.1821+1380C>T:p.(=); KLC1:ENST00000557450.5:c.1624-6850C>T:p.(=); KLC1:ENST00000634686.1:c.*187C>T:p.(=)

Pathogenicity Data:: Best Score: 0.10525352; CADD: 0.105 (0.483)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.6706%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1835%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.9199%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103695341A>* [-/1]

Variant score: 0.000

Transcripts:: KLC1:ENST00000334553.10:c.1848+2916A>*:p.(=); KLC1:ENST00000348520.10:c.1651-5314A>*:p.(=); KLC1:ENST00000452929.6:c.1782-5314A>*:p.(=); KLC1:ENST00000554280.5:c.1755-5314A>*:p.(=); KLC1:ENST00000555836.5:c.1821+2916A>*:p.(=); KLC1:ENST00000557450.5:c.1624-5314A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103695343A>* [-/1]

Variant score: 0.000

Transcripts:: KLC1:ENST00000334553.10:c.1848+2918A>*:p.(=); KLC1:ENST00000348520.10:c.1651-5312A>*:p.(=); KLC1:ENST00000452929.6:c.1782-5312A>*:p.(=); KLC1:ENST00000554280.5:c.1755-5312A>*:p.(=); KLC1:ENST00000555836.5:c.1821+2918A>*:p.(=); KLC1:ENST00000557450.5:c.1624-5312A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103696096CCG>* [-/1]

Variant score: 0.000

Transcripts:: KLC1:ENST00000334553.10:c.1848+3671_1848+3673delCCGins*:p.(=); KLC1:ENST00000348520.10:c.1651-4559_1651-4557delCCGins*:p.(=); KLC1:ENST00000452929.6:c.1782-4559_1782-4557delCCGins*:p.(=); KLC1:ENST00000554280.5:c.1755-4559_1755-4557delCCGins*:p.(=); KLC1:ENST00000555836.5:c.1821+3671_1821+3673delCCGins*:p.(=); KLC1:ENST00000557450.5:c.1624-4559_1624-4557delCCGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UBXN7

Exomiser Score: 0.408

Phenotype Score: 0.505

Variant Score: 0.835

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.408

Phenotype Score: 0.505

Variant Score: 0.835

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr3:g.196345350A>G [0/1] rs990058873 (variation viewer)

Variant score: 0.835 CONTRIBUTING VARIANT

Transcripts:: UBXN7:ENST00000296328.9::; UBXN7:ENST00000454715.5::

Pathogenicity Data:: Best Score: 0.83495593; CADD: 0.835 (7.824)

Frequency Data:: TOPMed: 0.0040%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.131

Phenotype Score: 0.505

Variant Score: 0.669

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr3:g.196345350A>G [0/1] rs990058873 (variation viewer)

Variant score: 0.835 CONTRIBUTING VARIANT

Transcripts:: UBXN7:ENST00000296328.9::; UBXN7:ENST00000454715.5::

Pathogenicity Data:: Best Score: 0.83495593; CADD: 0.835 (7.824)

Frequency Data:: TOPMed: 0.0040%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.196422371C>T [0/1] rs866444030 (variation viewer)

Variant score: 0.503 CONTRIBUTING VARIANT

Transcripts:: UBXN7:ENST00000296328.9:c.73+9956G>A:p.(=); UBXN7:ENST00000428095.1:c.-19+9956G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5050059; CADD: 0.505 (3.054)

Frequency Data:: TOPMed: 0.0287%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0134%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr3:g.196346751CTTT>C [1/1] rs769521419 (variation viewer)

Variant score: 0.162

Transcripts:: UBXN7:ENST00000296328.9::; UBXN7:ENST00000454715.5::

Pathogenicity Data:: Best Score: 0.17224842; CADD: 0.172 (0.821)

Frequency Data:: gnomAD_G_AFR: 0.1719%; gnomAD_G_NFE: 0.3587%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.196376545C>CAAA [0/1] rs777458391 (variation viewer)

Variant score: 0.089

Transcripts:: UBXN7:ENST00000296328.9:c.469-4504_469-4503insTTT:p.(=); UBXN7:ENST00000428095.1:c.-18-4504_-18-4503insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.088618934; CADD: 0.089 (0.403)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.196408097CA>C [0/1] rs71621241 (variation viewer)

Variant score: 0.083

Transcripts:: UBXN7:ENST00000296328.9:c.74-705del:p.(=); UBXN7:ENST00000428095.1:c.-19+24229del:p.(=)

Pathogenicity Data:: Best Score: 0.082724094; CADD: 0.083 (0.375)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.196372300T>TTCTCTCTCTCTCTCTCTC [0/1] rs144595952 (variation viewer)

Variant score: 0.049

Transcripts:: UBXN7:ENST00000296328.9:c.469-259_469-258insGAGAGAGAGAGAGAGAGA:p.(=); UBXN7:ENST00000428095.1:c.-18-259_-18-258insGAGAGAGAGAGAGAGAGA:p.(=)

Pathogenicity Data:: Best Score: 0.049395204; CADD: 0.049 (0.220)

Frequency Data:: No frequency data

UTRN

Exomiser Score: 0.397

Phenotype Score: 0.501

Variant Score: 0.834

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.397

Phenotype Score: 0.501

Variant Score: 0.834

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144437892T>C [0/1] rs913047453 (variation viewer)

Variant score: 0.834 CONTRIBUTING VARIANT

Transcripts:: UTRN:ENST00000367545.7:c.1241+146T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8353734; CADD: 0.835 (7.835)

Frequency Data:: TOPMed: 0.0096%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.236

Phenotype Score: 0.501

Variant Score: 0.752

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144437892T>C [0/1] rs913047453 (variation viewer)

Variant score: 0.834 CONTRIBUTING VARIANT

Transcripts:: UTRN:ENST00000367545.7:c.1241+146T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8353734; CADD: 0.835 (7.835)

Frequency Data:: TOPMed: 0.0096%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144502681C>T [0/1] rs140063573 (variation viewer)

Variant score: 0.670 CONTRIBUTING VARIANT

Transcripts:: UTRN:ENST00000367545.7:c.4764+3254C>T:p.(=)

Pathogenicity Data:: Best Score: 0.696541; CADD: 0.697 (5.179)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1832%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.2466%; gnomAD_G_OTH: 0.1022%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144645392T>C [0/1] rs149338693 (variation viewer)

Variant score: 0.571

Transcripts:: UTRN:ENST00000367526.8:c.145-33014T>C:p.(=); UTRN:ENST00000367545.7:c.7480-33014T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5825543; CADD: 0.583 (3.794)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1226%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.1399%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144849752T>C [0/1] rs548601257 (variation viewer)

Variant score: 0.318

Transcripts:: UTRN:ENST00000367526.8:c.2959-1237T>C:p.(=); UTRN:ENST00000367545.7:c.10294-1237T>C:p.(=)

Pathogenicity Data:: Best Score: 0.50739366; CADD: 0.507 (3.075)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.1513%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0114%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.1467%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144721703T>G [0/1] rs1011423930 (variation viewer)

Variant score: 0.316

Transcripts:: UTRN:ENST00000367526.8:c.475-8654T>G:p.(=); UTRN:ENST00000367545.7:c.7810-8654T>G:p.(=)

Pathogenicity Data:: Best Score: 0.3164032; CADD: 0.316 (1.652)

Frequency Data:: TOPMed: 0.0032%

DOWNSTREAM_GENE_VARIANT chr6:g.144854226T>TATAGATAGATAGATAG [-/1] rs71028316 (variation viewer)

Variant score: 0.294

Transcripts:: UTRN:ENST00000367545.7::; UTRN:ENST00000404707.2::

Pathogenicity Data:: Best Score: 0.29449517; CADD: 0.294 (1.515)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144653951A>G [0/1] rs866183333 (variation viewer)

Variant score: 0.277

Transcripts:: UTRN:ENST00000367526.8:c.145-24455A>G:p.(=); UTRN:ENST00000367545.7:c.7480-24455A>G:p.(=)

Pathogenicity Data:: Best Score: 0.27739662; CADD: 0.277 (1.411)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0133%

INTERGENIC_VARIANT chr6:g.144280835CAA>C [0/1] rs34347508 (variation viewer)

Variant score: 0.266

Transcripts:: UTRN:ENST00000367545.7::; UTRN:ENST00000404655.1::

Pathogenicity Data:: Best Score: 0.26616234; CADD: 0.266 (1.344)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144451633A>G [0/1]

Variant score: 0.260

Transcripts:: UTRN:ENST00000367545.7:c.2196+140A>G:p.(=)

Pathogenicity Data:: Best Score: 0.2602244; CADD: 0.260 (1.309)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.144870580C>T [0|1] rs146404887 (variation viewer)

Variant score: 0.251

Transcripts:: UTRN:ENST00000367545.7::; UTRN:ENST00000404707.2::

Pathogenicity Data:: Best Score: 0.40089905; CADD: 0.401 (2.225)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.6076%; UK10K: 0.8463%; gnomAD_G_AFR: 0.1606%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.9273%; gnomAD_G_OTH: 0.8147%

INTERGENIC_VARIANT chr6:g.144282661C>T [0/1] rs1358301165 (variation viewer)

Variant score: 0.244

Transcripts:: UTRN:ENST00000367545.7::; UTRN:ENST00000404655.1::

Pathogenicity Data:: Best Score: 0.24403793; CADD: 0.244 (1.215)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144610217A>G [0/1] rs138027475 (variation viewer)

Variant score: 0.221

Transcripts:: UTRN:ENST00000367526.8:c.144+26617A>G:p.(=); UTRN:ENST00000367545.7:c.7479+32929A>G:p.(=)

Pathogenicity Data:: Best Score: 0.39535564; CADD: 0.395 (2.185)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.2196%; UK10K: 0.9786%; gnomAD_G_AFR: 0.0918%; gnomAD_G_AMR: 0.6143%; gnomAD_G_ASJ: 0.3356%; gnomAD_G_FIN: 0.5316%; gnomAD_G_NFE: 1.4507%; gnomAD_G_OTH: 1.1530%

UPSTREAM_GENE_VARIANT chr6:g.144290752CTTTTT>C [1/1] rs200477118 (variation viewer)

Variant score: 0.192

Transcripts:: UTRN:ENST00000367545.7::; UTRN:ENST00000404655.1::

Pathogenicity Data:: Best Score: 0.19202113; CADD: 0.192 (0.926)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144622184G>GT [1/1] rs1199579909 (variation viewer)

Variant score: 0.180

Transcripts:: UTRN:ENST00000367526.8:c.144+38584_144+38585insT:p.(=); UTRN:ENST00000367545.7:c.7479+44896_7479+44897insT:p.(=)

Pathogenicity Data:: Best Score: 0.18002617; CADD: 0.180 (0.862)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.144872272T>C [0/1] rs562043695 (variation viewer)

Variant score: 0.166

Transcripts:: UTRN:ENST00000367545.7::; UTRN:ENST00000404707.2::

Pathogenicity Data:: Best Score: 0.2648093; CADD: 0.265 (1.336)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.3616%; UK10K: 0.4628%; gnomAD_G_AFR: 0.0919%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.4138%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144824572T>TTATATA [1/1] rs71028314 (variation viewer)

Variant score: 0.136

Transcripts:: UTRN:ENST00000367526.8:c.2160-2776_2160-2775insTATATA:p.(=); UTRN:ENST00000367545.7:c.9495-2776_9495-2775insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.13642514; CADD: 0.136 (0.637)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144631237G>GGTGTGTGT [1/1] rs67332744 (variation viewer)

Variant score: 0.133

Transcripts:: UTRN:ENST00000367526.8:c.145-47169_145-47168insGTGTGTGT:p.(=); UTRN:ENST00000367545.7:c.7480-47169_7480-47168insGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.1330381; CADD: 0.133 (0.620)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144590217C>T [0/1] rs148347105 (variation viewer)

Variant score: 0.103

Transcripts:: UTRN:ENST00000367526.8:c.144+6617C>T:p.(=); UTRN:ENST00000367545.7:c.7479+12929C>T:p.(=)

Pathogenicity Data:: Best Score: 0.11630988; CADD: 0.116 (0.537)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.2262%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1196%; gnomAD_G_EAS: 0.6196%; gnomAD_G_NFE: 0.1533%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144780418T>G [1/1] rs545738835 (variation viewer)

Variant score: 0.097

Transcripts:: UTRN:ENST00000367526.8:c.1298-1504T>G:p.(=); UTRN:ENST00000367545.7:c.8633-1504T>G:p.(=)

Pathogenicity Data:: Best Score: 0.15452647; CADD: 0.155 (0.729)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.1832%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.1867%; gnomAD_G_OTH: 0.2053%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144301536CTTTT>C [1/1] rs200484231 (variation viewer)

Variant score: 0.078

Transcripts:: UTRN:ENST00000367545.7:c.79+9630_79+9633del:p.(=)

Pathogenicity Data:: Best Score: 0.07849008; CADD: 0.078 (0.355)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144732241T>TATATATATATATATATATATATAC [-/1]

Variant score: 0.071

Transcripts:: UTRN:ENST00000367526.8:c.604+1755_604+1756insATATATATATATATATATATATAC:p.(=); UTRN:ENST00000367545.7:c.7939+1755_7939+1756insATATATATATATATATATATATAC:p.(=)

Pathogenicity Data:: Best Score: 0.070605695; CADD: 0.071 (0.318)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144732241T>TATATATATATATATATATATAC [-/1] rs6910394 (variation viewer)

Variant score: 0.067

Transcripts:: UTRN:ENST00000367526.8:c.604+1755_604+1756insATATATATATATATATATATAC:p.(=); UTRN:ENST00000367545.7:c.7939+1755_7939+1756insATATATATATATATATATATAC:p.(=)

Pathogenicity Data:: Best Score: 0.07338357; CADD: 0.073 (0.331)

Frequency Data:: gnomAD_G_AFR: 0.0193%; gnomAD_G_ASJ: 0.5155%; gnomAD_G_NFE: 0.3000%; gnomAD_G_OTH: 0.1946%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144781109C>T [1/1] rs565488768 (variation viewer)

Variant score: 0.066

Transcripts:: UTRN:ENST00000367526.8:c.1298-813C>T:p.(=); UTRN:ENST00000367545.7:c.8633-813C>T:p.(=)

Pathogenicity Data:: Best Score: 0.105047464; CADD: 0.105 (0.482)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.1776%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0114%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.1865%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144751067A>C [0/1] rs778502618 (variation viewer)

Variant score: 0.056

Transcripts:: UTRN:ENST00000367526.8:c.874-739A>C:p.(=); UTRN:ENST00000367545.7:c.8209-739A>C:p.(=)

Pathogenicity Data:: Best Score: 0.0557217; CADD: 0.056 (0.249)

Frequency Data:: TOPMed: 0.0032%; UK10K: 0.0132%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144322502C>A [0/1] rs185477854 (variation viewer)

Variant score: 0.016

Transcripts:: UTRN:ENST00000367545.7:c.79+30595C>A:p.(=)

Pathogenicity Data:: Best Score: 0.016441941; CADD: 0.016 (0.072)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0398%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0400%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144446231G>A [0/1] rs144000098 (variation viewer)

Variant score: 0.004

Transcripts:: UTRN:ENST00000367545.7:c.1615-980G>A:p.(=)

Pathogenicity Data:: Best Score: 0.00985229; CADD: 0.010 (0.043)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.2031%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0344%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.2134%; gnomAD_G_OTH: 0.3074%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144317225A>G [0/1] rs569486028 (variation viewer)

Variant score: 0.003

Transcripts:: UTRN:ENST00000367545.7:c.79+25318A>G:p.(=)

Pathogenicity Data:: Best Score: 0.0027592778; CADD: 0.003 (0.012)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0414%; UK10K: 0.0264%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0400%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.144433479AGGCAGAGGGTCTCCTCACTTCCCAGACGGGGTGGCTGCCG>A [0/1]

Variant score: 0.000

Transcripts:: UTRN:ENST00000367545.7:c.856-2455_856-2416del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TMED7

Exomiser Score: 0.396

Phenotype Score: 0.505

Variant Score: 0.830

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.396

Phenotype Score: 0.505

Variant Score: 0.830

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.115624610G>A [0/1] rs779132555 (variation viewer)

Variant score: 0.830 CONTRIBUTING VARIANT

Transcripts:: TMED7:ENST00000456936.4:c.192+991C>T:p.(=); TMED7:ENST00000282382.8:c.192+991C>T:p.(=); TMED7:ENST00000333314.3:c.192+991C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8335438; CADD: 0.834 (7.787)

Frequency Data:: TOPMed: 0.0175%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.259

Phenotype Score: 0.505

Variant Score: 0.761

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.115624610G>A [0/1] rs779132555 (variation viewer)

Variant score: 0.830 CONTRIBUTING VARIANT

Transcripts:: TMED7:ENST00000456936.4:c.192+991C>T:p.(=); TMED7:ENST00000282382.8:c.192+991C>T:p.(=); TMED7:ENST00000333314.3:c.192+991C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8335438; CADD: 0.834 (7.787)

Frequency Data:: TOPMed: 0.0175%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.0200%

CUSTOM chr5:g.115703003CTATATATATATA>C [-/1] rs59095437 (variation viewer)

Variant score: 0.693 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.6931685; CADD: 0.693 (5.131)

Frequency Data:: No frequency data

Other passed variants:

CUSTOM chr5:g.115547937G>GTGTGTGTGTATA [0/1] rs1284559247 (variation viewer)

Variant score: 0.136

Transcripts:

Pathogenicity Data:: Best Score: 0.13582838; CADD: 0.136 (0.634)

Frequency Data:: No frequency data

CUSTOM chr5:g.115699595A>ATATATATATATATATATATATTTTTTTTTT [0/1]

Variant score: 0.116

Transcripts:

Pathogenicity Data:: Best Score: 0.11590284; CADD: 0.116 (0.535)

Frequency Data:: No frequency data

CUSTOM chr5:g.115642784A>T [0|1] rs11956382 (variation viewer)

Variant score: 0.097

Transcripts:

Pathogenicity Data:: Best Score: 0.10195106; CADD: 0.102 (0.467)

Frequency Data:: gnomAD_G_AFR: 0.0700%; gnomAD_G_AMR: 0.1229%; gnomAD_G_FIN: 0.0885%; gnomAD_G_NFE: 0.1640%; gnomAD_G_OTH: 0.3158%

STOM

Exomiser Score: 0.395

Phenotype Score: 0.502

Variant Score: 0.833

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.038

Phenotype Score: 0.502

Variant Score: 0.528

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr9:g.121336838T>A [0/1]

Variant score: 0.528 CONTRIBUTING VARIANT

Transcripts:: STOM:ENST00000286713.7::; STOM:ENST00000449733.7::

Pathogenicity Data:: Best Score: 0.52793694; CADD: 0.528 (3.260)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.395

Phenotype Score: 0.502

Variant Score: 0.833

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr9:g.121334772TTGTGTGTGTG>T [1/1] rs55834253 (variation viewer)

Variant score: 0.833 CONTRIBUTING VARIANT

Transcripts:: STOM:ENST00000286713.7::; STOM:ENST00000449733.7::

Pathogenicity Data:: Best Score: 0.83258283; CADD: 0.833 (7.762)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121340988A>C [0/1] rs141027021 (variation viewer)

Variant score: 0.855

Transcripts:: STOM:ENST00000538954.5:c.487-1347T>G:p.(=); STOM:ENST00000286713.7:c.*214T>G:p.(=); STOM:ENST00000347359.3:c.*214T>G:p.(=)

Pathogenicity Data:: Best Score: 0.93176615; CADD: 0.932 (11.660)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0446%; UK10K: 0.0529%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121349046G>A [0/1] rs551351325 (variation viewer)

Variant score: 0.802

Transcripts:: STOM:ENST00000286713.7:c.525+74C>T:p.(=); STOM:ENST00000347359.3:c.165+7007C>T:p.(=); STOM:ENST00000538954.5:c.486+113C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8826184; CADD: 0.883 (9.304)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.2763%; UK10K: 0.5157%; gnomAD_G_AFR: 0.1490%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.3472%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121355620G>A [0/1] rs141928363 (variation viewer)

Variant score: 0.527

Transcripts:: STOM:ENST00000286713.7:c.165+433C>T:p.(=); STOM:ENST00000347359.3:c.165+433C>T:p.(=); STOM:ENST00000538954.5:c.165+433C>T:p.(=)

Pathogenicity Data:: Best Score: 0.57469547; CADD: 0.575 (3.713)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0422%; UK10K: 0.0529%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0666%

REGULATORY_REGION_VARIANT chr9:g.121372981TGTG>T [0|1] rs536031308 (variation viewer)

Variant score: 0.488

Transcripts:: STOM:ENST00000538954.5::; STOM:ENST00000481534.5::

Pathogenicity Data:: Best Score: 0.53172606; CADD: 0.532 (3.295)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0430%; UK10K: 0.0529%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121344789C>T [0/1] rs149988163 (variation viewer)

Variant score: 0.311

Transcripts:: STOM:ENST00000286713.7:c.660+3226G>A:p.(=); STOM:ENST00000347359.3:c.166-3381G>A:p.(=); STOM:ENST00000538954.5:c.486+4370G>A:p.(=)

Pathogenicity Data:: Best Score: 0.33900225; CADD: 0.339 (1.798)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.0581%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0572%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121347744C>T [0/1] rs139793249 (variation viewer)

Variant score: 0.296

Transcripts:: STOM:ENST00000286713.7:c.660+271G>A:p.(=); STOM:ENST00000347359.3:c.166-6336G>A:p.(=); STOM:ENST00000538954.5:c.486+1415G>A:p.(=)

Pathogenicity Data:: Best Score: 0.32251453; CADD: 0.323 (1.691)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0422%; UK10K: 0.0529%; gnomAD_G_AMR: 0.4785%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121355231C>CAATA [0/1] rs1554830881 (variation viewer)

Variant score: 0.281

Transcripts:: STOM:ENST00000286713.7:c.166-559_166-558insTATT:p.(=); STOM:ENST00000347359.3:c.165+821_165+822insTATT:p.(=); STOM:ENST00000538954.5:c.166-559_166-558insTATT:p.(=)

Pathogenicity Data:: Best Score: 0.28104782; CADD: 0.281 (1.433)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121359088G>A [0/1] rs144953283 (variation viewer)

Variant score: 0.219

Transcripts:: STOM:ENST00000286713.7:c.62-2932C>T:p.(=); STOM:ENST00000347359.3:c.62-2932C>T:p.(=); STOM:ENST00000538954.5:c.62-2932C>T:p.(=)

Pathogenicity Data:: Best Score: 0.23879784; CADD: 0.239 (1.185)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1398%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0733%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121345890C>T [0/1] rs145850601 (variation viewer)

Variant score: 0.157

Transcripts:: STOM:ENST00000286713.7:c.660+2125G>A:p.(=); STOM:ENST00000347359.3:c.166-4482G>A:p.(=); STOM:ENST00000538954.5:c.486+3269G>A:p.(=)

Pathogenicity Data:: Best Score: 0.17110407; CADD: 0.171 (0.815)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0502%; UK10K: 0.0793%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121352418A>G [0|1] rs143601053 (variation viewer)

Variant score: 0.142

Transcripts:: STOM:ENST00000286713.7:c.321+802T>C:p.(=); STOM:ENST00000347359.3:c.165+3635T>C:p.(=); STOM:ENST00000538954.5:c.321+802T>C:p.(=)

Pathogenicity Data:: Best Score: 0.15530485; CADD: 0.155 (0.733)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.0549%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0666%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.121357424G>GATATATATATATATATATATATATATATATATATATAT [0/1]

Variant score: 0.093

Transcripts:: STOM:ENST00000286713.7:c.62-1269_62-1268insATATATATATATATATATATATATATATATATATATAT:p.(=); STOM:ENST00000347359.3:c.62-1269_62-1268insATATATATATATATATATATATATATATATATATATAT:p.(=); STOM:ENST00000538954.5:c.62-1269_62-1268insATATATATATATATATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.09280634; CADD: 0.093 (0.423)

Frequency Data:: No frequency data

UGT8

Exomiser Score: 0.395

Phenotype Score: 0.505

Variant Score: 0.829

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.395

Phenotype Score: 0.505

Variant Score: 0.829

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.114606294A>C [0/1] rs976011743 (variation viewer)

Variant score: 0.829 CONTRIBUTING VARIANT

Transcripts:: UGT8:ENST00000310836.11:c.-3+7320A>C:p.(=)

Pathogenicity Data:: Best Score: 0.82923454; CADD: 0.829 (7.676)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.273

Phenotype Score: 0.505

Variant Score: 0.769

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.114606294A>C [0/1] rs976011743 (variation viewer)

Variant score: 0.829 CONTRIBUTING VARIANT

Transcripts:: UGT8:ENST00000310836.11:c.-3+7320A>C:p.(=)

Pathogenicity Data:: Best Score: 0.82923454; CADD: 0.829 (7.676)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.114638515T>C [0/1] rs771382013 (variation viewer)

Variant score: 0.708 CONTRIBUTING VARIANT

Transcripts:: UGT8:ENST00000310836.11:c.822+14813T>C:p.(=); UGT8:ENST00000394511.3:c.822+14813T>C:p.(=)

Pathogenicity Data:: Best Score: 0.72061694; CADD: 0.721 (5.538)

Frequency Data:: TOPMed: 0.0223%; UK10K: 0.0132%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0533%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.114670430C>CA [1/1] rs70964319 (variation viewer)

Variant score: 0.138

Transcripts:: UGT8:ENST00000310836.11:c.1262+2126_1262+2127insA:p.(=); UGT8:ENST00000394511.3:c.1262+2126_1262+2127insA:p.(=)

Pathogenicity Data:: Best Score: 0.13841128; CADD: 0.138 (0.647)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.114674452T>A [0/1] rs80253942 (variation viewer)

Variant score: 0.029

Transcripts:: UGT8:ENST00000310836.11:c.1263-1473T>A:p.(=); UGT8:ENST00000394511.3:c.1263-1473T>A:p.(=)

Pathogenicity Data:: Best Score: 0.060060263; CADD: 0.060 (0.269)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.6849%; UK10K: 1.1902%; gnomAD_G_AFR: 0.2404%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 1.5741%; gnomAD_G_NFE: 0.9999%; gnomAD_G_OTH: 1.2220%

CERS3

Exomiser Score: 0.392

Phenotype Score: 0.505

Variant Score: 0.828

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615023 Ichthyosis, congenital, autosomal recessive 9 - autosomal recessive; ORPHA:79394 Congenital non-bullous ichthyosiform erythroderma

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.051

Phenotype Score: 0.252

Variant Score: 0.843

Variants contributing to score:

FIVE_PRIME_UTR_EXON_VARIANT chr15:g.100544394CCGCGGGGACACGGGCCCTCTCTCGGCCTTGACCTG>C [0/1] rs369214990 (variation viewer)

Variant score: 0.843 CONTRIBUTING VARIANT

Transcripts:: CERS3:ENST00000394113.5:c.-707_-673del:p.(=); CERS3:ENST00000284382.8:c.-355+222_-355+256del:p.(=)

Pathogenicity Data:: Best Score: 0.8429637; CADD: 0.843 (8.040)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.392

Phenotype Score: 0.505

Variant Score: 0.828

Variants contributing to score:

FIVE_PRIME_UTR_EXON_VARIANT chr15:g.100544394CCGCGGGGACACGGGCCCTCTCTCGGCCTTGACCTG>C [0/1] rs369214990 (variation viewer)

Variant score: 0.843 CONTRIBUTING VARIANT

Transcripts:: CERS3:ENST00000394113.5:c.-707_-673del:p.(=); CERS3:ENST00000284382.8:c.-355+222_-355+256del:p.(=)

Pathogenicity Data:: Best Score: 0.8429637; CADD: 0.843 (8.040)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.100544461T>C [0|1] rs79818657 (variation viewer)

Variant score: 0.813 CONTRIBUTING VARIANT

Transcripts:: CERS3:ENST00000284382.8:c.-355+190A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8128887; CADD: 0.813 (7.279)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.100526478C>CTGTGTGTGTGTGTG [-/1] rs1217852084 (variation viewer)

Variant score: 0.526

Transcripts:: CERS3:ENST00000284382.8:c.-92+2334_-92+2335insCACACACACACACA:p.(=); CERS3:ENST00000394113.5:c.-231+2334_-231+2335insCACACACACACACA:p.(=); CERS3:ENST00000538112.6:c.-92+2334_-92+2335insCACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.5264127; CADD: 0.526 (3.246)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100450416CA>C [0/1] rs34873483 (variation viewer)

Variant score: 0.213

Transcripts:: CERS3:ENST00000284382.8:c.999+5476del:p.(=); CERS3:ENST00000394113.5:c.999+5476del:p.(=); CERS3:ENST00000538112.6:c.999+5476del:p.(=)

Pathogenicity Data:: Best Score: 0.21331656; CADD: 0.213 (1.042)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100467850T>TATAG [0/1] rs1555528323 (variation viewer)

Variant score: 0.144

Transcripts:: CERS3:ENST00000284382.8:c.845+1527_845+1528insCTAT:p.(=); CERS3:ENST00000394113.5:c.845+1527_845+1528insCTAT:p.(=); CERS3:ENST00000538112.6:c.845+1527_845+1528insCTAT:p.(=)

Pathogenicity Data:: Best Score: 0.14414537; CADD: 0.144 (0.676)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr15:g.100397435C>CA [0/1] rs200691619 (variation viewer)

Variant score: 0.135

Transcripts:: CERS3:ENST00000284382.8::; CERS3:ENST00000268070.9::

Pathogenicity Data:: Best Score: 0.454619; CADD: 0.455 (2.633)

Frequency Data:: gnomAD_G_AFR: 0.2727%; gnomAD_G_AMR: 1.0610%; gnomAD_G_ASJ: 0.3597%; gnomAD_G_EAS: 0.1916%; gnomAD_G_FIN: 1.6103%; gnomAD_G_NFE: 1.8226%; gnomAD_G_OTH: 1.4184%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100440479A>G [0/1] rs149089562 (variation viewer)

Variant score: 0.102

Transcripts:: CERS3:ENST00000284382.8:c.999+15414T>C:p.(=); CERS3:ENST00000394113.5:c.999+15414T>C:p.(=); CERS3:ENST00000538112.6:c.999+15414T>C:p.(=)

Pathogenicity Data:: Best Score: 0.31071317; CADD: 0.311 (1.616)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.9174%; UK10K: 1.7852%; gnomAD_G_AFR: 0.2295%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.2307%; gnomAD_G_NFE: 1.6370%; gnomAD_G_OTH: 1.3238%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100466737TTTCCTTCCTTCC>T [0/1] rs1197426230 (variation viewer)

Variant score: 0.101

Transcripts:: CERS3:ENST00000284382.8:c.845+2629_845+2640del:p.(=); CERS3:ENST00000394113.5:c.845+2629_845+2640del:p.(=); CERS3:ENST00000538112.6:c.845+2629_845+2640del:p.(=)

Pathogenicity Data:: Best Score: 0.11182201; CADD: 0.112 (0.515)

Frequency Data:: gnomAD_G_AFR: 0.0279%; gnomAD_G_EAS: 0.5415%; gnomAD_G_NFE: 0.0404%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100483787A>T [1|1] rs12901777 (variation viewer)

Variant score: 0.098

Transcripts:: CERS3:ENST00000284382.8:c.407+763T>A:p.(=); CERS3:ENST00000394113.5:c.407+763T>A:p.(=); CERS3:ENST00000538112.6:c.407+763T>A:p.(=)

Pathogenicity Data:: Best Score: 0.097598135; CADD: 0.098 (0.446)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100494247ATATATATATATT>A [-/1] rs1383069478 (variation viewer)

Variant score: 0.073

Transcripts:: CERS3:ENST00000284382.8:c.174-3328_174-3317del:p.(=); CERS3:ENST00000394113.5:c.174-3328_174-3317del:p.(=); CERS3:ENST00000538112.6:c.174-3328_174-3317del:p.(=)

Pathogenicity Data:: Best Score: 0.1081332; CADD: 0.108 (0.497)

Frequency Data:: gnomAD_G_AFR: 0.7401%; gnomAD_G_AMR: 1.2295%; gnomAD_G_ASJ: 0.9524%; gnomAD_G_EAS: 0.2768%; gnomAD_G_NFE: 0.8007%; gnomAD_G_OTH: 0.1818%

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.100511847T>C [1|1] rs183955611 (variation viewer)

Variant score: 0.069

Transcripts:: CERS3:ENST00000284382.8:c.-2+9820A>G:p.(=); CERS3:ENST00000394113.5:c.-140-7999A>G:p.(=); CERS3:ENST00000538112.6:c.-2+9820A>G:p.(=)

Pathogenicity Data:: Best Score: 0.37280875; CADD: 0.373 (2.026)

Frequency Data:: gnomAD_G_AFR: 0.7660%; gnomAD_G_AMR: 0.6024%; gnomAD_G_EAS: 1.9481%; gnomAD_G_FIN: 0.1678%; gnomAD_G_NFE: 0.9284%; gnomAD_G_OTH: 0.9804%

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.100544493C>T [0|1] rs28513799 (variation viewer)

Variant score: 0.033

Transcripts:: CERS3:ENST00000284382.8:c.-355+158G>A:p.(=)

Pathogenicity Data:: Best Score: 0.058110416; CADD: 0.058 (0.260)

Frequency Data:: gnomAD_G_AFR: 1.4401%; gnomAD_G_AMR: 0.3717%; gnomAD_G_ASJ: 0.6410%; gnomAD_G_EAS: 0.3472%; gnomAD_G_FIN: 0.3021%; gnomAD_G_NFE: 0.4759%; gnomAD_G_OTH: 0.1761%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100482611TA>* [-/1]

Variant score: 0.000

Transcripts:: CERS3:ENST00000284382.8:c.407+1938_407+1939delTAins:p.(=); CERS3:ENST00000394113.5:c.407+1938_407+1939delTAins:p.(=); CERS3:ENST00000538112.6:c.407+1938_407+1939delTAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100494247ATATATATATATT>* [-/1]

Variant score: 0.000

Transcripts:: CERS3:ENST00000284382.8:c.174-3328_174-3316delAATATATATATATins:p.(=); CERS3:ENST00000394113.5:c.174-3328_174-3316delAATATATATATATins:p.(=); CERS3:ENST00000538112.6:c.174-3328_174-3316delAATATATATATATins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PIK3CB

Exomiser Score: 0.387

Phenotype Score: 0.507

Variant Score: 0.823

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.387

Phenotype Score: 0.507

Variant Score: 0.823

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.138714390A>C [0/1] rs1425843303 (variation viewer)

Variant score: 0.823 CONTRIBUTING VARIANT

Transcripts:: PIK3CB:ENST00000289153.6:c.1302+78T>G:p.(=); PIK3CB:ENST00000477593.5:c.1302+78T>G:p.(=); PIK3CB:ENST00000674063.1:c.1302+78T>G:p.(=); PIK3CB:ENST00000544716.5:c.-230+78T>G:p.(=)

Pathogenicity Data:: Best Score: 0.824329; CADD: 0.824 (7.553)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.036

Phenotype Score: 0.507

Variant Score: 0.515

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.138714390A>C [0/1] rs1425843303 (variation viewer)

Variant score: 0.823 CONTRIBUTING VARIANT

Transcripts:: PIK3CB:ENST00000289153.6:c.1302+78T>G:p.(=); PIK3CB:ENST00000477593.5:c.1302+78T>G:p.(=); PIK3CB:ENST00000674063.1:c.1302+78T>G:p.(=); PIK3CB:ENST00000544716.5:c.-230+78T>G:p.(=)

Pathogenicity Data:: Best Score: 0.824329; CADD: 0.824 (7.553)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0133%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.138797420C>T [0/1] rs1408937995 (variation viewer)

Variant score: 0.206 CONTRIBUTING VARIANT

Transcripts:: PIK3CB:ENST00000477593.5:c.-17+37275G>A:p.(=); PIK3CB:ENST00000674063.1:c.-121-853G>A:p.(=)

Pathogenicity Data:: Best Score: 0.20640302; CADD: 0.206 (1.004)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.138703425G>C [0/1] rs145296073 (variation viewer)

Variant score: 0.132

Transcripts:: PIK3CB:ENST00000289153.6:c.1581+1018C>G:p.(=); PIK3CB:ENST00000477593.5:c.1581+1018C>G:p.(=); PIK3CB:ENST00000674063.1:c.1581+1018C>G:p.(=); PIK3CB:ENST00000544716.5:c.-82+1018C>G:p.(=)

Pathogenicity Data:: Best Score: 0.13582838; CADD: 0.136 (0.634)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0199%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1196%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.0467%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.138747054TTA>T [-/1] rs59299476 (variation viewer)

Variant score: 0.129

Transcripts:: PIK3CB:ENST00000289153.6:c.398-4275_398-4274del:p.(=); PIK3CB:ENST00000477593.5:c.398-4275_398-4274del:p.(=); PIK3CB:ENST00000674063.1:c.398-4275_398-4274del:p.(=)

Pathogenicity Data:: Best Score: 0.12903643; CADD: 0.129 (0.600)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.138737394CA>C [1|1] rs11344311 (variation viewer)

Variant score: 0.100

Transcripts:: PIK3CB:ENST00000289153.6:c.801+312del:p.(=); PIK3CB:ENST00000477593.5:c.801+312del:p.(=); PIK3CB:ENST00000674063.1:c.801+312del:p.(=)

Pathogenicity Data:: Best Score: 0.10008812; CADD: 0.100 (0.458)

Frequency Data:: No frequency data

NDUFS4

Exomiser Score: 0.380

Phenotype Score: 0.504

Variant Score: 0.823

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFS4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:252010 Mitochondrial complex I deficiency, nuclear type 1 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.018

Phenotype Score: 0.252

Variant Score: 0.723

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.53699141A>G [0/1] rs945640478 (variation viewer)

Variant score: 0.723 CONTRIBUTING VARIANT

Transcripts:: NDUFS4:ENST00000296684.10::; NDUFS4:ENST00000513426.1::

Pathogenicity Data:: Best Score: 0.7231784; CADD: 0.723 (5.578)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.380

Phenotype Score: 0.504

Variant Score: 0.823

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.53568792TCTCTA>T [0/1] rs771457410 (variation viewer)

Variant score: 0.922 CONTRIBUTING VARIANT

Transcripts:: NDUFS4:ENST00000296684.10:c.98+8033_98+8037del:p.(=)

Pathogenicity Data:: Best Score: 0.9742368; CADD: 0.974 (15.890)

Frequency Data:: TOPMed: 0.0350%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.0333%

INTERGENIC_VARIANT chr5:g.53699141A>G [0/1] rs945640478 (variation viewer)

Variant score: 0.723 CONTRIBUTING VARIANT

Transcripts:: NDUFS4:ENST00000296684.10::; NDUFS4:ENST00000513426.1::

Pathogenicity Data:: Best Score: 0.7231784; CADD: 0.723 (5.578)

Frequency Data:: TOPMed: 0.0016%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.53563034C>A [0|1] rs1165245656 (variation viewer)

Variant score: 0.685

Transcripts:: NDUFS4:ENST00000296684.10:c.98+2274C>A:p.(=)

Pathogenicity Data:: Best Score: 0.73097044; CADD: 0.731 (5.702)

Frequency Data:: gnomAD_G_AFR: 0.0348%; gnomAD_G_AMR: 0.3797%; gnomAD_G_FIN: 0.0880%; gnomAD_G_NFE: 0.0271%

REGULATORY_REGION_VARIANT chr5:g.53337910G>GAAAAAAA [1|1] rs1561251360 (variation viewer)

Variant score: 0.467

Transcripts:

Pathogenicity Data:: Best Score: 0.46727878; CADD: 0.467 (2.735)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.53563102GCCTGTAGTC>G [0/1] rs10940323 (variation viewer)

Variant score: 0.311

Transcripts:: NDUFS4:ENST00000296684.10:c.98+2343_98+2351del:p.(=)

Pathogenicity Data:: Best Score: 0.32298237; CADD: 0.323 (1.694)

Frequency Data:: gnomAD_G_AFR: 0.0242%; gnomAD_G_AMR: 0.2506%; gnomAD_G_FIN: 0.1786%; gnomAD_G_NFE: 0.0274%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.53586329C>CAA [0/1] rs539748080 (variation viewer)

Variant score: 0.114

Transcripts:: NDUFS4:ENST00000296684.10:c.99-17123_99-17122insAA:p.(=)

Pathogenicity Data:: Best Score: 0.32220244; CADD: 0.322 (1.689)

Frequency Data:: gnomAD_G_AFR: 1.3598%; gnomAD_G_NFE: 0.3491%; gnomAD_G_OTH: 1.7544%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.53657672A>C [0/1] rs184370571 (variation viewer)

Variant score: 0.092

Transcripts:: NDUFS4:ENST00000296684.10:c.351-879A>C:p.(=)

Pathogenicity Data:: Best Score: 0.12642539; CADD: 0.126 (0.587)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.2469%; UK10K: 0.1322%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 1.1111%; gnomAD_G_FIN: 0.3155%; gnomAD_G_NFE: 0.3401%; gnomAD_G_OTH: 0.6122%

FA2H

Exomiser Score: 0.378

Phenotype Score: 0.864

Variant Score: 0.415

Phenotype matches:

Phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612319 Spastic paraplegia 35, autosomal recessive - autosomal recessive; ORPHA:171629 Autosomal recessive spastic paraplegia type 35; ORPHA:329308 Fatty acid hydroxylase-associated neurodegeneration

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.432

Variant Score: 0.005

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.74745799AT>A [0/1] rs11365398 (variation viewer)

Variant score: 0.005 CONTRIBUTING VARIANT

Transcripts:: FA2H:ENST00000219368.8:c.271-5685del:p.(=)

Pathogenicity Data:: Best Score: 0.0050528646; CADD: 0.005 (0.022)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.378

Phenotype Score: 0.864

Variant Score: 0.415

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.74750761C>CTGTGTGTGTGTGTG [1/1] rs55799456 (variation viewer)

Variant score: 0.415 CONTRIBUTING VARIANT

Transcripts:: FA2H:ENST00000219368.8:c.271-10647_271-10646insCACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.41467106; CADD: 0.415 (2.326)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.74744983C>T [0/1] rs549494397 (variation viewer)

Variant score: 0.490

Transcripts:: FA2H:ENST00000219368.8:c.271-4868G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5617721; CADD: 0.562 (3.583)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.0366%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0133%; gnomAD_G_OTH: 0.2037%

DOWNSTREAM_GENE_VARIANT chr16:g.74711200CTTTTTT>C [1/1] rs869235859 (variation viewer)

Variant score: 0.278

Transcripts:: FA2H:ENST00000219368.8::; FA2H:ENST00000308807.12::

Pathogenicity Data:: Best Score: 0.27772927; CADD: 0.278 (1.413)

Frequency Data:: No frequency data

GNB1L

Exomiser Score: 0.377

Phenotype Score: 0.506

Variant Score: 0.820

Phenotype matches:

Proximity score 0.506 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.377

Phenotype Score: 0.506

Variant Score: 0.820

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19789850A>G [0|1]

Variant score: 0.820 CONTRIBUTING VARIANT

Transcripts:: GNB1L:ENST00000329517.11:c.733-890T>C:p.(=); GNB1L:ENST00000403325.5:c.733-890T>C:p.(=); GNB1L:ENST00000405009.5:c.631-1224T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8195321; CADD: 0.820 (7.436)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.226

Phenotype Score: 0.506

Variant Score: 0.740

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19789850A>G [0|1]

Variant score: 0.820 CONTRIBUTING VARIANT

Transcripts:: GNB1L:ENST00000329517.11:c.733-890T>C:p.(=); GNB1L:ENST00000403325.5:c.733-890T>C:p.(=); GNB1L:ENST00000405009.5:c.631-1224T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8195321; CADD: 0.820 (7.436)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19789843A>C [0|1]

Variant score: 0.661 CONTRIBUTING VARIANT

Transcripts:: GNB1L:ENST00000329517.11:c.733-883T>G:p.(=); GNB1L:ENST00000403325.5:c.733-883T>G:p.(=); GNB1L:ENST00000405009.5:c.631-1217T>G:p.(=)

Pathogenicity Data:: Best Score: 0.66053104; CADD: 0.661 (4.692)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19789851A>G [0|1]

Variant score: 0.174

Transcripts:: GNB1L:ENST00000329517.11:c.733-891T>C:p.(=); GNB1L:ENST00000403325.5:c.733-891T>C:p.(=); GNB1L:ENST00000405009.5:c.631-1225T>C:p.(=)

Pathogenicity Data:: Best Score: 0.17358154; CADD: 0.174 (0.828)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19806479C>T [0/1] rs138872781 (variation viewer)

Variant score: 0.073

Transcripts:: GNB1L:ENST00000329517.11:c.516+180G>A:p.(=); GNB1L:ENST00000403325.5:c.516+180G>A:p.(=); GNB1L:ENST00000405009.5:c.516+180G>A:p.(=)

Pathogenicity Data:: Best Score: 0.1707223; CADD: 0.171 (0.813)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.5455%; UK10K: 0.5290%; gnomAD_G_AFR: 0.1719%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.5404%; gnomAD_G_OTH: 0.4082%

HEXA

Exomiser Score: 0.374

Phenotype Score: 0.502

Variant Score: 0.823

Phenotype matches:

Proximity score 0.502 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:272800 GM2-gangliosidosis, several forms - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.374

Phenotype Score: 0.502

Variant Score: 0.823

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.72366323T>C [0/1] rs182975856 (variation viewer)

Variant score: 0.853 CONTRIBUTING VARIANT

Transcripts:: HEXA:ENST00000268097.9:c.253+9397A>G:p.(=); HEXA:ENST00000566304.5:c.253+9397A>G:p.(=); HEXA:ENST00000567159.5:c.253+9397A>G:p.(=); HEXA:ENST00000379915.4:c.253+9397A>G:p.(=)

Pathogenicity Data:: Best Score: 0.89062953; CADD: 0.891 (9.611)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.1362%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0230%; gnomAD_G_NFE: 0.2703%; gnomAD_G_OTH: 0.2066%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.72348664A>G [0/1] rs192794313 (variation viewer)

Variant score: 0.792 CONTRIBUTING VARIANT

Transcripts:: HEXA:ENST00000268097.9:c.986+415T>C:p.(=); HEXA:ENST00000566304.5:c.1019+415T>C:p.(=); HEXA:ENST00000567159.5:c.986+415T>C:p.(=); HEXA:ENST00000379915.4:c.413-2339T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8266595; CADD: 0.827 (7.611)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.1378%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.2666%; gnomAD_G_OTH: 0.2037%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.72365249C>T [0/1] rs368243018 (variation viewer)

Variant score: 0.026

Transcripts:: HEXA:ENST00000268097.9:c.254-8632G>A:p.(=); HEXA:ENST00000566304.5:c.254-8599G>A:p.(=); HEXA:ENST00000567159.5:c.254-8632G>A:p.(=); HEXA:ENST00000379915.4:c.254-8632G>A:p.(=)

Pathogenicity Data:: Best Score: 0.026580572; CADD: 0.027 (0.117)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.1306%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.2407%; gnomAD_G_OTH: 0.2045%

VMA21

Exomiser Score: 0.373

Phenotype Score: 0.505

Variant Score: 0.819

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:310440 Myopathy, X-linked, with excessive autophagy - X-linked recessive

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.373

Phenotype Score: 0.505

Variant Score: 0.819

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr23:g.151411249TCTCA>T [1/1] rs1297955506 (variation viewer)

Variant score: 0.819 CONTRIBUTING VARIANT

Transcripts:: VMA21:ENST00000330374.6::; VMA21:ENST00000370357.5::

Pathogenicity Data:: Best Score: 0.82102185; CADD: 0.821 (7.472)

Frequency Data:: gnomAD_G_AFR: 0.0171%

X_DOMINANT

Exomiser Score: 0.041

Phenotype Score: 0.252

Variant Score: 0.819

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr23:g.151411249TCTCA>T [1/1] rs1297955506 (variation viewer)

Variant score: 0.819 CONTRIBUTING VARIANT

Transcripts:: VMA21:ENST00000330374.6::; VMA21:ENST00000370357.5::

Pathogenicity Data:: Best Score: 0.82102185; CADD: 0.821 (7.472)

Frequency Data:: gnomAD_G_AFR: 0.0171%

Other passed variants:

GAB2

Exomiser Score: 0.373

Phenotype Score: 0.504

Variant Score: 0.820

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.198

Phenotype Score: 0.504

Variant Score: 0.725

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78233040G>GTTTTTTTT [0/1] rs372693456 (variation viewer)

Variant score: 0.725 CONTRIBUTING VARIANT

Transcripts:: GAB2:ENST00000340149.6:c.507-5990_507-5989insAAAAAAAA:p.(=); GAB2:ENST00000361507.5:c.621-5990_621-5989insAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.7245137; CADD: 0.725 (5.599)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.373

Phenotype Score: 0.504

Variant Score: 0.820

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78355680T>TAA [1/1] rs67850407 (variation viewer)

Variant score: 0.820 CONTRIBUTING VARIANT

Transcripts:: GAB2:ENST00000361507.5:c.75+61965_75+61966insTT:p.(=)

Pathogenicity Data:: Best Score: 0.8198227; CADD: 0.820 (7.443)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78235829GTCT>G [0/1] rs543000587 (variation viewer)

Variant score: 0.619

Transcripts:: GAB2:ENST00000340149.6:c.507-8781_507-8779del:p.(=); GAB2:ENST00000361507.5:c.621-8781_621-8779del:p.(=)

Pathogenicity Data:: Best Score: 0.641986; CADD: 0.642 (4.461)

Frequency Data:: gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78378777C>T [0/1] rs867384865 (variation viewer)

Variant score: 0.484

Transcripts:: GAB2:ENST00000361507.5:c.75+38869G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5024921; CADD: 0.502 (3.032)

Frequency Data:: TOPMed: 0.0127%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78366585C>CA [1/1] rs33997665 (variation viewer)

Variant score: 0.274

Transcripts:: GAB2:ENST00000361507.5:c.75+51060_75+51061insT:p.(=)

Pathogenicity Data:: Best Score: 0.27439547; CADD: 0.274 (1.393)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78414087CA>C [0/1] rs34915163 (variation viewer)

Variant score: 0.267

Transcripts:: GAB2:ENST00000361507.5:c.75+3558del:p.(=)

Pathogenicity Data:: Best Score: 0.2666691; CADD: 0.267 (1.347)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78233085G>A [0/1] rs868614375 (variation viewer)

Variant score: 0.255

Transcripts:: GAB2:ENST00000340149.6:c.507-6034C>T:p.(=); GAB2:ENST00000361507.5:c.621-6034C>T:p.(=)

Pathogenicity Data:: Best Score: 0.26548612; CADD: 0.265 (1.340)

Frequency Data:: gnomAD_G_AMR: 0.2506%; gnomAD_G_NFE: 0.0139%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78405091ATT>A [0/1] rs1174366754 (variation viewer)

Variant score: 0.228

Transcripts:: GAB2:ENST00000361507.5:c.75+12553_75+12554del:p.(=)

Pathogenicity Data:: Best Score: 0.22803074; CADD: 0.228 (1.124)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78323790C>CTTTT [0/1] rs749282969 (variation viewer)

Variant score: 0.226

Transcripts:: GAB2:ENST00000361507.5:c.76-42890_76-42889insAAAA:p.(=); GAB2:ENST00000340149.6:c.-40+17969_-40+17970insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.22607303; CADD: 0.226 (1.113)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78370725A>ATGTGTGTGTGTGTG [0/1] rs113823389 (variation viewer)

Variant score: 0.159

Transcripts:: GAB2:ENST00000361507.5:c.75+46920_75+46921insCACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.15879858; CADD: 0.159 (0.751)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78227631C>CAAAAAAAAAAAAA [0/1] rs55716895 (variation viewer)

Variant score: 0.149

Transcripts:: GAB2:ENST00000340149.6:c.507-581_507-580insTTTTTTTTTTTTT:p.(=); GAB2:ENST00000361507.5:c.621-581_621-580insTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14866596; CADD: 0.149 (0.699)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78317558C>CAAAA [0/1] rs370515492 (variation viewer)

Variant score: 0.142

Transcripts:: GAB2:ENST00000361507.5:c.76-36658_76-36657insTTTT:p.(=); GAB2:ENST00000340149.6:c.-40+24201_-40+24202insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14236993; CADD: 0.142 (0.667)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78266214C>CAAAAA [1/1] rs11445907 (variation viewer)

Variant score: 0.139

Transcripts:: GAB2:ENST00000340149.6:c.262+14386_262+14387insTTTTT:p.(=); GAB2:ENST00000361507.5:c.376+14386_376+14387insTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.13900626; CADD: 0.139 (0.650)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78231336G>GGTGTGTGTGTGTGTGTGTGTGT [0/1] rs58651538 (variation viewer)

Variant score: 0.135

Transcripts:: GAB2:ENST00000340149.6:c.507-4286_507-4285insACACACACACACACACACACAC:p.(=); GAB2:ENST00000361507.5:c.621-4286_621-4285insACACACACACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.13503206; CADD: 0.135 (0.630)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78289724AG>A [0/1] rs532524881 (variation viewer)

Variant score: 0.130

Transcripts:: GAB2:ENST00000361507.5:c.76-8824del:p.(=); GAB2:ENST00000340149.6:c.-39-8824del:p.(=)

Pathogenicity Data:: Best Score: 0.169002; CADD: 0.169 (0.804)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.1887%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0345%; gnomAD_G_AMR: 0.3597%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0290%; gnomAD_G_NFE: 0.2067%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78336326CAAA>C [1/1] rs71046966 (variation viewer)

Variant score: 0.120

Transcripts:: GAB2:ENST00000361507.5:c.76-55428_76-55426del:p.(=); GAB2:ENST00000340149.6:c.-40+5431_-40+5433del:p.(=)

Pathogenicity Data:: Best Score: 0.120167494; CADD: 0.120 (0.556)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78238206CA>C [1/1] rs10541492 (variation viewer)

Variant score: 0.114

Transcripts:: GAB2:ENST00000340149.6:c.507-11156del:p.(=); GAB2:ENST00000361507.5:c.621-11156del:p.(=)

Pathogenicity Data:: Best Score: 0.114068806; CADD: 0.114 (0.526)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78322298CAAAAAAAA>C [0/1] rs56709163 (variation viewer)

Variant score: 0.111

Transcripts:: GAB2:ENST00000361507.5:c.76-41405_76-41398del:p.(=); GAB2:ENST00000340149.6:c.-40+19454_-40+19461del:p.(=)

Pathogenicity Data:: Best Score: 0.11141288; CADD: 0.111 (0.513)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78300695G>GTT [0/1] rs769243672 (variation viewer)

Variant score: 0.060

Transcripts:: GAB2:ENST00000361507.5:c.76-19795_76-19794insAA:p.(=); GAB2:ENST00000340149.6:c.-39-19795_-39-19794insAA:p.(=)

Pathogenicity Data:: Best Score: 0.05984384; CADD: 0.060 (0.268)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78276111C>CAAA [0/1] rs539148797 (variation viewer)

Variant score: 0.029

Transcripts:: GAB2:ENST00000340149.6:c.262+4489_262+4490insTTT:p.(=); GAB2:ENST00000361507.5:c.376+4489_376+4490insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.060493052; CADD: 0.060 (0.271)

Frequency Data:: gnomAD_G_AFR: 0.2878%; gnomAD_G_AMR: 0.4274%; gnomAD_G_ASJ: 1.5873%; gnomAD_G_EAS: 0.5495%; gnomAD_G_FIN: 0.5682%; gnomAD_G_NFE: 0.0558%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78263899ATT>A [0/1] rs74630302 (variation viewer)

Variant score: 0.018

Transcripts:: GAB2:ENST00000340149.6:c.263-13501_263-13500del:p.(=); GAB2:ENST00000361507.5:c.377-13501_377-13500del:p.(=)

Pathogenicity Data:: Best Score: 0.07657844; CADD: 0.077 (0.346)

Frequency Data:: gnomAD_G_AFR: 0.6750%; gnomAD_G_AMR: 1.7241%; gnomAD_G_ASJ: 1.8939%; gnomAD_G_EAS: 0.7692%; gnomAD_G_FIN: 1.0676%; gnomAD_G_NFE: 0.9165%; gnomAD_G_OTH: 1.6624%

ADGRV1

Exomiser Score: 0.373

Phenotype Score: 0.512

Variant Score: 0.810

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 2 associated with ADGRV1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.512 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.512 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:604352 ?Febrile seizures, familial, 4 (unconfirmed); OMIM:605472 Usher syndrome, type 2C - autosomal recessive; ORPHA:231178 Usher syndrome type 2; ORPHA:36387 Generalized epilepsy with febrile seizures-plus

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.373

Phenotype Score: 0.512

Variant Score: 0.810

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90648592T>A [0/1]

Variant score: 0.810 CONTRIBUTING VARIANT

Transcripts:: ADGRV1:ENST00000405460.9:c.3289+828T>A:p.(=)

Pathogenicity Data:: Best Score: 0.8102857; CADD: 0.810 (7.219)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.171

Phenotype Score: 0.512

Variant Score: 0.695

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90648592T>A [0/1]

Variant score: 0.810 CONTRIBUTING VARIANT

Transcripts:: ADGRV1:ENST00000405460.9:c.3289+828T>A:p.(=)

Pathogenicity Data:: Best Score: 0.8102857; CADD: 0.810 (7.219)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.91014176C>CACACACACACA [-/1]

Variant score: 0.580 CONTRIBUTING VARIANT

Transcripts:: ADGRV1:ENST00000405460.9:c.18152+28654_18152+28655insACACACACACA:p.(=); ADGRV1:ENST00000639821.1:c.236+28654_236+28655insACACACACACA:p.(=); ADGRV1:ENST00000640815.1:c.236+28654_236+28655insACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.5799509; CADD: 0.580 (3.767)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.91014176C>CACACACACACACACACACACACA [-/1] rs56292568 (variation viewer)

Variant score: 0.518

Transcripts:: ADGRV1:ENST00000405460.9:c.18152+28654_18152+28655insACACACACACACACACACACACA:p.(=); ADGRV1:ENST00000639821.1:c.236+28654_236+28655insACACACACACACACACACACACA:p.(=); ADGRV1:ENST00000640815.1:c.236+28654_236+28655insACACACACACACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.51816314; CADD: 0.518 (3.171)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90809293T>TACACACAC [-/1] rs60659185 (variation viewer)

Variant score: 0.467

Transcripts:: ADGRV1:ENST00000405460.9:c.14973-940_14973-939insACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.4670334; CADD: 0.467 (2.733)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90809293T>TACACACACACACACAC [-/1] rs60659185 (variation viewer)

Variant score: 0.422

Transcripts:: ADGRV1:ENST00000405460.9:c.14973-940_14973-939insACACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.42190397; CADD: 0.422 (2.380)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90646152A>G [0/1]

Variant score: 0.416

Transcripts:: ADGRV1:ENST00000405460.9:c.3022+61A>G:p.(=)

Pathogenicity Data:: Best Score: 0.41642052; CADD: 0.416 (2.339)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90763890G>A [0|1] rs541739121 (variation viewer)

Variant score: 0.390

Transcripts:: ADGRV1:ENST00000405460.9:c.12285+421G>A:p.(=)

Pathogenicity Data:: Best Score: 0.39979446; CADD: 0.400 (2.217)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0987%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0229%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0799%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90721576T>TATAAA [1|1] rs1554094715 (variation viewer)

Variant score: 0.384

Transcripts:: ADGRV1:ENST00000405460.9:c.9748+517_9748+518insATAAA:p.(=)

Pathogenicity Data:: Best Score: 0.3838308; CADD: 0.384 (2.103)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90961515T>C [1|1] rs6896106 (variation viewer)

Variant score: 0.263

Transcripts:: ADGRV1:ENST00000405460.9:c.17857-3900T>C:p.(=); ADGRV1:ENST00000639821.1:c.-60-3900T>C:p.(=); ADGRV1:ENST00000640815.1:c.-60-3900T>C:p.(=)

Pathogenicity Data:: Best Score: 0.26987034; CADD: 0.270 (1.366)

Frequency Data:: gnomAD_G_OTH: 0.1812%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90771220C>T [0|1] rs946716544 (variation viewer)

Variant score: 0.239

Transcripts:: ADGRV1:ENST00000405460.9:c.12286-2966C>T:p.(=)

Pathogenicity Data:: Best Score: 0.24351555; CADD: 0.244 (1.212)

Frequency Data:: TOPMed: 0.0120%; gnomAD_G_NFE: 0.0089%; gnomAD_G_OTH: 0.1397%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.91028732G>GT [1/1] rs397998676 (variation viewer)

Variant score: 0.202

Transcripts:: ADGRV1:ENST00000405460.9:c.18152+43210_18152+43211insT:p.(=); ADGRV1:ENST00000639821.1:c.236+43210_236+43211insT:p.(=); ADGRV1:ENST00000640815.1:c.236+43210_236+43211insT:p.(=)

Pathogenicity Data:: Best Score: 0.20163774; CADD: 0.202 (0.978)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.91035861T>TA [-/1] rs368479509 (variation viewer)

Variant score: 0.153

Transcripts:: ADGRV1:ENST00000405460.9:c.18153-36586_18153-36585insA:p.(=); ADGRV1:ENST00000639821.1:c.237-36586_237-36585insA:p.(=); ADGRV1:ENST00000640815.1:c.237-36586_237-36585insA:p.(=)

Pathogenicity Data:: Best Score: 0.15316266; CADD: 0.153 (0.722)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90571061TTTG>T [0/1] rs1322415654 (variation viewer)

Variant score: 0.139

Transcripts:: ADGRV1:ENST00000405460.9:c.22+12145_22+12147del:p.(=)

Pathogenicity Data:: Best Score: 0.13900626; CADD: 0.139 (0.650)

Frequency Data:: TOPMed: 0.0032%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90639071A>AACACACACACAC [-/1] rs67813883 (variation viewer)

Variant score: 0.136

Transcripts:: ADGRV1:ENST00000405460.9:c.2240+1123_2240+1124insACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.13642514; CADD: 0.136 (0.637)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90722716CAAAAAAAAAAAAAAAAA>C [1/1] rs55761821 (variation viewer)

Variant score: 0.127

Transcripts:: ADGRV1:ENST00000405460.9:c.9748+1658_9748+1674del:p.(=)

Pathogenicity Data:: Best Score: 0.12662655; CADD: 0.127 (0.588)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90639071A>AACACACACACACACAC [-/1] rs67813883 (variation viewer)

Variant score: 0.126

Transcripts:: ADGRV1:ENST00000405460.9:c.2240+1123_2240+1124insACACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.12642539; CADD: 0.126 (0.587)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90813132CA>C [1|1] rs5869522 (variation viewer)

Variant score: 0.113

Transcripts:: ADGRV1:ENST00000405460.9:c.16078+1795del:p.(=)

Pathogenicity Data:: Best Score: 0.113048255; CADD: 0.113 (0.521)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90976322G>GTGTGTA [0/1] rs1420288881 (variation viewer)

Variant score: 0.107

Transcripts:: ADGRV1:ENST00000405460.9:c.17974-9022_17974-9021insTGTGTA:p.(=); ADGRV1:ENST00000639821.1:c.58-9022_58-9021insTGTGTA:p.(=); ADGRV1:ENST00000640815.1:c.58-9022_58-9021insTGTGTA:p.(=)

Pathogenicity Data:: Best Score: 0.10669452; CADD: 0.107 (0.490)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.91035861T>TAATATATATATATATATATATA [-/1]

Variant score: 0.102

Transcripts:: ADGRV1:ENST00000405460.9:c.18153-36586_18153-36585insAATATATATATATATATATATA:p.(=); ADGRV1:ENST00000639821.1:c.237-36586_237-36585insAATATATATATATATATATATA:p.(=); ADGRV1:ENST00000640815.1:c.237-36586_237-36585insAATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.101744235; CADD: 0.102 (0.466)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90958283CA>C [1/1] rs34676985 (variation viewer)

Variant score: 0.055

Transcripts:: ADGRV1:ENST00000405460.9:c.17857-7131del:p.(=); ADGRV1:ENST00000639821.1:c.-60-7131del:p.(=); ADGRV1:ENST00000640815.1:c.-60-7131del:p.(=)

Pathogenicity Data:: Best Score: 0.05506921; CADD: 0.055 (0.246)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90656313C>T [0/1] rs1012366528 (variation viewer)

Variant score: 0.024

Transcripts:: ADGRV1:ENST00000405460.9:c.4379-1592C>T:p.(=)

Pathogenicity Data:: Best Score: 0.024336636; CADD: 0.024 (0.107)

Frequency Data:: TOPMed: 0.0120%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.91054102T>A [1/1] rs4990550 (variation viewer)

Variant score: 0.010

Transcripts:: ADGRV1:ENST00000405460.9:c.18153-18345T>A:p.(=); ADGRV1:ENST00000639821.1:c.237-18345T>A:p.(=); ADGRV1:ENST00000640815.1:c.237-18345T>A:p.(=)

Pathogenicity Data:: Best Score: 0.010080218; CADD: 0.010 (0.044)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90564625AT>* [-/1]

Variant score: 0.000

Transcripts:: ADGRV1:ENST00000405460.9:c.22+5708_22+5709delATins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90681825A>* [-/1]

Variant score: 0.000

Transcripts:: ADGRV1:ENST00000405460.9:c.5664+371A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.90721531A>* [-/1]

Variant score: 0.000

Transcripts:: ADGRV1:ENST00000405460.9:c.9748+472A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PCDH15

Exomiser Score: 0.370

Phenotype Score: 0.517

Variant Score: 0.803

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 1 associated with PCDH15.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.517 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.517 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:601067 Usher syndrome, type 1D/F digenic - autosomal recessive; OMIM:602083 Usher syndrome, type 1F - autosomal recessive; OMIM:609533 Deafness, autosomal recessive 23 - autosomal recessive; ORPHA:231169 Usher syndrome type 1; ORPHA:231169 Usher syndrome type 1

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.049

Phenotype Score: 0.259

Variant Score: 0.830

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53994157C>T [0/1] rs1324056084 (variation viewer)

Variant score: 0.830 CONTRIBUTING VARIANT

Transcripts:: PCDH15:ENST00000320301.10:c.2868+1492G>A:p.(=); PCDH15:ENST00000361849.7:c.2868+1492G>A:p.(=); PCDH15:ENST00000373957.7:c.2883+1492G>A:p.(=); PCDH15:ENST00000373965.6:c.2868+1492G>A:p.(=); PCDH15:ENST00000395430.5:c.2868+1492G>A:p.(=); PCDH15:ENST00000395432.6:c.2757+1492G>A:p.(=); PCDH15:ENST00000395433.5:c.2802+1492G>A:p.(=); PCDH15:ENST00000395438.5:c.2868+1492G>A:p.(=); PCDH15:ENST00000395440.5:c.1306-184611G>A:p.(=); PCDH15:ENST00000395442.5:c.1099-184611G>A:p.(=); PCDH15:ENST00000395445.5:c.2889+1492G>A:p.(=); PCDH15:ENST00000395446.5:c.2091+85174G>A:p.(=); PCDH15:ENST00000409834.5:c.1701+1492G>A:p.(=); PCDH15:ENST00000414778.5:c.2868+1492G>A:p.(=); PCDH15:ENST00000437009.5:c.2655+1492G>A:p.(=); PCDH15:ENST00000612394.4:c.2904+1492G>A:p.(=); PCDH15:ENST00000613657.4:c.2904+1492G>A:p.(=); PCDH15:ENST00000614895.4:c.2883+1492G>A:p.(=); PCDH15:ENST00000616114.4:c.2868+1492G>A:p.(=); PCDH15:ENST00000617051.4:c.2883+1492G>A:p.(=); PCDH15:ENST00000617271.4:c.2868+1492G>A:p.(=); PCDH15:ENST00000621708.4:c.2883+1492G>A:p.(=); PCDH15:ENST00000622048.4:c.2655+1492G>A:p.(=); PCDH15:ENST00000644397.1:c.2868+1492G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-136894G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8308002; CADD: 0.831 (7.716)

Frequency Data:: TOPMed: 0.0048%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.370

Phenotype Score: 0.517

Variant Score: 0.803

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53994157C>T [0/1] rs1324056084 (variation viewer)

Variant score: 0.830 CONTRIBUTING VARIANT

Transcripts:: PCDH15:ENST00000320301.10:c.2868+1492G>A:p.(=); PCDH15:ENST00000361849.7:c.2868+1492G>A:p.(=); PCDH15:ENST00000373957.7:c.2883+1492G>A:p.(=); PCDH15:ENST00000373965.6:c.2868+1492G>A:p.(=); PCDH15:ENST00000395430.5:c.2868+1492G>A:p.(=); PCDH15:ENST00000395432.6:c.2757+1492G>A:p.(=); PCDH15:ENST00000395433.5:c.2802+1492G>A:p.(=); PCDH15:ENST00000395438.5:c.2868+1492G>A:p.(=); PCDH15:ENST00000395440.5:c.1306-184611G>A:p.(=); PCDH15:ENST00000395442.5:c.1099-184611G>A:p.(=); PCDH15:ENST00000395445.5:c.2889+1492G>A:p.(=); PCDH15:ENST00000395446.5:c.2091+85174G>A:p.(=); PCDH15:ENST00000409834.5:c.1701+1492G>A:p.(=); PCDH15:ENST00000414778.5:c.2868+1492G>A:p.(=); PCDH15:ENST00000437009.5:c.2655+1492G>A:p.(=); PCDH15:ENST00000612394.4:c.2904+1492G>A:p.(=); PCDH15:ENST00000613657.4:c.2904+1492G>A:p.(=); PCDH15:ENST00000614895.4:c.2883+1492G>A:p.(=); PCDH15:ENST00000616114.4:c.2868+1492G>A:p.(=); PCDH15:ENST00000617051.4:c.2883+1492G>A:p.(=); PCDH15:ENST00000617271.4:c.2868+1492G>A:p.(=); PCDH15:ENST00000621708.4:c.2883+1492G>A:p.(=); PCDH15:ENST00000622048.4:c.2655+1492G>A:p.(=); PCDH15:ENST00000644397.1:c.2868+1492G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-136894G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8308002; CADD: 0.831 (7.716)

Frequency Data:: TOPMed: 0.0048%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54011155T>C [0/1] rs77635219 (variation viewer)

Variant score: 0.776 CONTRIBUTING VARIANT

Transcripts:: PCDH15:ENST00000320301.10:c.2751+9037A>G:p.(=); PCDH15:ENST00000361849.7:c.2751+9037A>G:p.(=); PCDH15:ENST00000373955.5:c.2751+9037A>G:p.(=); PCDH15:ENST00000373957.7:c.2766+9037A>G:p.(=); PCDH15:ENST00000373965.6:c.2751+9037A>G:p.(=); PCDH15:ENST00000395430.5:c.2751+9037A>G:p.(=); PCDH15:ENST00000395432.6:c.2640+9037A>G:p.(=); PCDH15:ENST00000395433.5:c.2685+9037A>G:p.(=); PCDH15:ENST00000395438.5:c.2751+9037A>G:p.(=); PCDH15:ENST00000395440.5:c.1305+184528A>G:p.(=); PCDH15:ENST00000395442.5:c.1099-201609A>G:p.(=); PCDH15:ENST00000395445.5:c.2772+9037A>G:p.(=); PCDH15:ENST00000395446.5:c.2091+68176A>G:p.(=); PCDH15:ENST00000409834.5:c.1584+9037A>G:p.(=); PCDH15:ENST00000414778.5:c.2751+9037A>G:p.(=); PCDH15:ENST00000437009.5:c.2538+9037A>G:p.(=); PCDH15:ENST00000612394.4:c.2787+9037A>G:p.(=); PCDH15:ENST00000613657.4:c.2787+9037A>G:p.(=); PCDH15:ENST00000614895.4:c.2766+9037A>G:p.(=); PCDH15:ENST00000616114.4:c.2751+9037A>G:p.(=); PCDH15:ENST00000617051.4:c.2766+9037A>G:p.(=); PCDH15:ENST00000617271.4:c.2751+9037A>G:p.(=); PCDH15:ENST00000621708.4:c.2766+9037A>G:p.(=); PCDH15:ENST00000622048.4:c.2538+9037A>G:p.(=); PCDH15:ENST00000644397.1:c.2751+9037A>G:p.(=); PCDH15:ENST00000495484.5:c.-24-153892A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8199057; CADD: 0.820 (7.445)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.0486%; UK10K: 0.0264%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_NFE: 0.0400%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54363470A>G [0/1] rs937176786 (variation viewer)

Variant score: 0.740

Transcripts:: PCDH15:ENST00000320301.10:c.474+5650T>C:p.(=); PCDH15:ENST00000361849.7:c.474+5650T>C:p.(=); PCDH15:ENST00000373955.5:c.474+5650T>C:p.(=); PCDH15:ENST00000373957.7:c.489+5650T>C:p.(=); PCDH15:ENST00000373965.6:c.474+5650T>C:p.(=); PCDH15:ENST00000395430.5:c.474+5650T>C:p.(=); PCDH15:ENST00000395432.6:c.474+5650T>C:p.(=); PCDH15:ENST00000395433.5:c.408+5650T>C:p.(=); PCDH15:ENST00000395438.5:c.474+5650T>C:p.(=); PCDH15:ENST00000395440.5:c.474+5650T>C:p.(=); PCDH15:ENST00000395442.5:c.474+5650T>C:p.(=); PCDH15:ENST00000395445.5:c.474+5650T>C:p.(=); PCDH15:ENST00000395446.5:c.474+5650T>C:p.(=); PCDH15:ENST00000414778.5:c.474+5650T>C:p.(=); PCDH15:ENST00000437009.5:c.474+5650T>C:p.(=); PCDH15:ENST00000612394.4:c.489+5650T>C:p.(=); PCDH15:ENST00000613657.4:c.489+5650T>C:p.(=); PCDH15:ENST00000614895.4:c.489+5650T>C:p.(=); PCDH15:ENST00000616114.4:c.474+5650T>C:p.(=); PCDH15:ENST00000617051.4:c.489+5650T>C:p.(=); PCDH15:ENST00000617271.4:c.474+5650T>C:p.(=); PCDH15:ENST00000621708.4:c.489+5650T>C:p.(=); PCDH15:ENST00000622048.4:c.474+5650T>C:p.(=); PCDH15:ENST00000644397.1:c.474+5650T>C:p.(=); PCDH15:ENST00000409834.5:c.-90-167581T>C:p.(=); PCDH15:ENST00000495484.5:c.-25+437455T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7405821; CADD: 0.741 (5.860)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54026764A>G [0/1] rs1050968714 (variation viewer)

Variant score: 0.718

Transcripts:: PCDH15:ENST00000320301.10:c.2221-3567T>C:p.(=); PCDH15:ENST00000361849.7:c.2221-3567T>C:p.(=); PCDH15:ENST00000373955.5:c.2221-3567T>C:p.(=); PCDH15:ENST00000373957.7:c.2236-3567T>C:p.(=); PCDH15:ENST00000373965.6:c.2221-3567T>C:p.(=); PCDH15:ENST00000395430.5:c.2221-3567T>C:p.(=); PCDH15:ENST00000395432.6:c.2110-3567T>C:p.(=); PCDH15:ENST00000395433.5:c.2155-3567T>C:p.(=); PCDH15:ENST00000395438.5:c.2221-3567T>C:p.(=); PCDH15:ENST00000395440.5:c.1305+168919T>C:p.(=); PCDH15:ENST00000395442.5:c.1098+187172T>C:p.(=); PCDH15:ENST00000395445.5:c.2242-3567T>C:p.(=); PCDH15:ENST00000395446.5:c.2091+52567T>C:p.(=); PCDH15:ENST00000409834.5:c.1054-3567T>C:p.(=); PCDH15:ENST00000414778.5:c.2221-3567T>C:p.(=); PCDH15:ENST00000437009.5:c.2008-3567T>C:p.(=); PCDH15:ENST00000612394.4:c.2257-3567T>C:p.(=); PCDH15:ENST00000613657.4:c.2257-3567T>C:p.(=); PCDH15:ENST00000614895.4:c.2236-3567T>C:p.(=); PCDH15:ENST00000616114.4:c.2221-3567T>C:p.(=); PCDH15:ENST00000617051.4:c.2236-3567T>C:p.(=); PCDH15:ENST00000617271.4:c.2221-3567T>C:p.(=); PCDH15:ENST00000621708.4:c.2236-3567T>C:p.(=); PCDH15:ENST00000622048.4:c.2008-3567T>C:p.(=); PCDH15:ENST00000644397.1:c.2221-3567T>C:p.(=); PCDH15:ENST00000495484.5:c.-24-169501T>C:p.(=)

Pathogenicity Data:: Best Score: 0.718486; CADD: 0.718 (5.505)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54013357C>A [0/1] rs752633306 (variation viewer)

Variant score: 0.665

Transcripts:: PCDH15:ENST00000320301.10:c.2751+6835G>T:p.(=); PCDH15:ENST00000361849.7:c.2751+6835G>T:p.(=); PCDH15:ENST00000373955.5:c.2751+6835G>T:p.(=); PCDH15:ENST00000373957.7:c.2766+6835G>T:p.(=); PCDH15:ENST00000373965.6:c.2751+6835G>T:p.(=); PCDH15:ENST00000395430.5:c.2751+6835G>T:p.(=); PCDH15:ENST00000395432.6:c.2640+6835G>T:p.(=); PCDH15:ENST00000395433.5:c.2685+6835G>T:p.(=); PCDH15:ENST00000395438.5:c.2751+6835G>T:p.(=); PCDH15:ENST00000395440.5:c.1305+182326G>T:p.(=); PCDH15:ENST00000395442.5:c.1098+200579G>T:p.(=); PCDH15:ENST00000395445.5:c.2772+6835G>T:p.(=); PCDH15:ENST00000395446.5:c.2091+65974G>T:p.(=); PCDH15:ENST00000409834.5:c.1584+6835G>T:p.(=); PCDH15:ENST00000414778.5:c.2751+6835G>T:p.(=); PCDH15:ENST00000437009.5:c.2538+6835G>T:p.(=); PCDH15:ENST00000612394.4:c.2787+6835G>T:p.(=); PCDH15:ENST00000613657.4:c.2787+6835G>T:p.(=); PCDH15:ENST00000614895.4:c.2766+6835G>T:p.(=); PCDH15:ENST00000616114.4:c.2751+6835G>T:p.(=); PCDH15:ENST00000617051.4:c.2766+6835G>T:p.(=); PCDH15:ENST00000617271.4:c.2751+6835G>T:p.(=); PCDH15:ENST00000621708.4:c.2766+6835G>T:p.(=); PCDH15:ENST00000622048.4:c.2538+6835G>T:p.(=); PCDH15:ENST00000644397.1:c.2751+6835G>T:p.(=); PCDH15:ENST00000495484.5:c.-24-156094G>T:p.(=)

Pathogenicity Data:: Best Score: 0.66787624; CADD: 0.668 (4.787)

Frequency Data:: TOPMed: 0.0191%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0268%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54702543C>CA [-/1] rs375110960 (variation viewer)

Variant score: 0.628

Transcripts:: PCDH15:ENST00000320301.10:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000361849.7:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000373955.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000373957.7:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000373965.6:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395430.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395432.6:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395433.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395438.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395440.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395442.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395445.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000395446.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000409834.5:c.-209-38254_-209-38253insT:p.(=); PCDH15:ENST00000414778.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000437009.5:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000495484.5:c.-25+98381_-25+98382insT:p.(=); PCDH15:ENST00000612394.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000613657.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000614895.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000616114.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000617051.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000617271.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000621708.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000622048.4:c.-28-38254_-28-38253insT:p.(=); PCDH15:ENST00000644397.1:c.-28-38254_-28-38253insT:p.(=)

Pathogenicity Data:: Best Score: 0.6275225; CADD: 0.628 (4.289)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54039522T>C [1/1] rs186920203 (variation viewer)

Variant score: 0.566

Transcripts:: PCDH15:ENST00000320301.10:c.2221-16325A>G:p.(=); PCDH15:ENST00000361849.7:c.2221-16325A>G:p.(=); PCDH15:ENST00000373955.5:c.2221-16325A>G:p.(=); PCDH15:ENST00000373957.7:c.2236-16325A>G:p.(=); PCDH15:ENST00000373965.6:c.2221-16325A>G:p.(=); PCDH15:ENST00000395430.5:c.2221-16325A>G:p.(=); PCDH15:ENST00000395432.6:c.2110-16325A>G:p.(=); PCDH15:ENST00000395433.5:c.2155-16325A>G:p.(=); PCDH15:ENST00000395438.5:c.2221-16325A>G:p.(=); PCDH15:ENST00000395440.5:c.1305+156161A>G:p.(=); PCDH15:ENST00000395442.5:c.1098+174414A>G:p.(=); PCDH15:ENST00000395445.5:c.2242-16325A>G:p.(=); PCDH15:ENST00000395446.5:c.2091+39809A>G:p.(=); PCDH15:ENST00000409834.5:c.1054-16325A>G:p.(=); PCDH15:ENST00000414778.5:c.2221-16325A>G:p.(=); PCDH15:ENST00000437009.5:c.2008-16325A>G:p.(=); PCDH15:ENST00000612394.4:c.2257-16325A>G:p.(=); PCDH15:ENST00000613657.4:c.2257-16325A>G:p.(=); PCDH15:ENST00000614895.4:c.2236-16325A>G:p.(=); PCDH15:ENST00000616114.4:c.2221-16325A>G:p.(=); PCDH15:ENST00000617051.4:c.2236-16325A>G:p.(=); PCDH15:ENST00000617271.4:c.2221-16325A>G:p.(=); PCDH15:ENST00000621708.4:c.2236-16325A>G:p.(=); PCDH15:ENST00000622048.4:c.2008-16325A>G:p.(=); PCDH15:ENST00000644397.1:c.2221-16325A>G:p.(=); PCDH15:ENST00000495484.5:c.-24-182259A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6484395; CADD: 0.648 (4.540)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.3345%; UK10K: 0.4232%; gnomAD_G_AFR: 0.1030%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3871%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54146980A>G [0|1] rs556970948 (variation viewer)

Variant score: 0.548

Transcripts:: PCDH15:ENST00000320301.10:c.1784+6120T>C:p.(=); PCDH15:ENST00000361849.7:c.1784+6120T>C:p.(=); PCDH15:ENST00000373955.5:c.1784+6120T>C:p.(=); PCDH15:ENST00000373957.7:c.1799+6120T>C:p.(=); PCDH15:ENST00000373965.6:c.1784+6120T>C:p.(=); PCDH15:ENST00000395430.5:c.1784+6120T>C:p.(=); PCDH15:ENST00000395432.6:c.1673+6120T>C:p.(=); PCDH15:ENST00000395433.5:c.1718+6120T>C:p.(=); PCDH15:ENST00000395438.5:c.1784+6120T>C:p.(=); PCDH15:ENST00000395440.5:c.1305+48703T>C:p.(=); PCDH15:ENST00000395442.5:c.1098+66956T>C:p.(=); PCDH15:ENST00000395445.5:c.1805+6120T>C:p.(=); PCDH15:ENST00000395446.5:c.1784+6120T>C:p.(=); PCDH15:ENST00000409834.5:c.617+6120T>C:p.(=); PCDH15:ENST00000414778.5:c.1784+6120T>C:p.(=); PCDH15:ENST00000437009.5:c.1784+6120T>C:p.(=); PCDH15:ENST00000612394.4:c.1820+6120T>C:p.(=); PCDH15:ENST00000613657.4:c.1820+6120T>C:p.(=); PCDH15:ENST00000614895.4:c.1799+6120T>C:p.(=); PCDH15:ENST00000616114.4:c.1784+6120T>C:p.(=); PCDH15:ENST00000617051.4:c.1799+6120T>C:p.(=); PCDH15:ENST00000617271.4:c.1784+6120T>C:p.(=); PCDH15:ENST00000621708.4:c.1799+6120T>C:p.(=); PCDH15:ENST00000622048.4:c.1784+6120T>C:p.(=); PCDH15:ENST00000644397.1:c.1784+6120T>C:p.(=); PCDH15:ENST00000495484.5:c.-24-289717T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6767042; CADD: 0.677 (4.904)

Frequency Data:: gnomAD_G_AFR: 0.0178%; gnomAD_G_ASJ: 0.8772%; gnomAD_G_FIN: 0.1131%; gnomAD_G_NFE: 0.0243%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54447123A>G [0/1] rs773584919 (variation viewer)

Variant score: 0.545

Transcripts:: PCDH15:ENST00000320301.10:c.158-68181T>C:p.(=); PCDH15:ENST00000361849.7:c.158-68181T>C:p.(=); PCDH15:ENST00000373955.5:c.158-68181T>C:p.(=); PCDH15:ENST00000373957.7:c.173-68181T>C:p.(=); PCDH15:ENST00000373965.6:c.158-68181T>C:p.(=); PCDH15:ENST00000395430.5:c.158-68181T>C:p.(=); PCDH15:ENST00000395432.6:c.158-68181T>C:p.(=); PCDH15:ENST00000395433.5:c.92-68181T>C:p.(=); PCDH15:ENST00000395438.5:c.158-68181T>C:p.(=); PCDH15:ENST00000395440.5:c.158-68181T>C:p.(=); PCDH15:ENST00000395442.5:c.158-68181T>C:p.(=); PCDH15:ENST00000395445.5:c.158-68181T>C:p.(=); PCDH15:ENST00000395446.5:c.158-68181T>C:p.(=); PCDH15:ENST00000414778.5:c.158-68181T>C:p.(=); PCDH15:ENST00000437009.5:c.158-68181T>C:p.(=); PCDH15:ENST00000612394.4:c.173-68181T>C:p.(=); PCDH15:ENST00000613657.4:c.173-68181T>C:p.(=); PCDH15:ENST00000614895.4:c.173-68181T>C:p.(=); PCDH15:ENST00000616114.4:c.158-68181T>C:p.(=); PCDH15:ENST00000617051.4:c.173-68181T>C:p.(=); PCDH15:ENST00000617271.4:c.158-68181T>C:p.(=); PCDH15:ENST00000621708.4:c.173-68181T>C:p.(=); PCDH15:ENST00000622048.4:c.158-68181T>C:p.(=); PCDH15:ENST00000644397.1:c.158-68181T>C:p.(=); PCDH15:ENST00000409834.5:c.-91+217049T>C:p.(=); PCDH15:ENST00000495484.5:c.-25+353802T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5461629; CADD: 0.546 (3.431)

Frequency Data:: TOPMed: 0.0016%; UK10K: 0.0132%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53851671AAT>A [0/1] rs71004485 (variation viewer)

Variant score: 0.514

Transcripts:: PCDH15:ENST00000320301.10:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000361849.7:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000373957.7:c.3821+5502_3821+5503del:p.(=); PCDH15:ENST00000373965.6:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000395430.5:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000395432.6:c.3695+5502_3695+5503del:p.(=); PCDH15:ENST00000395433.5:c.3740+5502_3740+5503del:p.(=); PCDH15:ENST00000395438.5:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000395440.5:c.1306-42127_1306-42126del:p.(=); PCDH15:ENST00000395442.5:c.1099-42127_1099-42126del:p.(=); PCDH15:ENST00000395445.5:c.3827+5502_3827+5503del:p.(=); PCDH15:ENST00000395446.5:c.2092-42127_2092-42126del:p.(=); PCDH15:ENST00000409834.5:c.2639+5502_2639+5503del:p.(=); PCDH15:ENST00000414778.5:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000437009.5:c.3593+5502_3593+5503del:p.(=); PCDH15:ENST00000495484.5:c.65+5502_65+5503del:p.(=); PCDH15:ENST00000612394.4:c.3842+5502_3842+5503del:p.(=); PCDH15:ENST00000613657.4:c.3842+5502_3842+5503del:p.(=); PCDH15:ENST00000614895.4:c.3821+5502_3821+5503del:p.(=); PCDH15:ENST00000616114.4:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000617051.4:c.3821+5502_3821+5503del:p.(=); PCDH15:ENST00000617271.4:c.3806+5502_3806+5503del:p.(=); PCDH15:ENST00000621708.4:c.3821+5502_3821+5503del:p.(=); PCDH15:ENST00000622048.4:c.3593+5502_3593+5503del:p.(=); PCDH15:ENST00000644397.1:c.3806+5502_3806+5503del:p.(=)

Pathogenicity Data:: Best Score: 0.51359284; CADD: 0.514 (3.130)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54167840T>C [1|1] rs1164459040 (variation viewer)

Variant score: 0.481

Transcripts:: PCDH15:ENST00000320301.10:c.1591-14547A>G:p.(=); PCDH15:ENST00000361849.7:c.1591-14547A>G:p.(=); PCDH15:ENST00000373955.5:c.1591-14547A>G:p.(=); PCDH15:ENST00000373957.7:c.1606-14547A>G:p.(=); PCDH15:ENST00000373965.6:c.1591-14547A>G:p.(=); PCDH15:ENST00000395430.5:c.1591-14547A>G:p.(=); PCDH15:ENST00000395432.6:c.1480-14547A>G:p.(=); PCDH15:ENST00000395433.5:c.1525-14547A>G:p.(=); PCDH15:ENST00000395438.5:c.1591-14547A>G:p.(=); PCDH15:ENST00000395440.5:c.1305+27843A>G:p.(=); PCDH15:ENST00000395442.5:c.1098+46096A>G:p.(=); PCDH15:ENST00000395445.5:c.1612-14547A>G:p.(=); PCDH15:ENST00000395446.5:c.1591-14547A>G:p.(=); PCDH15:ENST00000409834.5:c.424-14547A>G:p.(=); PCDH15:ENST00000414778.5:c.1591-14547A>G:p.(=); PCDH15:ENST00000437009.5:c.1591-14547A>G:p.(=); PCDH15:ENST00000612394.4:c.1627-14547A>G:p.(=); PCDH15:ENST00000613657.4:c.1627-14547A>G:p.(=); PCDH15:ENST00000614895.4:c.1606-14547A>G:p.(=); PCDH15:ENST00000616114.4:c.1591-14547A>G:p.(=); PCDH15:ENST00000617051.4:c.1606-14547A>G:p.(=); PCDH15:ENST00000617271.4:c.1591-14547A>G:p.(=); PCDH15:ENST00000621708.4:c.1606-14547A>G:p.(=); PCDH15:ENST00000622048.4:c.1591-14547A>G:p.(=); PCDH15:ENST00000644397.1:c.1591-14547A>G:p.(=); PCDH15:ENST00000495484.5:c.-24-310577A>G:p.(=)

Pathogenicity Data:: Best Score: 0.53312564; CADD: 0.533 (3.308)

Frequency Data:: gnomAD_G_AFR: 0.4710%; gnomAD_G_AMR: 0.2857%; gnomAD_G_EAS: 0.1403%; gnomAD_G_FIN: 0.0795%; gnomAD_G_NFE: 0.4156%; gnomAD_G_OTH: 0.5435%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54031323C>T [0/1] rs138631667 (variation viewer)

Variant score: 0.451

Transcripts:: PCDH15:ENST00000320301.10:c.2221-8126G>A:p.(=); PCDH15:ENST00000361849.7:c.2221-8126G>A:p.(=); PCDH15:ENST00000373955.5:c.2221-8126G>A:p.(=); PCDH15:ENST00000373957.7:c.2236-8126G>A:p.(=); PCDH15:ENST00000373965.6:c.2221-8126G>A:p.(=); PCDH15:ENST00000395430.5:c.2221-8126G>A:p.(=); PCDH15:ENST00000395432.6:c.2110-8126G>A:p.(=); PCDH15:ENST00000395433.5:c.2155-8126G>A:p.(=); PCDH15:ENST00000395438.5:c.2221-8126G>A:p.(=); PCDH15:ENST00000395440.5:c.1305+164360G>A:p.(=); PCDH15:ENST00000395442.5:c.1098+182613G>A:p.(=); PCDH15:ENST00000395445.5:c.2242-8126G>A:p.(=); PCDH15:ENST00000395446.5:c.2091+48008G>A:p.(=); PCDH15:ENST00000409834.5:c.1054-8126G>A:p.(=); PCDH15:ENST00000414778.5:c.2221-8126G>A:p.(=); PCDH15:ENST00000437009.5:c.2008-8126G>A:p.(=); PCDH15:ENST00000612394.4:c.2257-8126G>A:p.(=); PCDH15:ENST00000613657.4:c.2257-8126G>A:p.(=); PCDH15:ENST00000614895.4:c.2236-8126G>A:p.(=); PCDH15:ENST00000616114.4:c.2221-8126G>A:p.(=); PCDH15:ENST00000617051.4:c.2236-8126G>A:p.(=); PCDH15:ENST00000617271.4:c.2221-8126G>A:p.(=); PCDH15:ENST00000621708.4:c.2236-8126G>A:p.(=); PCDH15:ENST00000622048.4:c.2008-8126G>A:p.(=); PCDH15:ENST00000644397.1:c.2221-8126G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-174060G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5166074; CADD: 0.517 (3.157)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.3154%; UK10K: 0.3967%; gnomAD_G_AFR: 0.0804%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1150%; gnomAD_G_NFE: 0.3548%; gnomAD_G_OTH: 0.2049%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53821730GA>G [0/1] rs548021914 (variation viewer)

Variant score: 0.407

Transcripts:: PCDH15:ENST00000373965.6:c.4373+3405del:p.(=); PCDH15:ENST00000395438.5:c.4371+5661del:p.(=); PCDH15:ENST00000395440.5:c.1306-12185del:p.(=); PCDH15:ENST00000395442.5:c.1099-12185del:p.(=); PCDH15:ENST00000395445.5:c.4388+5662del:p.(=); PCDH15:ENST00000395446.5:c.2092-12185del:p.(=); PCDH15:ENST00000409834.5:c.3206+3405del:p.(=); PCDH15:ENST00000414778.5:c.4370+5662del:p.(=); PCDH15:ENST00000495484.5:c.462-3718del:p.(=); PCDH15:ENST00000612394.4:c.4406+5662del:p.(=); PCDH15:ENST00000613657.4:c.4409+3405del:p.(=); PCDH15:ENST00000614895.4:c.4385+5662del:p.(=); PCDH15:ENST00000616114.4:c.4367+5662del:p.(=); PCDH15:ENST00000617271.4:c.4373+3405del:p.(=); PCDH15:ENST00000621708.4:c.4388+3405del:p.(=); PCDH15:ENST00000644397.1:c.4368-1501del:p.(=); PCDH15:ENST00000320301.10:c.*127del:p.(=); PCDH15:ENST00000361849.7:c.*127del:p.(=); PCDH15:ENST00000373957.7:c.*127del:p.(=); PCDH15:ENST00000395430.5:c.*127del:p.(=); PCDH15:ENST00000395432.6:c.*127del:p.(=); PCDH15:ENST00000395433.5:c.*127del:p.(=); PCDH15:ENST00000437009.5:c.*127del:p.(=); PCDH15:ENST00000617051.4:c.*127del:p.(=); PCDH15:ENST00000622048.4:c.*127del:p.(=)

Pathogenicity Data:: Best Score: 0.41789675; CADD: 0.418 (2.350)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.1797%; gnomAD_G_AFR: 0.0692%; gnomAD_G_AMR: 0.1202%; gnomAD_G_NFE: 0.0405%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54715945A>G [0/1] rs144106996 (variation viewer)

Variant score: 0.404

Transcripts:: PCDH15:ENST00000320301.10:c.-28-51655T>C:p.(=); PCDH15:ENST00000361849.7:c.-28-51655T>C:p.(=); PCDH15:ENST00000373955.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000373957.7:c.-28-51655T>C:p.(=); PCDH15:ENST00000373965.6:c.-28-51655T>C:p.(=); PCDH15:ENST00000395430.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000395432.6:c.-28-51655T>C:p.(=); PCDH15:ENST00000395433.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000395438.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000395440.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000395442.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000395445.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000395446.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000409834.5:c.-209-51655T>C:p.(=); PCDH15:ENST00000414778.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000437009.5:c.-28-51655T>C:p.(=); PCDH15:ENST00000495484.5:c.-25+84980T>C:p.(=); PCDH15:ENST00000612394.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000613657.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000614895.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000616114.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000617051.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000617271.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000621708.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000622048.4:c.-28-51655T>C:p.(=); PCDH15:ENST00000644397.1:c.-28-51655T>C:p.(=)

Pathogenicity Data:: Best Score: 0.72647315; CADD: 0.726 (5.630)

Frequency Data:: 1000Genomes: 0.7987%; TOPMed: 0.9373%; UK10K: 1.4546%; gnomAD_G_AFR: 0.2752%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.7446%; gnomAD_G_NFE: 1.1402%; gnomAD_G_OTH: 1.1202%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54167805C>T [1|1] rs12782614 (variation viewer)

Variant score: 0.396

Transcripts:: PCDH15:ENST00000320301.10:c.1591-14512G>A:p.(=); PCDH15:ENST00000361849.7:c.1591-14512G>A:p.(=); PCDH15:ENST00000373955.5:c.1591-14512G>A:p.(=); PCDH15:ENST00000373957.7:c.1606-14512G>A:p.(=); PCDH15:ENST00000373965.6:c.1591-14512G>A:p.(=); PCDH15:ENST00000395430.5:c.1591-14512G>A:p.(=); PCDH15:ENST00000395432.6:c.1480-14512G>A:p.(=); PCDH15:ENST00000395433.5:c.1525-14512G>A:p.(=); PCDH15:ENST00000395438.5:c.1591-14512G>A:p.(=); PCDH15:ENST00000395440.5:c.1305+27878G>A:p.(=); PCDH15:ENST00000395442.5:c.1098+46131G>A:p.(=); PCDH15:ENST00000395445.5:c.1612-14512G>A:p.(=); PCDH15:ENST00000395446.5:c.1591-14512G>A:p.(=); PCDH15:ENST00000409834.5:c.424-14512G>A:p.(=); PCDH15:ENST00000414778.5:c.1591-14512G>A:p.(=); PCDH15:ENST00000437009.5:c.1591-14512G>A:p.(=); PCDH15:ENST00000612394.4:c.1627-14512G>A:p.(=); PCDH15:ENST00000613657.4:c.1627-14512G>A:p.(=); PCDH15:ENST00000614895.4:c.1606-14512G>A:p.(=); PCDH15:ENST00000616114.4:c.1591-14512G>A:p.(=); PCDH15:ENST00000617051.4:c.1606-14512G>A:p.(=); PCDH15:ENST00000617271.4:c.1591-14512G>A:p.(=); PCDH15:ENST00000621708.4:c.1606-14512G>A:p.(=); PCDH15:ENST00000622048.4:c.1591-14512G>A:p.(=); PCDH15:ENST00000644397.1:c.1591-14512G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-310542G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3963294; CADD: 0.396 (2.192)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54296144CA>C [-/1] rs59721161 (variation viewer)

Variant score: 0.374

Transcripts:: PCDH15:ENST00000320301.10:c.876+21126del:p.(=); PCDH15:ENST00000361849.7:c.876+21126del:p.(=); PCDH15:ENST00000373955.5:c.876+21126del:p.(=); PCDH15:ENST00000373957.7:c.891+21126del:p.(=); PCDH15:ENST00000373965.6:c.876+21126del:p.(=); PCDH15:ENST00000395430.5:c.876+21126del:p.(=); PCDH15:ENST00000395432.6:c.765+21126del:p.(=); PCDH15:ENST00000395433.5:c.810+21126del:p.(=); PCDH15:ENST00000395438.5:c.876+21126del:p.(=); PCDH15:ENST00000395440.5:c.876+21126del:p.(=); PCDH15:ENST00000395442.5:c.876+21126del:p.(=); PCDH15:ENST00000395445.5:c.876+21126del:p.(=); PCDH15:ENST00000395446.5:c.876+21126del:p.(=); PCDH15:ENST00000414778.5:c.876+21126del:p.(=); PCDH15:ENST00000437009.5:c.876+21126del:p.(=); PCDH15:ENST00000612394.4:c.891+21126del:p.(=); PCDH15:ENST00000613657.4:c.891+21126del:p.(=); PCDH15:ENST00000614895.4:c.891+21126del:p.(=); PCDH15:ENST00000616114.4:c.876+21126del:p.(=); PCDH15:ENST00000617051.4:c.891+21126del:p.(=); PCDH15:ENST00000617271.4:c.876+21126del:p.(=); PCDH15:ENST00000621708.4:c.891+21126del:p.(=); PCDH15:ENST00000622048.4:c.876+21126del:p.(=); PCDH15:ENST00000644397.1:c.876+21126del:p.(=); PCDH15:ENST00000409834.5:c.-90-100256del:p.(=); PCDH15:ENST00000495484.5:c.-24-438882del:p.(=)

Pathogenicity Data:: Best Score: 0.3738188; CADD: 0.374 (2.033)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54296144CAA>C [-/1] rs59721161 (variation viewer)

Variant score: 0.367

Transcripts:: PCDH15:ENST00000320301.10:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000361849.7:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000373955.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000373957.7:c.891+21125_891+21126del:p.(=); PCDH15:ENST00000373965.6:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000395430.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000395432.6:c.765+21125_765+21126del:p.(=); PCDH15:ENST00000395433.5:c.810+21125_810+21126del:p.(=); PCDH15:ENST00000395438.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000395440.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000395442.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000395445.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000395446.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000414778.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000437009.5:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000612394.4:c.891+21125_891+21126del:p.(=); PCDH15:ENST00000613657.4:c.891+21125_891+21126del:p.(=); PCDH15:ENST00000614895.4:c.891+21125_891+21126del:p.(=); PCDH15:ENST00000616114.4:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000617051.4:c.891+21125_891+21126del:p.(=); PCDH15:ENST00000617271.4:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000621708.4:c.891+21125_891+21126del:p.(=); PCDH15:ENST00000622048.4:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000644397.1:c.876+21125_876+21126del:p.(=); PCDH15:ENST00000409834.5:c.-90-100257_-90-100256del:p.(=); PCDH15:ENST00000495484.5:c.-24-438883_-24-438882del:p.(=)

Pathogenicity Data:: Best Score: 0.36715114; CADD: 0.367 (1.987)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54559850T>TAAAAAA [1/1] rs80250003 (variation viewer)

Variant score: 0.359

Transcripts:: PCDH15:ENST00000320301.10:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000361849.7:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000373955.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000373957.7:c.92-31449_92-31448insTTTTTT:p.(=); PCDH15:ENST00000373965.6:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395430.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395432.6:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395433.5:c.91+104321_91+104322insTTTTTT:p.(=); PCDH15:ENST00000395438.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395440.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395442.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395445.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000395446.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000414778.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000437009.5:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000612394.4:c.92-31449_92-31448insTTTTTT:p.(=); PCDH15:ENST00000613657.4:c.92-31449_92-31448insTTTTTT:p.(=); PCDH15:ENST00000614895.4:c.92-31449_92-31448insTTTTTT:p.(=); PCDH15:ENST00000616114.4:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000617051.4:c.92-31449_92-31448insTTTTTT:p.(=); PCDH15:ENST00000617271.4:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000621708.4:c.92-31449_92-31448insTTTTTT:p.(=); PCDH15:ENST00000622048.4:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000644397.1:c.92-31974_92-31973insTTTTTT:p.(=); PCDH15:ENST00000409834.5:c.-91+104321_-91+104322insTTTTTT:p.(=); PCDH15:ENST00000495484.5:c.-25+241074_-25+241075insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.35908568; CADD: 0.359 (1.932)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54561980CTTTTTT>C [1/1] rs575547228 (variation viewer)

Variant score: 0.319

Transcripts:: PCDH15:ENST00000320301.10:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000361849.7:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000373955.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000373957.7:c.92-33584_92-33579del:p.(=); PCDH15:ENST00000373965.6:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395430.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395432.6:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395433.5:c.91+102186_91+102191del:p.(=); PCDH15:ENST00000395438.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395440.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395442.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395445.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000395446.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000414778.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000437009.5:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000612394.4:c.92-33584_92-33579del:p.(=); PCDH15:ENST00000613657.4:c.92-33584_92-33579del:p.(=); PCDH15:ENST00000614895.4:c.92-33584_92-33579del:p.(=); PCDH15:ENST00000616114.4:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000617051.4:c.92-33584_92-33579del:p.(=); PCDH15:ENST00000617271.4:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000621708.4:c.92-33584_92-33579del:p.(=); PCDH15:ENST00000622048.4:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000644397.1:c.92-34109_92-34104del:p.(=); PCDH15:ENST00000409834.5:c.-91+102186_-91+102191del:p.(=); PCDH15:ENST00000495484.5:c.-25+238939_-25+238944del:p.(=)

Pathogenicity Data:: Best Score: 0.31876022; CADD: 0.319 (1.667)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54286223T>C [0/1] rs111234620 (variation viewer)

Variant score: 0.308

Transcripts:: PCDH15:ENST00000320301.10:c.876+31048A>G:p.(=); PCDH15:ENST00000361849.7:c.876+31048A>G:p.(=); PCDH15:ENST00000373955.5:c.876+31048A>G:p.(=); PCDH15:ENST00000373957.7:c.891+31048A>G:p.(=); PCDH15:ENST00000373965.6:c.876+31048A>G:p.(=); PCDH15:ENST00000395430.5:c.876+31048A>G:p.(=); PCDH15:ENST00000395432.6:c.765+31048A>G:p.(=); PCDH15:ENST00000395433.5:c.810+31048A>G:p.(=); PCDH15:ENST00000395438.5:c.876+31048A>G:p.(=); PCDH15:ENST00000395440.5:c.876+31048A>G:p.(=); PCDH15:ENST00000395442.5:c.876+31048A>G:p.(=); PCDH15:ENST00000395445.5:c.876+31048A>G:p.(=); PCDH15:ENST00000395446.5:c.876+31048A>G:p.(=); PCDH15:ENST00000414778.5:c.876+31048A>G:p.(=); PCDH15:ENST00000437009.5:c.876+31048A>G:p.(=); PCDH15:ENST00000612394.4:c.891+31048A>G:p.(=); PCDH15:ENST00000613657.4:c.891+31048A>G:p.(=); PCDH15:ENST00000614895.4:c.891+31048A>G:p.(=); PCDH15:ENST00000616114.4:c.876+31048A>G:p.(=); PCDH15:ENST00000617051.4:c.891+31048A>G:p.(=); PCDH15:ENST00000617271.4:c.876+31048A>G:p.(=); PCDH15:ENST00000621708.4:c.891+31048A>G:p.(=); PCDH15:ENST00000622048.4:c.876+31048A>G:p.(=); PCDH15:ENST00000644397.1:c.876+31048A>G:p.(=); PCDH15:ENST00000409834.5:c.-90-90334A>G:p.(=); PCDH15:ENST00000495484.5:c.-24-428960A>G:p.(=)

Pathogenicity Data:: Best Score: 0.41709203; CADD: 0.417 (2.344)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.7104%; UK10K: 0.8596%; gnomAD_G_AFR: 0.1832%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.3729%; gnomAD_G_NFE: 0.9925%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53984122CTTTTTTTTTTTTTCTTTTTTCTTTTCT>C [1/1] rs1285707690 (variation viewer)

Variant score: 0.306

Transcripts:: PCDH15:ENST00000320301.10:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000361849.7:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000373957.7:c.2883+11500_2883+11526del:p.(=); PCDH15:ENST00000373965.6:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000395430.5:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000395432.6:c.2757+11500_2757+11526del:p.(=); PCDH15:ENST00000395433.5:c.2802+11500_2802+11526del:p.(=); PCDH15:ENST00000395438.5:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000395440.5:c.1306-174603_1306-174577del:p.(=); PCDH15:ENST00000395442.5:c.1099-174603_1099-174577del:p.(=); PCDH15:ENST00000395445.5:c.2889+11500_2889+11526del:p.(=); PCDH15:ENST00000395446.5:c.2091+95182_2091+95208del:p.(=); PCDH15:ENST00000409834.5:c.1701+11500_1701+11526del:p.(=); PCDH15:ENST00000414778.5:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000437009.5:c.2655+11500_2655+11526del:p.(=); PCDH15:ENST00000612394.4:c.2904+11500_2904+11526del:p.(=); PCDH15:ENST00000613657.4:c.2904+11500_2904+11526del:p.(=); PCDH15:ENST00000614895.4:c.2883+11500_2883+11526del:p.(=); PCDH15:ENST00000616114.4:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000617051.4:c.2883+11500_2883+11526del:p.(=); PCDH15:ENST00000617271.4:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000621708.4:c.2883+11500_2883+11526del:p.(=); PCDH15:ENST00000622048.4:c.2655+11500_2655+11526del:p.(=); PCDH15:ENST00000644397.1:c.2868+11500_2868+11526del:p.(=); PCDH15:ENST00000495484.5:c.-24-126886_-24-126860del:p.(=)

Pathogenicity Data:: Best Score: 0.30641448; CADD: 0.306 (1.589)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54167834C>T [1|1] rs1460111635 (variation viewer)

Variant score: 0.303

Transcripts:: PCDH15:ENST00000320301.10:c.1591-14541G>A:p.(=); PCDH15:ENST00000361849.7:c.1591-14541G>A:p.(=); PCDH15:ENST00000373955.5:c.1591-14541G>A:p.(=); PCDH15:ENST00000373957.7:c.1606-14541G>A:p.(=); PCDH15:ENST00000373965.6:c.1591-14541G>A:p.(=); PCDH15:ENST00000395430.5:c.1591-14541G>A:p.(=); PCDH15:ENST00000395432.6:c.1480-14541G>A:p.(=); PCDH15:ENST00000395433.5:c.1525-14541G>A:p.(=); PCDH15:ENST00000395438.5:c.1591-14541G>A:p.(=); PCDH15:ENST00000395440.5:c.1305+27849G>A:p.(=); PCDH15:ENST00000395442.5:c.1098+46102G>A:p.(=); PCDH15:ENST00000395445.5:c.1612-14541G>A:p.(=); PCDH15:ENST00000395446.5:c.1591-14541G>A:p.(=); PCDH15:ENST00000409834.5:c.424-14541G>A:p.(=); PCDH15:ENST00000414778.5:c.1591-14541G>A:p.(=); PCDH15:ENST00000437009.5:c.1591-14541G>A:p.(=); PCDH15:ENST00000612394.4:c.1627-14541G>A:p.(=); PCDH15:ENST00000613657.4:c.1627-14541G>A:p.(=); PCDH15:ENST00000614895.4:c.1606-14541G>A:p.(=); PCDH15:ENST00000616114.4:c.1591-14541G>A:p.(=); PCDH15:ENST00000617051.4:c.1606-14541G>A:p.(=); PCDH15:ENST00000617271.4:c.1591-14541G>A:p.(=); PCDH15:ENST00000621708.4:c.1606-14541G>A:p.(=); PCDH15:ENST00000622048.4:c.1591-14541G>A:p.(=); PCDH15:ENST00000644397.1:c.1591-14541G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-310571G>A:p.(=)

Pathogenicity Data:: Best Score: 0.36100125; CADD: 0.361 (1.945)

Frequency Data:: gnomAD_G_AFR: 0.6693%; gnomAD_G_AMR: 0.3145%; gnomAD_G_ASJ: 0.7812%; gnomAD_G_EAS: 0.1435%; gnomAD_G_FIN: 0.1880%; gnomAD_G_NFE: 0.6730%; gnomAD_G_OTH: 0.5780%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54484817C>T [0/1]

Variant score: 0.269

Transcripts:: PCDH15:ENST00000320301.10:c.157+42995G>A:p.(=); PCDH15:ENST00000361849.7:c.157+42995G>A:p.(=); PCDH15:ENST00000373955.5:c.157+42995G>A:p.(=); PCDH15:ENST00000373957.7:c.172+42995G>A:p.(=); PCDH15:ENST00000373965.6:c.157+42995G>A:p.(=); PCDH15:ENST00000395430.5:c.157+42995G>A:p.(=); PCDH15:ENST00000395432.6:c.157+42995G>A:p.(=); PCDH15:ENST00000395433.5:c.92-105875G>A:p.(=); PCDH15:ENST00000395438.5:c.157+42995G>A:p.(=); PCDH15:ENST00000395440.5:c.157+42995G>A:p.(=); PCDH15:ENST00000395442.5:c.157+42995G>A:p.(=); PCDH15:ENST00000395445.5:c.157+42995G>A:p.(=); PCDH15:ENST00000395446.5:c.157+42995G>A:p.(=); PCDH15:ENST00000414778.5:c.157+42995G>A:p.(=); PCDH15:ENST00000437009.5:c.157+42995G>A:p.(=); PCDH15:ENST00000612394.4:c.172+42995G>A:p.(=); PCDH15:ENST00000613657.4:c.172+42995G>A:p.(=); PCDH15:ENST00000614895.4:c.172+42995G>A:p.(=); PCDH15:ENST00000616114.4:c.157+42995G>A:p.(=); PCDH15:ENST00000617051.4:c.172+42995G>A:p.(=); PCDH15:ENST00000617271.4:c.157+42995G>A:p.(=); PCDH15:ENST00000621708.4:c.172+42995G>A:p.(=); PCDH15:ENST00000622048.4:c.157+42995G>A:p.(=); PCDH15:ENST00000644397.1:c.157+42995G>A:p.(=); PCDH15:ENST00000409834.5:c.-91+179355G>A:p.(=); PCDH15:ENST00000495484.5:c.-25+316108G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2693658; CADD: 0.269 (1.363)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54316556ACACACACACACACACACAC>A [0/1] rs748134298 (variation viewer)

Variant score: 0.257

Transcripts:: PCDH15:ENST00000320301.10:c.876+696_876+714del:p.(=); PCDH15:ENST00000361849.7:c.876+696_876+714del:p.(=); PCDH15:ENST00000373955.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000373957.7:c.891+696_891+714del:p.(=); PCDH15:ENST00000373965.6:c.876+696_876+714del:p.(=); PCDH15:ENST00000395430.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000395432.6:c.765+696_765+714del:p.(=); PCDH15:ENST00000395433.5:c.810+696_810+714del:p.(=); PCDH15:ENST00000395438.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000395440.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000395442.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000395445.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000395446.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000414778.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000437009.5:c.876+696_876+714del:p.(=); PCDH15:ENST00000612394.4:c.891+696_891+714del:p.(=); PCDH15:ENST00000613657.4:c.891+696_891+714del:p.(=); PCDH15:ENST00000614895.4:c.891+696_891+714del:p.(=); PCDH15:ENST00000616114.4:c.876+696_876+714del:p.(=); PCDH15:ENST00000617051.4:c.891+696_891+714del:p.(=); PCDH15:ENST00000617271.4:c.876+696_876+714del:p.(=); PCDH15:ENST00000621708.4:c.891+696_891+714del:p.(=); PCDH15:ENST00000622048.4:c.876+696_876+714del:p.(=); PCDH15:ENST00000644397.1:c.876+696_876+714del:p.(=); PCDH15:ENST00000409834.5:c.-90-120686_-90-120668del:p.(=); PCDH15:ENST00000495484.5:c.-24-459312_-24-459294del:p.(=)

Pathogenicity Data:: Best Score: 0.26886094; CADD: 0.269 (1.360)

Frequency Data:: gnomAD_G_AFR: 0.1129%; gnomAD_G_AMR: 0.2874%; gnomAD_G_NFE: 0.0288%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54618869A>G [0/1] rs944669513 (variation viewer)

Variant score: 0.254

Transcripts:: PCDH15:ENST00000320301.10:c.91+45303T>C:p.(=); PCDH15:ENST00000361849.7:c.91+45303T>C:p.(=); PCDH15:ENST00000373955.5:c.91+45303T>C:p.(=); PCDH15:ENST00000373957.7:c.91+45303T>C:p.(=); PCDH15:ENST00000373965.6:c.91+45303T>C:p.(=); PCDH15:ENST00000395430.5:c.91+45303T>C:p.(=); PCDH15:ENST00000395432.6:c.91+45303T>C:p.(=); PCDH15:ENST00000395433.5:c.91+45303T>C:p.(=); PCDH15:ENST00000395438.5:c.91+45303T>C:p.(=); PCDH15:ENST00000395440.5:c.91+45303T>C:p.(=); PCDH15:ENST00000395442.5:c.91+45303T>C:p.(=); PCDH15:ENST00000395445.5:c.91+45303T>C:p.(=); PCDH15:ENST00000395446.5:c.91+45303T>C:p.(=); PCDH15:ENST00000414778.5:c.91+45303T>C:p.(=); PCDH15:ENST00000437009.5:c.91+45303T>C:p.(=); PCDH15:ENST00000612394.4:c.91+45303T>C:p.(=); PCDH15:ENST00000613657.4:c.91+45303T>C:p.(=); PCDH15:ENST00000614895.4:c.91+45303T>C:p.(=); PCDH15:ENST00000616114.4:c.91+45303T>C:p.(=); PCDH15:ENST00000617051.4:c.91+45303T>C:p.(=); PCDH15:ENST00000617271.4:c.91+45303T>C:p.(=); PCDH15:ENST00000621708.4:c.91+45303T>C:p.(=); PCDH15:ENST00000622048.4:c.91+45303T>C:p.(=); PCDH15:ENST00000644397.1:c.91+45303T>C:p.(=); PCDH15:ENST00000409834.5:c.-91+45303T>C:p.(=); PCDH15:ENST00000495484.5:c.-25+182056T>C:p.(=)

Pathogenicity Data:: Best Score: 0.25389493; CADD: 0.254 (1.272)

Frequency Data:: TOPMed: 0.0016%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53981835C>A [0/1] rs1332644505 (variation viewer)

Variant score: 0.250

Transcripts:: PCDH15:ENST00000320301.10:c.2868+13814G>T:p.(=); PCDH15:ENST00000361849.7:c.2868+13814G>T:p.(=); PCDH15:ENST00000373957.7:c.2883+13814G>T:p.(=); PCDH15:ENST00000373965.6:c.2868+13814G>T:p.(=); PCDH15:ENST00000395430.5:c.2868+13814G>T:p.(=); PCDH15:ENST00000395432.6:c.2757+13814G>T:p.(=); PCDH15:ENST00000395433.5:c.2802+13814G>T:p.(=); PCDH15:ENST00000395438.5:c.2868+13814G>T:p.(=); PCDH15:ENST00000395440.5:c.1306-172289G>T:p.(=); PCDH15:ENST00000395442.5:c.1099-172289G>T:p.(=); PCDH15:ENST00000395445.5:c.2889+13814G>T:p.(=); PCDH15:ENST00000395446.5:c.2091+97496G>T:p.(=); PCDH15:ENST00000409834.5:c.1701+13814G>T:p.(=); PCDH15:ENST00000414778.5:c.2868+13814G>T:p.(=); PCDH15:ENST00000437009.5:c.2655+13814G>T:p.(=); PCDH15:ENST00000612394.4:c.2904+13814G>T:p.(=); PCDH15:ENST00000613657.4:c.2904+13814G>T:p.(=); PCDH15:ENST00000614895.4:c.2883+13814G>T:p.(=); PCDH15:ENST00000616114.4:c.2868+13814G>T:p.(=); PCDH15:ENST00000617051.4:c.2883+13814G>T:p.(=); PCDH15:ENST00000617271.4:c.2868+13814G>T:p.(=); PCDH15:ENST00000621708.4:c.2883+13814G>T:p.(=); PCDH15:ENST00000622048.4:c.2655+13814G>T:p.(=); PCDH15:ENST00000644397.1:c.2868+13814G>T:p.(=); PCDH15:ENST00000495484.5:c.-24-124572G>T:p.(=)

Pathogenicity Data:: Best Score: 0.2525193; CADD: 0.253 (1.264)

Frequency Data:: gnomAD_G_AFR: 0.0692%; gnomAD_G_NFE: 0.0073%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54796282GTATCTATC>G [-/1] rs57641746 (variation viewer)

Variant score: 0.249

Transcripts:: PCDH15:ENST00000320301.10:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000361849.7:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000373955.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000373957.7:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000373965.6:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395430.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395432.6:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395433.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395438.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395440.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395442.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395445.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000395446.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000409834.5:c.-210+4635_-210+4642del:p.(=); PCDH15:ENST00000414778.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000437009.5:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000495484.5:c.-25+4635_-25+4642del:p.(=); PCDH15:ENST00000612394.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000613657.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000614895.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000616114.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000617051.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000617271.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000621708.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000622048.4:c.-29+4635_-29+4642del:p.(=); PCDH15:ENST00000644397.1:c.-29+4635_-29+4642del:p.(=)

Pathogenicity Data:: Best Score: 0.24906904; CADD: 0.249 (1.244)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54796282GTATCTATCTATC>G [-/1] rs57641746 (variation viewer)

Variant score: 0.238

Transcripts:: PCDH15:ENST00000320301.10:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000361849.7:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000373955.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000373957.7:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000373965.6:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395430.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395432.6:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395433.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395438.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395440.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395442.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395445.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000395446.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000409834.5:c.-210+4631_-210+4642del:p.(=); PCDH15:ENST00000414778.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000437009.5:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000495484.5:c.-25+4631_-25+4642del:p.(=); PCDH15:ENST00000612394.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000613657.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000614895.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000616114.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000617051.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000617271.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000621708.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000622048.4:c.-29+4631_-29+4642del:p.(=); PCDH15:ENST00000644397.1:c.-29+4631_-29+4642del:p.(=)

Pathogenicity Data:: Best Score: 0.23809648; CADD: 0.238 (1.181)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54166497TTTTG>T [0/1] rs748077058 (variation viewer)

Variant score: 0.229

Transcripts:: PCDH15:ENST00000320301.10:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000361849.7:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000373955.5:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000373957.7:c.1606-13208_1606-13205del:p.(=); PCDH15:ENST00000373965.6:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000395430.5:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000395432.6:c.1480-13208_1480-13205del:p.(=); PCDH15:ENST00000395433.5:c.1525-13208_1525-13205del:p.(=); PCDH15:ENST00000395438.5:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000395440.5:c.1305+29182_1305+29185del:p.(=); PCDH15:ENST00000395442.5:c.1098+47435_1098+47438del:p.(=); PCDH15:ENST00000395445.5:c.1612-13208_1612-13205del:p.(=); PCDH15:ENST00000395446.5:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000409834.5:c.424-13208_424-13205del:p.(=); PCDH15:ENST00000414778.5:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000437009.5:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000612394.4:c.1627-13208_1627-13205del:p.(=); PCDH15:ENST00000613657.4:c.1627-13208_1627-13205del:p.(=); PCDH15:ENST00000614895.4:c.1606-13208_1606-13205del:p.(=); PCDH15:ENST00000616114.4:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000617051.4:c.1606-13208_1606-13205del:p.(=); PCDH15:ENST00000617271.4:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000621708.4:c.1606-13208_1606-13205del:p.(=); PCDH15:ENST00000622048.4:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000644397.1:c.1591-13208_1591-13205del:p.(=); PCDH15:ENST00000495484.5:c.-24-309238_-24-309235del:p.(=)

Pathogenicity Data:: Best Score: 0.44575727; CADD: 0.446 (2.563)

Frequency Data:: TOPMed: 0.4810%; UK10K: 0.2380%; gnomAD_G_AFR: 1.5245%; gnomAD_G_AMR: 0.1193%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54122034G>C [0|1] rs148137731 (variation viewer)

Variant score: 0.221

Transcripts:: PCDH15:ENST00000320301.10:c.1917+10841C>G:p.(=); PCDH15:ENST00000361849.7:c.1917+10841C>G:p.(=); PCDH15:ENST00000373955.5:c.1917+10841C>G:p.(=); PCDH15:ENST00000373957.7:c.1932+10841C>G:p.(=); PCDH15:ENST00000373965.6:c.1917+10841C>G:p.(=); PCDH15:ENST00000395430.5:c.1917+10841C>G:p.(=); PCDH15:ENST00000395432.6:c.1806+10841C>G:p.(=); PCDH15:ENST00000395433.5:c.1851+10841C>G:p.(=); PCDH15:ENST00000395438.5:c.1917+10841C>G:p.(=); PCDH15:ENST00000395440.5:c.1305+73649C>G:p.(=); PCDH15:ENST00000395442.5:c.1098+91902C>G:p.(=); PCDH15:ENST00000395445.5:c.1938+10841C>G:p.(=); PCDH15:ENST00000395446.5:c.1917+10841C>G:p.(=); PCDH15:ENST00000409834.5:c.750+10841C>G:p.(=); PCDH15:ENST00000414778.5:c.1917+10841C>G:p.(=); PCDH15:ENST00000437009.5:c.1784+31066C>G:p.(=); PCDH15:ENST00000612394.4:c.1953+10841C>G:p.(=); PCDH15:ENST00000613657.4:c.1953+10841C>G:p.(=); PCDH15:ENST00000614895.4:c.1932+10841C>G:p.(=); PCDH15:ENST00000616114.4:c.1917+10841C>G:p.(=); PCDH15:ENST00000617051.4:c.1932+10841C>G:p.(=); PCDH15:ENST00000617271.4:c.1917+10841C>G:p.(=); PCDH15:ENST00000621708.4:c.1932+10841C>G:p.(=); PCDH15:ENST00000622048.4:c.1784+31066C>G:p.(=); PCDH15:ENST00000644397.1:c.1917+10841C>G:p.(=); PCDH15:ENST00000495484.5:c.-24-264771C>G:p.(=)

Pathogenicity Data:: Best Score: 0.22339535; CADD: 0.223 (1.098)

Frequency Data:: gnomAD_G_AFR: 0.0190%; gnomAD_G_FIN: 0.0615%; gnomAD_G_NFE: 0.0162%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54008289A>G [0/1] rs75302753 (variation viewer)

Variant score: 0.213

Transcripts:: PCDH15:ENST00000320301.10:c.2751+11903T>C:p.(=); PCDH15:ENST00000361849.7:c.2751+11903T>C:p.(=); PCDH15:ENST00000373955.5:c.2751+11903T>C:p.(=); PCDH15:ENST00000373957.7:c.2766+11903T>C:p.(=); PCDH15:ENST00000373965.6:c.2751+11903T>C:p.(=); PCDH15:ENST00000395430.5:c.2751+11903T>C:p.(=); PCDH15:ENST00000395432.6:c.2640+11903T>C:p.(=); PCDH15:ENST00000395433.5:c.2685+11903T>C:p.(=); PCDH15:ENST00000395438.5:c.2751+11903T>C:p.(=); PCDH15:ENST00000395440.5:c.1305+187394T>C:p.(=); PCDH15:ENST00000395442.5:c.1099-198743T>C:p.(=); PCDH15:ENST00000395445.5:c.2772+11903T>C:p.(=); PCDH15:ENST00000395446.5:c.2091+71042T>C:p.(=); PCDH15:ENST00000409834.5:c.1584+11903T>C:p.(=); PCDH15:ENST00000414778.5:c.2751+11903T>C:p.(=); PCDH15:ENST00000437009.5:c.2538+11903T>C:p.(=); PCDH15:ENST00000612394.4:c.2787+11903T>C:p.(=); PCDH15:ENST00000613657.4:c.2787+11903T>C:p.(=); PCDH15:ENST00000614895.4:c.2766+11903T>C:p.(=); PCDH15:ENST00000616114.4:c.2751+11903T>C:p.(=); PCDH15:ENST00000617051.4:c.2766+11903T>C:p.(=); PCDH15:ENST00000617271.4:c.2751+11903T>C:p.(=); PCDH15:ENST00000621708.4:c.2766+11903T>C:p.(=); PCDH15:ENST00000622048.4:c.2538+11903T>C:p.(=); PCDH15:ENST00000644397.1:c.2751+11903T>C:p.(=); PCDH15:ENST00000495484.5:c.-24-151026T>C:p.(=)

Pathogenicity Data:: Best Score: 0.24351555; CADD: 0.244 (1.212)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.3002%; UK10K: 0.3967%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3199%; gnomAD_G_OTH: 0.1018%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54774007CT>C [-/1] rs763704132 (variation viewer)

Variant score: 0.204

Transcripts:: PCDH15:ENST00000320301.10:c.-29+26917del:p.(=); PCDH15:ENST00000361849.7:c.-29+26917del:p.(=); PCDH15:ENST00000373955.5:c.-29+26917del:p.(=); PCDH15:ENST00000373957.7:c.-29+26917del:p.(=); PCDH15:ENST00000373965.6:c.-29+26917del:p.(=); PCDH15:ENST00000395430.5:c.-29+26917del:p.(=); PCDH15:ENST00000395432.6:c.-29+26917del:p.(=); PCDH15:ENST00000395433.5:c.-29+26917del:p.(=); PCDH15:ENST00000395438.5:c.-29+26917del:p.(=); PCDH15:ENST00000395440.5:c.-29+26917del:p.(=); PCDH15:ENST00000395442.5:c.-29+26917del:p.(=); PCDH15:ENST00000395445.5:c.-29+26917del:p.(=); PCDH15:ENST00000395446.5:c.-29+26917del:p.(=); PCDH15:ENST00000409834.5:c.-210+26917del:p.(=); PCDH15:ENST00000414778.5:c.-29+26917del:p.(=); PCDH15:ENST00000437009.5:c.-29+26917del:p.(=); PCDH15:ENST00000495484.5:c.-25+26917del:p.(=); PCDH15:ENST00000612394.4:c.-29+26917del:p.(=); PCDH15:ENST00000613657.4:c.-29+26917del:p.(=); PCDH15:ENST00000614895.4:c.-29+26917del:p.(=); PCDH15:ENST00000616114.4:c.-29+26917del:p.(=); PCDH15:ENST00000617051.4:c.-29+26917del:p.(=); PCDH15:ENST00000617271.4:c.-29+26917del:p.(=); PCDH15:ENST00000621708.4:c.-29+26917del:p.(=); PCDH15:ENST00000622048.4:c.-29+26917del:p.(=); PCDH15:ENST00000644397.1:c.-29+26917del:p.(=)

Pathogenicity Data:: Best Score: 0.20365733; CADD: 0.204 (0.989)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54774007CTTTTTTTTTTTTT>C [-/1] rs763704132 (variation viewer)

Variant score: 0.199

Transcripts:: PCDH15:ENST00000320301.10:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000361849.7:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000373955.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000373957.7:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000373965.6:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395430.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395432.6:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395433.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395438.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395440.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395442.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395445.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000395446.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000409834.5:c.-210+26905_-210+26917del:p.(=); PCDH15:ENST00000414778.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000437009.5:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000495484.5:c.-25+26905_-25+26917del:p.(=); PCDH15:ENST00000612394.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000613657.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000614895.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000616114.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000617051.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000617271.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000621708.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000622048.4:c.-29+26905_-29+26917del:p.(=); PCDH15:ENST00000644397.1:c.-29+26905_-29+26917del:p.(=)

Pathogenicity Data:: Best Score: 0.19869107; CADD: 0.199 (0.962)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54718684C>CT [0/1] rs71461255 (variation viewer)

Variant score: 0.196

Transcripts:: PCDH15:ENST00000320301.10:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000361849.7:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000373955.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000373957.7:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000373965.6:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395430.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395432.6:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395433.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395438.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395440.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395442.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395445.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000395446.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000409834.5:c.-209-54395_-209-54394insA:p.(=); PCDH15:ENST00000414778.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000437009.5:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000495484.5:c.-25+82240_-25+82241insA:p.(=); PCDH15:ENST00000612394.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000613657.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000614895.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000616114.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000617051.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000617271.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000621708.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000622048.4:c.-28-54395_-28-54394insA:p.(=); PCDH15:ENST00000644397.1:c.-28-54395_-28-54394insA:p.(=)

Pathogenicity Data:: Best Score: 0.19591862; CADD: 0.196 (0.947)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54344904CAAA>C [1/1] rs57295345 (variation viewer)

Variant score: 0.189

Transcripts:: PCDH15:ENST00000320301.10:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000361849.7:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000373955.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000373957.7:c.609+1458_609+1460del:p.(=); PCDH15:ENST00000373965.6:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395430.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395432.6:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395433.5:c.528+1458_528+1460del:p.(=); PCDH15:ENST00000395438.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395440.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395442.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395445.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000395446.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000414778.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000437009.5:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000612394.4:c.609+1458_609+1460del:p.(=); PCDH15:ENST00000613657.4:c.609+1458_609+1460del:p.(=); PCDH15:ENST00000614895.4:c.609+1458_609+1460del:p.(=); PCDH15:ENST00000616114.4:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000617051.4:c.609+1458_609+1460del:p.(=); PCDH15:ENST00000617271.4:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000621708.4:c.609+1458_609+1460del:p.(=); PCDH15:ENST00000622048.4:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000644397.1:c.594+1458_594+1460del:p.(=); PCDH15:ENST00000409834.5:c.-90-149018_-90-149016del:p.(=); PCDH15:ENST00000495484.5:c.-25+456018_-25+456020del:p.(=)

Pathogenicity Data:: Best Score: 0.18866539; CADD: 0.189 (0.908)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54392468C>CA [1/1] rs71007849 (variation viewer)

Variant score: 0.179

Transcripts:: PCDH15:ENST00000320301.10:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000361849.7:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000373955.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000373957.7:c.173-13527_173-13526insT:p.(=); PCDH15:ENST00000373965.6:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395430.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395432.6:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395433.5:c.92-13527_92-13526insT:p.(=); PCDH15:ENST00000395438.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395440.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395442.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395445.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000395446.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000414778.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000437009.5:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000612394.4:c.173-13527_173-13526insT:p.(=); PCDH15:ENST00000613657.4:c.173-13527_173-13526insT:p.(=); PCDH15:ENST00000614895.4:c.173-13527_173-13526insT:p.(=); PCDH15:ENST00000616114.4:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000617051.4:c.173-13527_173-13526insT:p.(=); PCDH15:ENST00000617271.4:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000621708.4:c.173-13527_173-13526insT:p.(=); PCDH15:ENST00000622048.4:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000644397.1:c.158-13527_158-13526insT:p.(=); PCDH15:ENST00000409834.5:c.-90-196580_-90-196579insT:p.(=); PCDH15:ENST00000495484.5:c.-25+408456_-25+408457insT:p.(=)

Pathogenicity Data:: Best Score: 0.17870343; CADD: 0.179 (0.855)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54295116C>T [0/1] rs1028343192 (variation viewer)

Variant score: 0.178

Transcripts:: PCDH15:ENST00000320301.10:c.876+22155G>A:p.(=); PCDH15:ENST00000361849.7:c.876+22155G>A:p.(=); PCDH15:ENST00000373955.5:c.876+22155G>A:p.(=); PCDH15:ENST00000373957.7:c.891+22155G>A:p.(=); PCDH15:ENST00000373965.6:c.876+22155G>A:p.(=); PCDH15:ENST00000395430.5:c.876+22155G>A:p.(=); PCDH15:ENST00000395432.6:c.765+22155G>A:p.(=); PCDH15:ENST00000395433.5:c.810+22155G>A:p.(=); PCDH15:ENST00000395438.5:c.876+22155G>A:p.(=); PCDH15:ENST00000395440.5:c.876+22155G>A:p.(=); PCDH15:ENST00000395442.5:c.876+22155G>A:p.(=); PCDH15:ENST00000395445.5:c.876+22155G>A:p.(=); PCDH15:ENST00000395446.5:c.876+22155G>A:p.(=); PCDH15:ENST00000414778.5:c.876+22155G>A:p.(=); PCDH15:ENST00000437009.5:c.876+22155G>A:p.(=); PCDH15:ENST00000612394.4:c.891+22155G>A:p.(=); PCDH15:ENST00000613657.4:c.891+22155G>A:p.(=); PCDH15:ENST00000614895.4:c.891+22155G>A:p.(=); PCDH15:ENST00000616114.4:c.876+22155G>A:p.(=); PCDH15:ENST00000617051.4:c.891+22155G>A:p.(=); PCDH15:ENST00000617271.4:c.876+22155G>A:p.(=); PCDH15:ENST00000621708.4:c.891+22155G>A:p.(=); PCDH15:ENST00000622048.4:c.876+22155G>A:p.(=); PCDH15:ENST00000644397.1:c.876+22155G>A:p.(=); PCDH15:ENST00000409834.5:c.-90-99227G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-437853G>A:p.(=)

Pathogenicity Data:: Best Score: 0.1785143; CADD: 0.179 (0.854)

Frequency Data:: TOPMed: 0.0048%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54205481T>TTGTGTGTGTGTGTG [-/1] rs71461223 (variation viewer)

Variant score: 0.178

Transcripts:: PCDH15:ENST00000320301.10:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000361849.7:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000373955.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000373957.7:c.1113+8454_1113+8455insCACACACACACACA:p.(=); PCDH15:ENST00000373965.6:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395430.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395432.6:c.987+8454_987+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395433.5:c.1032+8454_1032+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395438.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395440.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395442.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395445.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000395446.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000414778.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000437009.5:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000612394.4:c.1113+8454_1113+8455insCACACACACACACA:p.(=); PCDH15:ENST00000613657.4:c.1113+8454_1113+8455insCACACACACACACA:p.(=); PCDH15:ENST00000614895.4:c.1113+8454_1113+8455insCACACACACACACA:p.(=); PCDH15:ENST00000616114.4:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000617051.4:c.1113+8454_1113+8455insCACACACACACACA:p.(=); PCDH15:ENST00000617271.4:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000621708.4:c.1113+8454_1113+8455insCACACACACACACA:p.(=); PCDH15:ENST00000622048.4:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000644397.1:c.1098+8454_1098+8455insCACACACACACACA:p.(=); PCDH15:ENST00000409834.5:c.-90-9593_-90-9592insCACACACACACACA:p.(=); PCDH15:ENST00000495484.5:c.-24-348219_-24-348218insCACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.17794669; CADD: 0.178 (0.851)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54205481T>TTGTGTGTGTGTGTGTGTG [-/1] rs71461223 (variation viewer)

Variant score: 0.165

Transcripts:: PCDH15:ENST00000320301.10:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000361849.7:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000373955.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000373957.7:c.1113+8454_1113+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000373965.6:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395430.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395432.6:c.987+8454_987+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395433.5:c.1032+8454_1032+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395438.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395440.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395442.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395445.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000395446.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000414778.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000437009.5:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000612394.4:c.1113+8454_1113+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000613657.4:c.1113+8454_1113+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000614895.4:c.1113+8454_1113+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000616114.4:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000617051.4:c.1113+8454_1113+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000617271.4:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000621708.4:c.1113+8454_1113+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000622048.4:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000644397.1:c.1098+8454_1098+8455insCACACACACACACACACA:p.(=); PCDH15:ENST00000409834.5:c.-90-9593_-90-9592insCACACACACACACACACA:p.(=); PCDH15:ENST00000495484.5:c.-24-348219_-24-348218insCACACACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.16535848; CADD: 0.165 (0.785)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54535709C>CAA [1/1] rs71010382 (variation viewer)

Variant score: 0.165

Transcripts:: PCDH15:ENST00000320301.10:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000361849.7:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000373955.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000373957.7:c.92-7308_92-7307insTT:p.(=); PCDH15:ENST00000373965.6:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395430.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395432.6:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395433.5:c.91+128462_91+128463insTT:p.(=); PCDH15:ENST00000395438.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395440.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395442.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395445.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000395446.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000414778.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000437009.5:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000612394.4:c.92-7308_92-7307insTT:p.(=); PCDH15:ENST00000613657.4:c.92-7308_92-7307insTT:p.(=); PCDH15:ENST00000614895.4:c.92-7308_92-7307insTT:p.(=); PCDH15:ENST00000616114.4:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000617051.4:c.92-7308_92-7307insTT:p.(=); PCDH15:ENST00000617271.4:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000621708.4:c.92-7308_92-7307insTT:p.(=); PCDH15:ENST00000622048.4:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000644397.1:c.92-7833_92-7832insTT:p.(=); PCDH15:ENST00000409834.5:c.-91+128462_-91+128463insTT:p.(=); PCDH15:ENST00000495484.5:c.-25+265215_-25+265216insTT:p.(=)

Pathogenicity Data:: Best Score: 0.16478169; CADD: 0.165 (0.782)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54174702C>CTT [-/1] rs1169302544 (variation viewer)

Variant score: 0.143

Transcripts:: PCDH15:ENST00000320301.10:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000361849.7:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000373955.5:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000373957.7:c.1605+8741_1605+8742insAA:p.(=); PCDH15:ENST00000373965.6:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000395430.5:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000395432.6:c.1479+8741_1479+8742insAA:p.(=); PCDH15:ENST00000395433.5:c.1524+8741_1524+8742insAA:p.(=); PCDH15:ENST00000395438.5:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000395440.5:c.1305+20980_1305+20981insAA:p.(=); PCDH15:ENST00000395442.5:c.1098+39233_1098+39234insAA:p.(=); PCDH15:ENST00000395445.5:c.1611+8741_1611+8742insAA:p.(=); PCDH15:ENST00000395446.5:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000409834.5:c.423+8741_423+8742insAA:p.(=); PCDH15:ENST00000414778.5:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000437009.5:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000612394.4:c.1626+8741_1626+8742insAA:p.(=); PCDH15:ENST00000613657.4:c.1626+8741_1626+8742insAA:p.(=); PCDH15:ENST00000614895.4:c.1605+8741_1605+8742insAA:p.(=); PCDH15:ENST00000616114.4:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000617051.4:c.1605+8741_1605+8742insAA:p.(=); PCDH15:ENST00000617271.4:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000621708.4:c.1605+8741_1605+8742insAA:p.(=); PCDH15:ENST00000622048.4:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000644397.1:c.1590+8741_1590+8742insAA:p.(=); PCDH15:ENST00000495484.5:c.-24-317440_-24-317439insAA:p.(=)

Pathogenicity Data:: Best Score: 0.1425674; CADD: 0.143 (0.668)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54644756G>A [0/1] rs148934337 (variation viewer)

Variant score: 0.143

Transcripts:: PCDH15:ENST00000320301.10:c.91+19416C>T:p.(=); PCDH15:ENST00000361849.7:c.91+19416C>T:p.(=); PCDH15:ENST00000373955.5:c.91+19416C>T:p.(=); PCDH15:ENST00000373957.7:c.91+19416C>T:p.(=); PCDH15:ENST00000373965.6:c.91+19416C>T:p.(=); PCDH15:ENST00000395430.5:c.91+19416C>T:p.(=); PCDH15:ENST00000395432.6:c.91+19416C>T:p.(=); PCDH15:ENST00000395433.5:c.91+19416C>T:p.(=); PCDH15:ENST00000395438.5:c.91+19416C>T:p.(=); PCDH15:ENST00000395440.5:c.91+19416C>T:p.(=); PCDH15:ENST00000395442.5:c.91+19416C>T:p.(=); PCDH15:ENST00000395445.5:c.91+19416C>T:p.(=); PCDH15:ENST00000395446.5:c.91+19416C>T:p.(=); PCDH15:ENST00000414778.5:c.91+19416C>T:p.(=); PCDH15:ENST00000437009.5:c.91+19416C>T:p.(=); PCDH15:ENST00000612394.4:c.91+19416C>T:p.(=); PCDH15:ENST00000613657.4:c.91+19416C>T:p.(=); PCDH15:ENST00000614895.4:c.91+19416C>T:p.(=); PCDH15:ENST00000616114.4:c.91+19416C>T:p.(=); PCDH15:ENST00000617051.4:c.91+19416C>T:p.(=); PCDH15:ENST00000617271.4:c.91+19416C>T:p.(=); PCDH15:ENST00000621708.4:c.91+19416C>T:p.(=); PCDH15:ENST00000622048.4:c.91+19416C>T:p.(=); PCDH15:ENST00000644397.1:c.91+19416C>T:p.(=); PCDH15:ENST00000409834.5:c.-91+19416C>T:p.(=); PCDH15:ENST00000495484.5:c.-25+156169C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3479213; CADD: 0.348 (1.857)

Frequency Data:: 1000Genomes: 0.8586%; TOPMed: 1.0670%; UK10K: 1.6794%; gnomAD_G_AFR: 0.2864%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.8591%; gnomAD_G_NFE: 1.2597%; gnomAD_G_OTH: 1.2245%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54174702C>CTTT [-/1] rs1169302544 (variation viewer)

Variant score: 0.140

Transcripts:: PCDH15:ENST00000320301.10:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000361849.7:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000373955.5:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000373957.7:c.1605+8741_1605+8742insAAA:p.(=); PCDH15:ENST00000373965.6:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000395430.5:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000395432.6:c.1479+8741_1479+8742insAAA:p.(=); PCDH15:ENST00000395433.5:c.1524+8741_1524+8742insAAA:p.(=); PCDH15:ENST00000395438.5:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000395440.5:c.1305+20980_1305+20981insAAA:p.(=); PCDH15:ENST00000395442.5:c.1098+39233_1098+39234insAAA:p.(=); PCDH15:ENST00000395445.5:c.1611+8741_1611+8742insAAA:p.(=); PCDH15:ENST00000395446.5:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000409834.5:c.423+8741_423+8742insAAA:p.(=); PCDH15:ENST00000414778.5:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000437009.5:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000612394.4:c.1626+8741_1626+8742insAAA:p.(=); PCDH15:ENST00000613657.4:c.1626+8741_1626+8742insAAA:p.(=); PCDH15:ENST00000614895.4:c.1605+8741_1605+8742insAAA:p.(=); PCDH15:ENST00000616114.4:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000617051.4:c.1605+8741_1605+8742insAAA:p.(=); PCDH15:ENST00000617271.4:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000621708.4:c.1605+8741_1605+8742insAAA:p.(=); PCDH15:ENST00000622048.4:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000644397.1:c.1590+8741_1590+8742insAAA:p.(=); PCDH15:ENST00000495484.5:c.-24-317440_-24-317439insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.13979888; CADD: 0.140 (0.654)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53828207CAA>C [1/1] rs71004480 (variation viewer)

Variant score: 0.139

Transcripts:: PCDH15:ENST00000320301.10:c.4211+356_4211+357del:p.(=); PCDH15:ENST00000361849.7:c.4211+356_4211+357del:p.(=); PCDH15:ENST00000373957.7:c.4226+356_4226+357del:p.(=); PCDH15:ENST00000373965.6:c.4211+356_4211+357del:p.(=); PCDH15:ENST00000395430.5:c.4203-661_4203-660del:p.(=); PCDH15:ENST00000395432.6:c.4092-661_4092-660del:p.(=); PCDH15:ENST00000395433.5:c.4137-661_4137-660del:p.(=); PCDH15:ENST00000395438.5:c.4214-660_4214-659del:p.(=); PCDH15:ENST00000395440.5:c.1306-18663_1306-18662del:p.(=); PCDH15:ENST00000395442.5:c.1099-18663_1099-18662del:p.(=); PCDH15:ENST00000395445.5:c.4232+356_4232+357del:p.(=); PCDH15:ENST00000395446.5:c.2092-18663_2092-18662del:p.(=); PCDH15:ENST00000409834.5:c.3044+356_3044+357del:p.(=); PCDH15:ENST00000414778.5:c.4214-660_4214-659del:p.(=); PCDH15:ENST00000437009.5:c.3998+356_3998+357del:p.(=); PCDH15:ENST00000495484.5:c.461+3106_461+3107del:p.(=); PCDH15:ENST00000612394.4:c.4250-660_4250-659del:p.(=); PCDH15:ENST00000613657.4:c.4247+356_4247+357del:p.(=); PCDH15:ENST00000614895.4:c.4229-660_4229-659del:p.(=); PCDH15:ENST00000616114.4:c.4211+356_4211+357del:p.(=); PCDH15:ENST00000617051.4:c.4229-660_4229-659del:p.(=); PCDH15:ENST00000617271.4:c.4211+356_4211+357del:p.(=); PCDH15:ENST00000621708.4:c.4226+356_4226+357del:p.(=); PCDH15:ENST00000622048.4:c.4001-660_4001-659del:p.(=); PCDH15:ENST00000644397.1:c.4211+356_4211+357del:p.(=)

Pathogenicity Data:: Best Score: 0.1392045; CADD: 0.139 (0.651)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53987323A>G [0/1] rs117514523 (variation viewer)

Variant score: 0.132

Transcripts:: PCDH15:ENST00000320301.10:c.2868+8326T>C:p.(=); PCDH15:ENST00000361849.7:c.2868+8326T>C:p.(=); PCDH15:ENST00000373957.7:c.2883+8326T>C:p.(=); PCDH15:ENST00000373965.6:c.2868+8326T>C:p.(=); PCDH15:ENST00000395430.5:c.2868+8326T>C:p.(=); PCDH15:ENST00000395432.6:c.2757+8326T>C:p.(=); PCDH15:ENST00000395433.5:c.2802+8326T>C:p.(=); PCDH15:ENST00000395438.5:c.2868+8326T>C:p.(=); PCDH15:ENST00000395440.5:c.1306-177777T>C:p.(=); PCDH15:ENST00000395442.5:c.1099-177777T>C:p.(=); PCDH15:ENST00000395445.5:c.2889+8326T>C:p.(=); PCDH15:ENST00000395446.5:c.2091+92008T>C:p.(=); PCDH15:ENST00000409834.5:c.1701+8326T>C:p.(=); PCDH15:ENST00000414778.5:c.2868+8326T>C:p.(=); PCDH15:ENST00000437009.5:c.2655+8326T>C:p.(=); PCDH15:ENST00000612394.4:c.2904+8326T>C:p.(=); PCDH15:ENST00000613657.4:c.2904+8326T>C:p.(=); PCDH15:ENST00000614895.4:c.2883+8326T>C:p.(=); PCDH15:ENST00000616114.4:c.2868+8326T>C:p.(=); PCDH15:ENST00000617051.4:c.2883+8326T>C:p.(=); PCDH15:ENST00000617271.4:c.2868+8326T>C:p.(=); PCDH15:ENST00000621708.4:c.2883+8326T>C:p.(=); PCDH15:ENST00000622048.4:c.2655+8326T>C:p.(=); PCDH15:ENST00000644397.1:c.2868+8326T>C:p.(=); PCDH15:ENST00000495484.5:c.-24-130060T>C:p.(=)

Pathogenicity Data:: Best Score: 0.15160131; CADD: 0.152 (0.714)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2716%; UK10K: 0.2645%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2404%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.1164%; gnomAD_G_NFE: 0.3134%; gnomAD_G_OTH: 0.1020%

REGULATORY_REGION_VARIANT chr10:g.53014838C>CTTTTTT [-/1] rs71032683 (variation viewer)

Variant score: 0.128

Transcripts:

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54408052C>CA [-/1] rs71461239 (variation viewer)

Variant score: 0.118

Transcripts:: PCDH15:ENST00000320301.10:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000361849.7:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000373955.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000373957.7:c.173-29111_173-29110insT:p.(=); PCDH15:ENST00000373965.6:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395430.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395432.6:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395433.5:c.92-29111_92-29110insT:p.(=); PCDH15:ENST00000395438.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395440.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395442.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395445.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000395446.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000414778.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000437009.5:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000612394.4:c.173-29111_173-29110insT:p.(=); PCDH15:ENST00000613657.4:c.173-29111_173-29110insT:p.(=); PCDH15:ENST00000614895.4:c.173-29111_173-29110insT:p.(=); PCDH15:ENST00000616114.4:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000617051.4:c.173-29111_173-29110insT:p.(=); PCDH15:ENST00000617271.4:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000621708.4:c.173-29111_173-29110insT:p.(=); PCDH15:ENST00000622048.4:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000644397.1:c.158-29111_158-29110insT:p.(=); PCDH15:ENST00000409834.5:c.-90-212164_-90-212163insT:p.(=); PCDH15:ENST00000495484.5:c.-25+392872_-25+392873insT:p.(=)

Pathogenicity Data:: Best Score: 0.11813927; CADD: 0.118 (0.546)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54442414C>CTTTATA [-/1] rs1491511066 (variation viewer)

Variant score: 0.115

Transcripts:: PCDH15:ENST00000320301.10:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000361849.7:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000373955.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000373957.7:c.173-63473_173-63472insTATAAA:p.(=); PCDH15:ENST00000373965.6:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395430.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395432.6:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395433.5:c.92-63473_92-63472insTATAAA:p.(=); PCDH15:ENST00000395438.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395440.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395442.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395445.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000395446.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000414778.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000437009.5:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000612394.4:c.173-63473_173-63472insTATAAA:p.(=); PCDH15:ENST00000613657.4:c.173-63473_173-63472insTATAAA:p.(=); PCDH15:ENST00000614895.4:c.173-63473_173-63472insTATAAA:p.(=); PCDH15:ENST00000616114.4:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000617051.4:c.173-63473_173-63472insTATAAA:p.(=); PCDH15:ENST00000617271.4:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000621708.4:c.173-63473_173-63472insTATAAA:p.(=); PCDH15:ENST00000622048.4:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000644397.1:c.158-63473_158-63472insTATAAA:p.(=); PCDH15:ENST00000409834.5:c.-91+221757_-91+221758insTATAAA:p.(=); PCDH15:ENST00000495484.5:c.-25+358510_-25+358511insTATAAA:p.(=)

Pathogenicity Data:: Best Score: 0.115088165; CADD: 0.115 (0.531)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr10:g.53014838C>CTTTTTTTTTTTT [-/1] rs71032683 (variation viewer)

Variant score: 0.114

Transcripts:

Pathogenicity Data:: Best Score: 0.11366069; CADD: 0.114 (0.524)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54242130TTATATATATATA>T [-/1] rs57729172 (variation viewer)

Variant score: 0.112

Transcripts:: PCDH15:ENST00000320301.10:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000361849.7:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000373955.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000373957.7:c.892-5211_892-5200del:p.(=); PCDH15:ENST00000373965.6:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000395430.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000395432.6:c.766-5211_766-5200del:p.(=); PCDH15:ENST00000395433.5:c.811-5211_811-5200del:p.(=); PCDH15:ENST00000395438.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000395440.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000395442.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000395445.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000395446.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000414778.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000437009.5:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000612394.4:c.892-5211_892-5200del:p.(=); PCDH15:ENST00000613657.4:c.892-5211_892-5200del:p.(=); PCDH15:ENST00000614895.4:c.892-5211_892-5200del:p.(=); PCDH15:ENST00000616114.4:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000617051.4:c.892-5211_892-5200del:p.(=); PCDH15:ENST00000617271.4:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000621708.4:c.892-5211_892-5200del:p.(=); PCDH15:ENST00000622048.4:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000644397.1:c.877-5211_877-5200del:p.(=); PCDH15:ENST00000409834.5:c.-90-46253_-90-46242del:p.(=); PCDH15:ENST00000495484.5:c.-24-384879_-24-384868del:p.(=)

Pathogenicity Data:: Best Score: 0.11182201; CADD: 0.112 (0.515)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54408052C>CAAAAAA [-/1] rs71461239 (variation viewer)

Variant score: 0.106

Transcripts:: PCDH15:ENST00000320301.10:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000361849.7:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000373955.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000373957.7:c.173-29111_173-29110insTTTTTT:p.(=); PCDH15:ENST00000373965.6:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395430.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395432.6:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395433.5:c.92-29111_92-29110insTTTTTT:p.(=); PCDH15:ENST00000395438.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395440.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395442.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395445.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000395446.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000414778.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000437009.5:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000612394.4:c.173-29111_173-29110insTTTTTT:p.(=); PCDH15:ENST00000613657.4:c.173-29111_173-29110insTTTTTT:p.(=); PCDH15:ENST00000614895.4:c.173-29111_173-29110insTTTTTT:p.(=); PCDH15:ENST00000616114.4:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000617051.4:c.173-29111_173-29110insTTTTTT:p.(=); PCDH15:ENST00000617271.4:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000621708.4:c.173-29111_173-29110insTTTTTT:p.(=); PCDH15:ENST00000622048.4:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000644397.1:c.158-29111_158-29110insTTTTTT:p.(=); PCDH15:ENST00000409834.5:c.-90-212164_-90-212163insTTTTTT:p.(=); PCDH15:ENST00000495484.5:c.-25+392872_-25+392873insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.106488824; CADD: 0.106 (0.489)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54442414C>CTTTATATATA [-/1] rs1491511066 (variation viewer)

Variant score: 0.106

Transcripts:: PCDH15:ENST00000320301.10:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000361849.7:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000373955.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000373957.7:c.173-63473_173-63472insTATATATAAA:p.(=); PCDH15:ENST00000373965.6:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395430.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395432.6:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395433.5:c.92-63473_92-63472insTATATATAAA:p.(=); PCDH15:ENST00000395438.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395440.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395442.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395445.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000395446.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000414778.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000437009.5:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000612394.4:c.173-63473_173-63472insTATATATAAA:p.(=); PCDH15:ENST00000613657.4:c.173-63473_173-63472insTATATATAAA:p.(=); PCDH15:ENST00000614895.4:c.173-63473_173-63472insTATATATAAA:p.(=); PCDH15:ENST00000616114.4:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000617051.4:c.173-63473_173-63472insTATATATAAA:p.(=); PCDH15:ENST00000617271.4:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000621708.4:c.173-63473_173-63472insTATATATAAA:p.(=); PCDH15:ENST00000622048.4:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000644397.1:c.158-63473_158-63472insTATATATAAA:p.(=); PCDH15:ENST00000409834.5:c.-91+221757_-91+221758insTATATATAAA:p.(=); PCDH15:ENST00000495484.5:c.-25+358510_-25+358511insTATATATAAA:p.(=)

Pathogenicity Data:: Best Score: 0.10628301; CADD: 0.106 (0.488)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr10:g.53803555C>T [0/1]

Variant score: 0.105

Transcripts:: PCDH15:ENST00000373965.6:c.*3024G>A:p.(=); PCDH15:ENST00000414778.5:c.*3024G>A:p.(=); PCDH15:ENST00000614895.4:c.*3024G>A:p.(=); PCDH15:ENST00000644397.1:c.*3024G>A:p.(=)

Pathogenicity Data:: Best Score: 0.10525352; CADD: 0.105 (0.483)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53812825G>C [0/1] rs140121877 (variation viewer)

Variant score: 0.101

Transcripts:: PCDH15:ENST00000373965.6:c.4374-2161C>G:p.(=); PCDH15:ENST00000395438.5:c.4372-1201C>G:p.(=); PCDH15:ENST00000395440.5:c.1306-3279C>G:p.(=); PCDH15:ENST00000395442.5:c.1099-3279C>G:p.(=); PCDH15:ENST00000395445.5:c.4389-2161C>G:p.(=); PCDH15:ENST00000395446.5:c.2092-3279C>G:p.(=); PCDH15:ENST00000409834.5:c.3207-1206C>G:p.(=); PCDH15:ENST00000414778.5:c.4371-2161C>G:p.(=); PCDH15:ENST00000495484.5:c.520-1206C>G:p.(=); PCDH15:ENST00000612394.4:c.4407-2161C>G:p.(=); PCDH15:ENST00000613657.4:c.4410-2161C>G:p.(=); PCDH15:ENST00000614895.4:c.4386-2161C>G:p.(=); PCDH15:ENST00000616114.4:c.4368-2161C>G:p.(=); PCDH15:ENST00000617271.4:c.4374-1206C>G:p.(=); PCDH15:ENST00000621708.4:c.4389-2161C>G:p.(=); PCDH15:ENST00000644397.1:c.4492-1206C>G:p.(=)

Pathogenicity Data:: Best Score: 0.11590284; CADD: 0.116 (0.535)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.2963%; UK10K: 0.4761%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1435%; gnomAD_G_NFE: 0.3400%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54686041A>AT [1/1] rs66539612 (variation viewer)

Variant score: 0.101

Transcripts:: PCDH15:ENST00000320301.10:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000361849.7:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000373955.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000373957.7:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000373965.6:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395430.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395432.6:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395433.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395438.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395440.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395442.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395445.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000395446.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000409834.5:c.-209-21752_-209-21751insA:p.(=); PCDH15:ENST00000414778.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000437009.5:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000495484.5:c.-25+114883_-25+114884insA:p.(=); PCDH15:ENST00000612394.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000613657.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000614895.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000616114.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000617051.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000617271.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000621708.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000622048.4:c.-28-21752_-28-21751insA:p.(=); PCDH15:ENST00000644397.1:c.-28-21752_-28-21751insA:p.(=)

Pathogenicity Data:: Best Score: 0.10050243; CADD: 0.101 (0.460)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54199570C>CAACAATAATAATAAT [-/1] rs142287657 (variation viewer)

Variant score: 0.064

Transcripts:: PCDH15:ENST00000320301.10:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000361849.7:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000373955.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000373957.7:c.1114-3682_1114-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000373965.6:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395430.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395432.6:c.988-3682_988-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395433.5:c.1033-3682_1033-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395438.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395440.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395442.5:c.1098+14365_1098+14366insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395445.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000395446.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000414778.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000437009.5:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000612394.4:c.1114-3682_1114-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000613657.4:c.1114-3682_1114-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000614895.4:c.1114-3682_1114-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000616114.4:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000617051.4:c.1114-3682_1114-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000617271.4:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000621708.4:c.1114-3682_1114-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000622048.4:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000644397.1:c.1099-3682_1099-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000409834.5:c.-90-3682_-90-3681insATTATTATTATTGTT:p.(=); PCDH15:ENST00000495484.5:c.-24-342308_-24-342307insATTATTATTATTGTT:p.(=)

Pathogenicity Data:: Best Score: 0.063516796; CADD: 0.064 (0.285)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54313894C>T [0/1] rs186914390 (variation viewer)

Variant score: 0.039

Transcripts:: PCDH15:ENST00000320301.10:c.876+3377G>A:p.(=); PCDH15:ENST00000361849.7:c.876+3377G>A:p.(=); PCDH15:ENST00000373955.5:c.876+3377G>A:p.(=); PCDH15:ENST00000373957.7:c.891+3377G>A:p.(=); PCDH15:ENST00000373965.6:c.876+3377G>A:p.(=); PCDH15:ENST00000395430.5:c.876+3377G>A:p.(=); PCDH15:ENST00000395432.6:c.765+3377G>A:p.(=); PCDH15:ENST00000395433.5:c.810+3377G>A:p.(=); PCDH15:ENST00000395438.5:c.876+3377G>A:p.(=); PCDH15:ENST00000395440.5:c.876+3377G>A:p.(=); PCDH15:ENST00000395442.5:c.876+3377G>A:p.(=); PCDH15:ENST00000395445.5:c.876+3377G>A:p.(=); PCDH15:ENST00000395446.5:c.876+3377G>A:p.(=); PCDH15:ENST00000414778.5:c.876+3377G>A:p.(=); PCDH15:ENST00000437009.5:c.876+3377G>A:p.(=); PCDH15:ENST00000612394.4:c.891+3377G>A:p.(=); PCDH15:ENST00000613657.4:c.891+3377G>A:p.(=); PCDH15:ENST00000614895.4:c.891+3377G>A:p.(=); PCDH15:ENST00000616114.4:c.876+3377G>A:p.(=); PCDH15:ENST00000617051.4:c.891+3377G>A:p.(=); PCDH15:ENST00000617271.4:c.876+3377G>A:p.(=); PCDH15:ENST00000621708.4:c.891+3377G>A:p.(=); PCDH15:ENST00000622048.4:c.876+3377G>A:p.(=); PCDH15:ENST00000644397.1:c.876+3377G>A:p.(=); PCDH15:ENST00000409834.5:c.-90-118005G>A:p.(=); PCDH15:ENST00000495484.5:c.-24-456631G>A:p.(=)

Pathogenicity Data:: Best Score: 0.039494157; CADD: 0.039 (0.175)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0342%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54240626C>CT [1/1] rs1228784141 (variation viewer)

Variant score: 0.036

Transcripts:: PCDH15:ENST00000320301.10:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000361849.7:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000373955.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000373957.7:c.892-3696_892-3695insA:p.(=); PCDH15:ENST00000373965.6:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000395430.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000395432.6:c.766-3696_766-3695insA:p.(=); PCDH15:ENST00000395433.5:c.811-3696_811-3695insA:p.(=); PCDH15:ENST00000395438.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000395440.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000395442.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000395445.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000395446.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000414778.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000437009.5:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000612394.4:c.892-3696_892-3695insA:p.(=); PCDH15:ENST00000613657.4:c.892-3696_892-3695insA:p.(=); PCDH15:ENST00000614895.4:c.892-3696_892-3695insA:p.(=); PCDH15:ENST00000616114.4:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000617051.4:c.892-3696_892-3695insA:p.(=); PCDH15:ENST00000617271.4:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000621708.4:c.892-3696_892-3695insA:p.(=); PCDH15:ENST00000622048.4:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000644397.1:c.877-3696_877-3695insA:p.(=); PCDH15:ENST00000409834.5:c.-90-44738_-90-44737insA:p.(=); PCDH15:ENST00000495484.5:c.-24-383364_-24-383363insA:p.(=)

Pathogenicity Data:: Best Score: 0.035504937; CADD: 0.036 (0.157)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.53818777T>C [0/1] rs547035451 (variation viewer)

Variant score: 0.020

Transcripts:: PCDH15:ENST00000373965.6:c.4373+6359A>G:p.(=); PCDH15:ENST00000395438.5:c.4372-7153A>G:p.(=); PCDH15:ENST00000395440.5:c.1306-9231A>G:p.(=); PCDH15:ENST00000395442.5:c.1099-9231A>G:p.(=); PCDH15:ENST00000395445.5:c.4389-8113A>G:p.(=); PCDH15:ENST00000395446.5:c.2092-9231A>G:p.(=); PCDH15:ENST00000409834.5:c.3206+6359A>G:p.(=); PCDH15:ENST00000414778.5:c.4371-8113A>G:p.(=); PCDH15:ENST00000495484.5:c.462-764A>G:p.(=); PCDH15:ENST00000612394.4:c.4407-8113A>G:p.(=); PCDH15:ENST00000613657.4:c.4409+6359A>G:p.(=); PCDH15:ENST00000614895.4:c.4386-8113A>G:p.(=); PCDH15:ENST00000616114.4:c.4368-8113A>G:p.(=); PCDH15:ENST00000617271.4:c.4373+6359A>G:p.(=); PCDH15:ENST00000621708.4:c.4388+6359A>G:p.(=); PCDH15:ENST00000644397.1:c.4434-764A>G:p.(=)

Pathogenicity Data:: Best Score: 0.02005881; CADD: 0.020 (0.088)

Frequency Data:: TOPMed: 0.0239%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0401%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54174927G>A [0/1] rs191331005 (variation viewer)

Variant score: 0.018

Transcripts:: PCDH15:ENST00000320301.10:c.1590+8517C>T:p.(=); PCDH15:ENST00000361849.7:c.1590+8517C>T:p.(=); PCDH15:ENST00000373955.5:c.1590+8517C>T:p.(=); PCDH15:ENST00000373957.7:c.1605+8517C>T:p.(=); PCDH15:ENST00000373965.6:c.1590+8517C>T:p.(=); PCDH15:ENST00000395430.5:c.1590+8517C>T:p.(=); PCDH15:ENST00000395432.6:c.1479+8517C>T:p.(=); PCDH15:ENST00000395433.5:c.1524+8517C>T:p.(=); PCDH15:ENST00000395438.5:c.1590+8517C>T:p.(=); PCDH15:ENST00000395440.5:c.1305+20756C>T:p.(=); PCDH15:ENST00000395442.5:c.1098+39009C>T:p.(=); PCDH15:ENST00000395445.5:c.1611+8517C>T:p.(=); PCDH15:ENST00000395446.5:c.1590+8517C>T:p.(=); PCDH15:ENST00000409834.5:c.423+8517C>T:p.(=); PCDH15:ENST00000414778.5:c.1590+8517C>T:p.(=); PCDH15:ENST00000437009.5:c.1590+8517C>T:p.(=); PCDH15:ENST00000612394.4:c.1626+8517C>T:p.(=); PCDH15:ENST00000613657.4:c.1626+8517C>T:p.(=); PCDH15:ENST00000614895.4:c.1605+8517C>T:p.(=); PCDH15:ENST00000616114.4:c.1590+8517C>T:p.(=); PCDH15:ENST00000617051.4:c.1605+8517C>T:p.(=); PCDH15:ENST00000617271.4:c.1590+8517C>T:p.(=); PCDH15:ENST00000621708.4:c.1605+8517C>T:p.(=); PCDH15:ENST00000622048.4:c.1590+8517C>T:p.(=); PCDH15:ENST00000644397.1:c.1590+8517C>T:p.(=); PCDH15:ENST00000495484.5:c.-24-317664C>T:p.(=)

Pathogenicity Data:: Best Score: 0.019607484; CADD: 0.020 (0.086)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.1625%; UK10K: 0.2116%; gnomAD_G_AMR: 0.4878%; gnomAD_G_NFE: 0.3760%; gnomAD_G_OTH: 0.4090%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54401400A>G [0/1] rs188912411 (variation viewer)

Variant score: 0.017

Transcripts:: PCDH15:ENST00000320301.10:c.158-22458T>C:p.(=); PCDH15:ENST00000361849.7:c.158-22458T>C:p.(=); PCDH15:ENST00000373955.5:c.158-22458T>C:p.(=); PCDH15:ENST00000373957.7:c.173-22458T>C:p.(=); PCDH15:ENST00000373965.6:c.158-22458T>C:p.(=); PCDH15:ENST00000395430.5:c.158-22458T>C:p.(=); PCDH15:ENST00000395432.6:c.158-22458T>C:p.(=); PCDH15:ENST00000395433.5:c.92-22458T>C:p.(=); PCDH15:ENST00000395438.5:c.158-22458T>C:p.(=); PCDH15:ENST00000395440.5:c.158-22458T>C:p.(=); PCDH15:ENST00000395442.5:c.158-22458T>C:p.(=); PCDH15:ENST00000395445.5:c.158-22458T>C:p.(=); PCDH15:ENST00000395446.5:c.158-22458T>C:p.(=); PCDH15:ENST00000414778.5:c.158-22458T>C:p.(=); PCDH15:ENST00000437009.5:c.158-22458T>C:p.(=); PCDH15:ENST00000612394.4:c.173-22458T>C:p.(=); PCDH15:ENST00000613657.4:c.173-22458T>C:p.(=); PCDH15:ENST00000614895.4:c.173-22458T>C:p.(=); PCDH15:ENST00000616114.4:c.158-22458T>C:p.(=); PCDH15:ENST00000617051.4:c.173-22458T>C:p.(=); PCDH15:ENST00000617271.4:c.158-22458T>C:p.(=); PCDH15:ENST00000621708.4:c.173-22458T>C:p.(=); PCDH15:ENST00000622048.4:c.158-22458T>C:p.(=); PCDH15:ENST00000644397.1:c.158-22458T>C:p.(=); PCDH15:ENST00000409834.5:c.-90-205511T>C:p.(=); PCDH15:ENST00000495484.5:c.-25+399525T>C:p.(=)

Pathogenicity Data:: Best Score: 0.01915586; CADD: 0.019 (0.084)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1330%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0534%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54618771AG>A [0/1] rs532145528 (variation viewer)

Variant score: 0.002

Transcripts:: PCDH15:ENST00000320301.10:c.91+45400del:p.(=); PCDH15:ENST00000361849.7:c.91+45400del:p.(=); PCDH15:ENST00000373955.5:c.91+45400del:p.(=); PCDH15:ENST00000373957.7:c.91+45400del:p.(=); PCDH15:ENST00000373965.6:c.91+45400del:p.(=); PCDH15:ENST00000395430.5:c.91+45400del:p.(=); PCDH15:ENST00000395432.6:c.91+45400del:p.(=); PCDH15:ENST00000395433.5:c.91+45400del:p.(=); PCDH15:ENST00000395438.5:c.91+45400del:p.(=); PCDH15:ENST00000395440.5:c.91+45400del:p.(=); PCDH15:ENST00000395442.5:c.91+45400del:p.(=); PCDH15:ENST00000395445.5:c.91+45400del:p.(=); PCDH15:ENST00000395446.5:c.91+45400del:p.(=); PCDH15:ENST00000414778.5:c.91+45400del:p.(=); PCDH15:ENST00000437009.5:c.91+45400del:p.(=); PCDH15:ENST00000612394.4:c.91+45400del:p.(=); PCDH15:ENST00000613657.4:c.91+45400del:p.(=); PCDH15:ENST00000614895.4:c.91+45400del:p.(=); PCDH15:ENST00000616114.4:c.91+45400del:p.(=); PCDH15:ENST00000617051.4:c.91+45400del:p.(=); PCDH15:ENST00000617271.4:c.91+45400del:p.(=); PCDH15:ENST00000621708.4:c.91+45400del:p.(=); PCDH15:ENST00000622048.4:c.91+45400del:p.(=); PCDH15:ENST00000644397.1:c.91+45400del:p.(=); PCDH15:ENST00000409834.5:c.-91+45400del:p.(=); PCDH15:ENST00000495484.5:c.-25+182153del:p.(=)

Pathogenicity Data:: Best Score: 0.0020701885; CADD: 0.002 (0.009)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1426%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1936%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54004425AC>* [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000361849.7:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000373955.5:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000373957.7:c.2767-8661_2767-8660delGTins:p.(=); PCDH15:ENST00000373965.6:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000395430.5:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000395432.6:c.2641-8661_2641-8660delGTins:p.(=); PCDH15:ENST00000395433.5:c.2686-8661_2686-8660delGTins:p.(=); PCDH15:ENST00000395438.5:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000395440.5:c.1305+191257_1305+191258delGTins:p.(=); PCDH15:ENST00000395442.5:c.1099-194880_1099-194879delGTins:p.(=); PCDH15:ENST00000395445.5:c.2773-8661_2773-8660delGTins:p.(=); PCDH15:ENST00000395446.5:c.2091+74905_2091+74906delGTins:p.(=); PCDH15:ENST00000409834.5:c.1585-8661_1585-8660delGTins:p.(=); PCDH15:ENST00000414778.5:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000437009.5:c.2539-8661_2539-8660delGTins:p.(=); PCDH15:ENST00000612394.4:c.2788-8661_2788-8660delGTins:p.(=); PCDH15:ENST00000613657.4:c.2788-8661_2788-8660delGTins:p.(=); PCDH15:ENST00000614895.4:c.2767-8661_2767-8660delGTins:p.(=); PCDH15:ENST00000616114.4:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000617051.4:c.2767-8661_2767-8660delGTins:p.(=); PCDH15:ENST00000617271.4:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000621708.4:c.2767-8661_2767-8660delGTins:p.(=); PCDH15:ENST00000622048.4:c.2539-8661_2539-8660delGTins:p.(=); PCDH15:ENST00000644397.1:c.2752-8661_2752-8660delGTins:p.(=); PCDH15:ENST00000495484.5:c.-24-147163_-24-147162delGTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54207370GTGTGTGTA>* [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000361849.7:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000373955.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000373957.7:c.1113+6558_1113+6566delTACACACACins:p.(=); PCDH15:ENST00000373965.6:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000395430.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000395432.6:c.987+6558_987+6566delTACACACACins:p.(=); PCDH15:ENST00000395433.5:c.1032+6558_1032+6566delTACACACACins:p.(=); PCDH15:ENST00000395438.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000395440.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000395442.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000395445.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000395446.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000414778.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000437009.5:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000612394.4:c.1113+6558_1113+6566delTACACACACins:p.(=); PCDH15:ENST00000613657.4:c.1113+6558_1113+6566delTACACACACins:p.(=); PCDH15:ENST00000614895.4:c.1113+6558_1113+6566delTACACACACins:p.(=); PCDH15:ENST00000616114.4:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000617051.4:c.1113+6558_1113+6566delTACACACACins:p.(=); PCDH15:ENST00000617271.4:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000621708.4:c.1113+6558_1113+6566delTACACACACins:p.(=); PCDH15:ENST00000622048.4:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000644397.1:c.1098+6558_1098+6566delTACACACACins:p.(=); PCDH15:ENST00000409834.5:c.-90-11489_-90-11481delTACACACACins:p.(=); PCDH15:ENST00000495484.5:c.-24-350115_-24-350107delTACACACACins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54307090A>* [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.876+10181T>:p.(=); PCDH15:ENST00000361849.7:c.876+10181T>:p.(=); PCDH15:ENST00000373955.5:c.876+10181T>:p.(=); PCDH15:ENST00000373957.7:c.891+10181T>:p.(=); PCDH15:ENST00000373965.6:c.876+10181T>:p.(=); PCDH15:ENST00000395430.5:c.876+10181T>:p.(=); PCDH15:ENST00000395432.6:c.765+10181T>:p.(=); PCDH15:ENST00000395433.5:c.810+10181T>:p.(=); PCDH15:ENST00000395438.5:c.876+10181T>:p.(=); PCDH15:ENST00000395440.5:c.876+10181T>:p.(=); PCDH15:ENST00000395442.5:c.876+10181T>:p.(=); PCDH15:ENST00000395445.5:c.876+10181T>:p.(=); PCDH15:ENST00000395446.5:c.876+10181T>:p.(=); PCDH15:ENST00000414778.5:c.876+10181T>:p.(=); PCDH15:ENST00000437009.5:c.876+10181T>:p.(=); PCDH15:ENST00000612394.4:c.891+10181T>:p.(=); PCDH15:ENST00000613657.4:c.891+10181T>:p.(=); PCDH15:ENST00000614895.4:c.891+10181T>:p.(=); PCDH15:ENST00000616114.4:c.876+10181T>:p.(=); PCDH15:ENST00000617051.4:c.891+10181T>:p.(=); PCDH15:ENST00000617271.4:c.876+10181T>:p.(=); PCDH15:ENST00000621708.4:c.891+10181T>:p.(=); PCDH15:ENST00000622048.4:c.876+10181T>:p.(=); PCDH15:ENST00000644397.1:c.876+10181T>:p.(=); PCDH15:ENST00000409834.5:c.-90-111201T>:p.(=); PCDH15:ENST00000495484.5:c.-24-449827T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54307092A>* [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.876+10179T>:p.(=); PCDH15:ENST00000361849.7:c.876+10179T>:p.(=); PCDH15:ENST00000373955.5:c.876+10179T>:p.(=); PCDH15:ENST00000373957.7:c.891+10179T>:p.(=); PCDH15:ENST00000373965.6:c.876+10179T>:p.(=); PCDH15:ENST00000395430.5:c.876+10179T>:p.(=); PCDH15:ENST00000395432.6:c.765+10179T>:p.(=); PCDH15:ENST00000395433.5:c.810+10179T>:p.(=); PCDH15:ENST00000395438.5:c.876+10179T>:p.(=); PCDH15:ENST00000395440.5:c.876+10179T>:p.(=); PCDH15:ENST00000395442.5:c.876+10179T>:p.(=); PCDH15:ENST00000395445.5:c.876+10179T>:p.(=); PCDH15:ENST00000395446.5:c.876+10179T>:p.(=); PCDH15:ENST00000414778.5:c.876+10179T>:p.(=); PCDH15:ENST00000437009.5:c.876+10179T>:p.(=); PCDH15:ENST00000612394.4:c.891+10179T>:p.(=); PCDH15:ENST00000613657.4:c.891+10179T>:p.(=); PCDH15:ENST00000614895.4:c.891+10179T>:p.(=); PCDH15:ENST00000616114.4:c.876+10179T>:p.(=); PCDH15:ENST00000617051.4:c.891+10179T>:p.(=); PCDH15:ENST00000617271.4:c.876+10179T>:p.(=); PCDH15:ENST00000621708.4:c.891+10179T>:p.(=); PCDH15:ENST00000622048.4:c.876+10179T>:p.(=); PCDH15:ENST00000644397.1:c.876+10179T>:p.(=); PCDH15:ENST00000409834.5:c.-90-111203T>:p.(=); PCDH15:ENST00000495484.5:c.-24-449829T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.54316560ACACACACACACACAC>* [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000361849.7:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000373955.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000373957.7:c.891+696_891+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000373965.6:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395430.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395432.6:c.765+696_765+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395433.5:c.810+696_810+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395438.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395440.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395442.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395445.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000395446.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000414778.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000437009.5:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000612394.4:c.891+696_891+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000613657.4:c.891+696_891+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000614895.4:c.891+696_891+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000616114.4:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000617051.4:c.891+696_891+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000617271.4:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000621708.4:c.891+696_891+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000622048.4:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000644397.1:c.876+696_876+711delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000409834.5:c.-90-120686_-90-120671delGTGTGTGTGTGTGTGTins:p.(=); PCDH15:ENST00000495484.5:c.-24-459312_-24-459297delGTGTGTGTGTGTGTGTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54756056AACAC>* [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000361849.7:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000373955.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000373957.7:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000373965.6:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395430.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395432.6:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395433.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395438.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395440.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395442.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395445.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000395446.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000409834.5:c.-210+44865_-210+44869delGTGTTins:p.(=); PCDH15:ENST00000414778.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000437009.5:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000495484.5:c.-25+44865_-25+44869delGTGTTins:p.(=); PCDH15:ENST00000612394.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000613657.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000614895.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000616114.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000617051.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000617271.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000621708.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000622048.4:c.-29+44865_-29+44869delGTGTTins:p.(=); PCDH15:ENST00000644397.1:c.-29+44865_-29+44869delGTGTTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54779488G>GTATATATATACACACATATATGTGTGTATATATATATACACACATATATGTGTGTA [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000361849.7:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000373955.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000373957.7:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000373965.6:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395430.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395432.6:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395433.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395438.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395440.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395442.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395445.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000395446.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000409834.5:c.-210+21436_-210+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000414778.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000437009.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000495484.5:c.-25+21436_-25+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000612394.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000613657.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000614895.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000616114.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000617051.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000617271.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000621708.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000622048.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=); PCDH15:ENST00000644397.1:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATATATACACACATATATGTGTGTATATATATA:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.54779488G>GTGTATATATACACACATATATGTGTGTATATATACACACATATATGTGTGTA [-/1]

Variant score: 0.000

Transcripts:: PCDH15:ENST00000320301.10:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000361849.7:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000373955.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000373957.7:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000373965.6:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395430.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395432.6:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395433.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395438.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395440.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395442.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395445.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000395446.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000409834.5:c.-210+21436_-210+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000414778.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000437009.5:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000495484.5:c.-25+21436_-25+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000612394.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000613657.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000614895.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000616114.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000617051.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000617271.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000621708.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000622048.4:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=); PCDH15:ENST00000644397.1:c.-29+21436_-29+21437insTACACACATATATGTGTGTATATATACACACATATATGTGTGTATATATACA:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TMC1

Exomiser Score: 0.364

Phenotype Score: 0.511

Variant Score: 0.808

Phenotype matches:

Proximity score 0.511 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.511 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:600974 Deafness, autosomal recessive 7 - autosomal recessive; OMIM:606705 Deafness, autosomal dominant 36 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.364

Phenotype Score: 0.511

Variant Score: 0.808

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72525375A>G [0/1]

Variant score: 0.808 CONTRIBUTING VARIANT

Transcripts:: TMC1:ENST00000297784.9:c.-428+3462A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8084862; CADD: 0.808 (7.178)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.173

Phenotype Score: 0.511

Variant Score: 0.699

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72525375A>G [0/1]

Variant score: 0.808 CONTRIBUTING VARIANT

Transcripts:: TMC1:ENST00000297784.9:c.-428+3462A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8084862; CADD: 0.808 (7.178)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr9:g.72839547T>C [0/1] rs368550129 (variation viewer)

Variant score: 0.589 CONTRIBUTING VARIANT

Transcripts:: TMC1:ENST00000645208.2::; TMC1:ENST00000297785.8::

Pathogenicity Data:: Best Score: 0.67476296; CADD: 0.675 (4.878)

Frequency Data:: TOPMed: 0.1378%; gnomAD_G_AFR: 0.1164%; gnomAD_G_AMR: 0.2740%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.2275%; gnomAD_G_OTH: 0.1092%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72589712T>C [0/1] rs35583217 (variation viewer)

Variant score: 0.579

Transcripts:: TMC1:ENST00000297784.9:c.-306+11689T>C:p.(=); TMC1:ENST00000645208.2:c.-306+11689T>C:p.(=); TMC1:ENST00000651183.1:c.-407+11689T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7423085; CADD: 0.742 (5.889)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.6371%; UK10K: 0.9654%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1717%; gnomAD_G_NFE: 0.7726%; gnomAD_G_OTH: 0.7128%

INTERGENIC_VARIANT chr9:g.72851127C>G [0/1] rs1315681984 (variation viewer)

Variant score: 0.531

Transcripts:: TMC1:ENST00000645208.2::; TMC1:ENST00000297785.8::

Pathogenicity Data:: Best Score: 0.53140247; CADD: 0.531 (3.292)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72634104G>A [0/1] rs77022845 (variation viewer)

Variant score: 0.475

Transcripts:: TMC1:ENST00000297784.9:c.-53+6041G>A:p.(=); TMC1:ENST00000340019.4:c.-53+6041G>A:p.(=); TMC1:ENST00000645208.2:c.-53+6041G>A:p.(=); TMC1:ENST00000651183.1:c.-297+17627G>A:p.(=)

Pathogenicity Data:: Best Score: 0.89217985; CADD: 0.892 (9.673)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.8999%; UK10K: 1.4943%; gnomAD_G_AFR: 0.2176%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.3721%; gnomAD_G_NFE: 1.0525%; gnomAD_G_OTH: 1.0183%

INTERGENIC_VARIANT chr9:g.72515436C>CAAAAAAA [0/1] rs759751959 (variation viewer)

Variant score: 0.462

Transcripts:: TMC1:ENST00000297784.9::; TMC1:ENST00000415024.1::

Pathogenicity Data:: Best Score: 0.46173018; CADD: 0.462 (2.690)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72555973CAAAA>C [0/1] rs59431883 (variation viewer)

Variant score: 0.332

Transcripts:: TMC1:ENST00000297784.9:c.-427-21928_-427-21925del:p.(=)

Pathogenicity Data:: Best Score: 0.33150214; CADD: 0.332 (1.749)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.72846393C>T [0/1] rs192573728 (variation viewer)

Variant score: 0.328

Transcripts:: TMC1:ENST00000645208.2::; TMC1:ENST00000297785.8::

Pathogenicity Data:: Best Score: 0.37612152; CADD: 0.376 (2.049)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0717%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0667%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.72765260A>G [0/1] rs906778536 (variation viewer)

Variant score: 0.272

Transcripts:: TMC1:ENST00000297784.9:c.742-7153A>G:p.(=); TMC1:ENST00000340019.4:c.742-7153A>G:p.(=); TMC1:ENST00000645208.2:c.742-7153A>G:p.(=); TMC1:ENST00000651183.1:c.304-7153A>G:p.(=)

Pathogenicity Data:: Best Score: 0.2720526; CADD: 0.272 (1.379)

Frequency Data:: TOPMed: 0.0040%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.72685100CTTT>C [0/1] rs71359515 (variation viewer)

Variant score: 0.266

Transcripts:: TMC1:ENST00000297784.9:c.17-3608_17-3606del:p.(=); TMC1:ENST00000340019.4:c.17-3608_17-3606del:p.(=); TMC1:ENST00000645208.2:c.17-3608_17-3606del:p.(=); TMC1:ENST00000651183.1:c.-296-3608_-296-3606del:p.(=)

Pathogenicity Data:: Best Score: 0.26616234; CADD: 0.266 (1.344)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72570676CTTT>C [0/1] rs529953890 (variation viewer)

Variant score: 0.213

Transcripts:: TMC1:ENST00000297784.9:c.-427-7225_-427-7223del:p.(=)

Pathogenicity Data:: Best Score: 0.21313542; CADD: 0.213 (1.041)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72584784C>CTTTTTTT [0/1] rs71357591 (variation viewer)

Variant score: 0.164

Transcripts:: TMC1:ENST00000297784.9:c.-306+6761_-306+6762insTTTTTTT:p.(=); TMC1:ENST00000645208.2:c.-306+6761_-306+6762insTTTTTTT:p.(=); TMC1:ENST00000651183.1:c.-407+6761_-407+6762insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.16381955; CADD: 0.164 (0.777)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.72856973G>A [0/1] rs188982537 (variation viewer)

Variant score: 0.126

Transcripts:: TMC1:ENST00000645208.2::; TMC1:ENST00000297785.8::

Pathogenicity Data:: Best Score: 0.14846992; CADD: 0.148 (0.698)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0764%; gnomAD_G_AFR: 0.0635%; gnomAD_G_AMR: 0.3916%; gnomAD_G_ASJ: 0.7519%; gnomAD_G_NFE: 0.0692%; gnomAD_G_OTH: 0.1124%

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72623147GTT>G [0/1] rs1162181237 (variation viewer)

Variant score: 0.101

Transcripts:: TMC1:ENST00000297784.9:c.-195-4773_-195-4772del:p.(=); TMC1:ENST00000340019.4:c.-195-4773_-195-4772del:p.(=); TMC1:ENST00000645208.2:c.-195-4773_-195-4772del:p.(=); TMC1:ENST00000651183.1:c.-297+6671_-297+6672del:p.(=)

Pathogenicity Data:: Best Score: 0.10133052; CADD: 0.101 (0.464)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.72725325G>GTA [0|1] rs57562145 (variation viewer)

Variant score: 0.092

Transcripts:: TMC1:ENST00000297784.9:c.363-14794_363-14793insTA:p.(=); TMC1:ENST00000340019.4:c.363-14794_363-14793insTA:p.(=); TMC1:ENST00000645208.2:c.363-14794_363-14793insTA:p.(=); TMC1:ENST00000651183.1:c.-76-14794_-76-14793insTA:p.(=)

Pathogenicity Data:: Best Score: 0.09217948; CADD: 0.092 (0.420)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72607002T>G [0/1] rs10781104 (variation viewer)

Variant score: 0.082

Transcripts:: TMC1:ENST00000297784.9:c.-305-9366T>G:p.(=); TMC1:ENST00000645208.2:c.-305-9366T>G:p.(=); TMC1:ENST00000651183.1:c.-406-9366T>G:p.(=)

Pathogenicity Data:: Best Score: 0.08166742; CADD: 0.082 (0.370)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72528124C>A [0/1]

Variant score: 0.067

Transcripts:: TMC1:ENST00000297784.9:c.-428+6211C>A:p.(=)

Pathogenicity Data:: Best Score: 0.067390144; CADD: 0.067 (0.303)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.72775383C>T [0/1] rs13299110 (variation viewer)

Variant score: 0.052

Transcripts:: TMC1:ENST00000297784.9:c.884+2828C>T:p.(=); TMC1:ENST00000340019.4:c.884+2828C>T:p.(=); TMC1:ENST00000645208.2:c.884+2828C>T:p.(=); TMC1:ENST00000651183.1:c.446+2828C>T:p.(=)

Pathogenicity Data:: Best Score: 0.052018225; CADD: 0.052 (0.232)

Frequency Data:: TOPMed: 0.0143%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.72683733T>TATATATATA [-/1]

Variant score: 0.051

Transcripts:: TMC1:ENST00000297784.9:c.17-4976_17-4975insATATATATA:p.(=); TMC1:ENST00000340019.4:c.17-4976_17-4975insATATATATA:p.(=); TMC1:ENST00000645208.2:c.17-4976_17-4975insATATATATA:p.(=); TMC1:ENST00000651183.1:c.-296-4976_-296-4975insATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.05136311; CADD: 0.051 (0.229)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.72596539T>TA [0/1] rs35140344 (variation viewer)

Variant score: 0.034

Transcripts:: TMC1:ENST00000297784.9:c.-306+18516_-306+18517insA:p.(=); TMC1:ENST00000645208.2:c.-306+18516_-306+18517insA:p.(=); TMC1:ENST00000651183.1:c.-407+18516_-407+18517insA:p.(=)

Pathogenicity Data:: Best Score: 0.034393907; CADD: 0.034 (0.152)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.72831374C>T [0/1] rs981651431 (variation viewer)

Variant score: 0.002

Transcripts:: TMC1:ENST00000297784.9:c.2260+692C>T:p.(=); TMC1:ENST00000340019.4:c.2260+692C>T:p.(=); TMC1:ENST00000645208.2:c.2260+692C>T:p.(=); TMC1:ENST00000651183.1:c.1770+845C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0020701885; CADD: 0.002 (0.009)

Frequency Data:: TOPMed: 0.0048%

PRKCE

Exomiser Score: 0.362

Phenotype Score: 0.516

Variant Score: 0.801

Phenotype matches:

Proximity score 0.516 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.179

Phenotype Score: 0.516

Variant Score: 0.697

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45888465C>CT [-/1] rs34871432 (variation viewer)

Variant score: 0.697 CONTRIBUTING VARIANT

Transcripts:: PRKCE:ENST00000306156.8:c.412+45402_412+45403insT:p.(=)

Pathogenicity Data:: Best Score: 0.6970297; CADD: 0.697 (5.186)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.362

Phenotype Score: 0.516

Variant Score: 0.801

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46149547T>C [0/1] rs180871297 (variation viewer)

Variant score: 0.905 CONTRIBUTING VARIANT

Transcripts:: PRKCE:ENST00000306156.8:c.1732-1494T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9384823; CADD: 0.938 (12.110)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1561%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.1208%; gnomAD_G_NFE: 0.2333%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45888465C>CT [-/1] rs34871432 (variation viewer)

Variant score: 0.697 CONTRIBUTING VARIANT

Transcripts:: PRKCE:ENST00000306156.8:c.412+45402_412+45403insT:p.(=)

Pathogenicity Data:: Best Score: 0.6970297; CADD: 0.697 (5.186)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45974279A>G [0/1] rs181933619 (variation viewer)

Variant score: 0.662

Transcripts:: PRKCE:ENST00000306156.8:c.413-2150A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7097983; CADD: 0.710 (5.373)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1911%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.2331%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45888465CTT>C [-/1] rs34871432 (variation viewer)

Variant score: 0.643

Transcripts:: PRKCE:ENST00000306156.8:c.412+45403_412+45404del:p.(=)

Pathogenicity Data:: Best Score: 0.64272714; CADD: 0.643 (4.470)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45980432C>T [0/1] rs78545113 (variation viewer)

Variant score: 0.632

Transcripts:: PRKCE:ENST00000306156.8:c.693+51C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6522237; CADD: 0.652 (4.587)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0319%; UK10K: 0.0264%; ESP EA: 0.0397%; ESP All: 0.0269%; ExAC AFR: 0.0109%; ExAC AMR: 0.0620%; ExAC NFE: 0.0283%; gnomAD_E_AMR: 0.1051%; gnomAD_E_ASJ: 0.1651%; gnomAD_E_NFE: 0.0321%; gnomAD_E_OTH: 0.1126%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0333%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45981132A>G [0/1]

Variant score: 0.446

Transcripts:: PRKCE:ENST00000306156.8:c.693+751A>G:p.(=)

Pathogenicity Data:: Best Score: 0.44550198; CADD: 0.446 (2.561)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46070672G>A [0/1] rs187763304 (variation viewer)

Variant score: 0.425

Transcripts:: PRKCE:ENST00000306156.8:c.1438-15536G>A:p.(=)

Pathogenicity Data:: Best Score: 0.45109147; CADD: 0.451 (2.605)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1529%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0691%; gnomAD_G_AMR: 0.3606%; gnomAD_G_FIN: 0.0582%; gnomAD_G_NFE: 0.1548%; gnomAD_G_OTH: 0.3093%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45940640ACT>A [0/1] rs796581408 (variation viewer)

Variant score: 0.403

Transcripts:: PRKCE:ENST00000306156.8:c.413-35788_413-35787del:p.(=)

Pathogenicity Data:: Best Score: 0.4093911; CADD: 0.409 (2.287)

Frequency Data:: TOPMed: 0.0239%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.1018%

INTERGENIC_VARIANT chr2:g.46203576CT>C [1/1] rs34489488 (variation viewer)

Variant score: 0.374

Transcripts:: PRKCE:ENST00000306156.8::; PRKCE:ENST00000446949.1::

Pathogenicity Data:: Best Score: 0.37425125; CADD: 0.374 (2.036)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45681288C>CAA [0/1] rs10532828 (variation viewer)

Variant score: 0.373

Transcripts:: PRKCE:ENST00000306156.8:c.348+28840_348+28841insAA:p.(=)

Pathogenicity Data:: Best Score: 0.37266433; CADD: 0.373 (2.025)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46015691C>CA [0|1] rs749060776 (variation viewer)

Variant score: 0.356

Transcripts:: PRKCE:ENST00000306156.8:c.1437+5174_1437+5175insA:p.(=)

Pathogenicity Data:: Best Score: 0.35597903; CADD: 0.356 (1.911)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45885002T>TTG [0|1] rs1553440408 (variation viewer)

Variant score: 0.274

Transcripts:: PRKCE:ENST00000306156.8:c.412+41939_412+41940insTG:p.(=)

Pathogenicity Data:: Best Score: 0.27372688; CADD: 0.274 (1.389)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45786149T>G [0/1] rs757232262 (variation viewer)

Variant score: 0.259

Transcripts:: PRKCE:ENST00000306156.8:c.349-56851T>G:p.(=)

Pathogenicity Data:: Best Score: 0.25937223; CADD: 0.259 (1.304)

Frequency Data:: TOPMed: 0.0127%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46023089C>CAAAAAAA [1/1] rs397984467 (variation viewer)

Variant score: 0.256

Transcripts:: PRKCE:ENST00000306156.8:c.1437+12572_1437+12573insAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.2564674; CADD: 0.256 (1.287)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46172365C>T [0/1] rs773226396 (variation viewer)

Variant score: 0.256

Transcripts:: PRKCE:ENST00000306156.8:c.2068-12370C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2564674; CADD: 0.256 (1.287)

Frequency Data:: TOPMed: 0.0104%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46062668CTT>C [0/1] rs71394871 (variation viewer)

Variant score: 0.233

Transcripts:: PRKCE:ENST00000306156.8:c.1438-23539_1438-23538del:p.(=)

Pathogenicity Data:: Best Score: 0.23334497; CADD: 0.233 (1.154)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45944655A>ATTTT [1/1] rs71394861 (variation viewer)

Variant score: 0.170

Transcripts:: PRKCE:ENST00000306156.8:c.413-31774_413-31773insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.1701492; CADD: 0.170 (0.810)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46123214C>CT [-/1] rs70937991 (variation viewer)

Variant score: 0.170

Transcripts:: PRKCE:ENST00000306156.8:c.1593-21879_1593-21878insT:p.(=)

Pathogenicity Data:: Best Score: 0.16995811; CADD: 0.170 (0.809)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45933464C>CTT [0/1] rs59991455 (variation viewer)

Variant score: 0.155

Transcripts:: PRKCE:ENST00000306156.8:c.413-42965_413-42964insTT:p.(=)

Pathogenicity Data:: Best Score: 0.15472114; CADD: 0.155 (0.730)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45958190C>CA [0/1] rs60711691 (variation viewer)

Variant score: 0.147

Transcripts:: PRKCE:ENST00000306156.8:c.413-18239_413-18238insA:p.(=)

Pathogenicity Data:: Best Score: 0.1465069; CADD: 0.147 (0.688)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46123214CT>C [-/1] rs70937991 (variation viewer)

Variant score: 0.131

Transcripts:: PRKCE:ENST00000306156.8:c.1593-21878del:p.(=)

Pathogenicity Data:: Best Score: 0.13063931; CADD: 0.131 (0.608)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46002656C>T [0/1] rs189525454 (variation viewer)

Variant score: 0.114

Transcripts:: PRKCE:ENST00000306156.8:c.966+1110C>T:p.(=); PRKCE:ENST00000394874.1:c.135+1110C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14846992; CADD: 0.148 (0.698)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.5224%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1146%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.6261%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46092680C>T [0/1] rs34473961 (variation viewer)

Variant score: 0.108

Transcripts:: PRKCE:ENST00000306156.8:c.1592+6318C>T:p.(=)

Pathogenicity Data:: Best Score: 0.72514737; CADD: 0.725 (5.609)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.7159%; UK10K: 1.0976%; gnomAD_G_AFR: 0.1603%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.4579%; gnomAD_G_NFE: 1.1261%; gnomAD_G_OTH: 1.0183%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45958814ATATTTTTTTTTTT>A [0/1] rs1321616641 (variation viewer)

Variant score: 0.072

Transcripts:: PRKCE:ENST00000306156.8:c.413-17614_413-17602del:p.(=)

Pathogenicity Data:: Best Score: 0.07231617; CADD: 0.072 (0.326)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45751494A>G [0/1] rs1401442810 (variation viewer)

Variant score: 0.072

Transcripts:: PRKCE:ENST00000306156.8:c.349-91506A>G:p.(=)

Pathogenicity Data:: Best Score: 0.071888804; CADD: 0.072 (0.324)

Frequency Data:: TOPMed: 0.0040%

INTERGENIC_VARIANT chr2:g.45644148G>A [0/1] rs72796635 (variation viewer)

Variant score: 0.072

Transcripts:: PRKCE:ENST00000306156.8::

Pathogenicity Data:: Best Score: 0.19887555; CADD: 0.199 (0.963)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.6514%; UK10K: 0.9521%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.7459%; gnomAD_G_NFE: 1.0596%; gnomAD_G_OTH: 1.2295%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46182329G>A [0/1] rs527743328 (variation viewer)

Variant score: 0.041

Transcripts:: PRKCE:ENST00000306156.8:c.2068-2406G>A:p.(=)

Pathogenicity Data:: Best Score: 0.045666873; CADD: 0.046 (0.203)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.3321%; UK10K: 0.5422%; gnomAD_G_AFR: 0.1147%; gnomAD_G_NFE: 0.4670%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45968248T>TAC [0/1] rs796079621 (variation viewer)

Variant score: 0.039

Transcripts:: PRKCE:ENST00000306156.8:c.413-8181_413-8180insAC:p.(=)

Pathogenicity Data:: Best Score: 0.05354494; CADD: 0.054 (0.239)

Frequency Data:: gnomAD_G_AFR: 1.0907%; gnomAD_G_AMR: 0.2513%; gnomAD_G_FIN: 0.1186%; gnomAD_G_NFE: 0.2909%; gnomAD_G_OTH: 0.6356%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46085736GT>G [-/1] rs1170933914 (variation viewer)

Variant score: 0.034

Transcripts:: PRKCE:ENST00000306156.8:c.1438-471del:p.(=)

Pathogenicity Data:: Best Score: 0.033726633; CADD: 0.034 (0.149)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45713980G>A [0/1] rs146169588 (variation viewer)

Variant score: 0.033

Transcripts:: PRKCE:ENST00000306156.8:c.348+61532G>A:p.(=)

Pathogenicity Data:: Best Score: 0.22428894; CADD: 0.224 (1.103)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 1.0800%; UK10K: 1.7456%; gnomAD_G_AFR: 0.3206%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.2576%; gnomAD_G_NFE: 1.8195%; gnomAD_G_OTH: 1.3265%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45667303T>C [0/1] rs145672903 (variation viewer)

Variant score: 0.032

Transcripts:: PRKCE:ENST00000306156.8:c.348+14855T>C:p.(=)

Pathogenicity Data:: Best Score: 0.21855211; CADD: 0.219 (1.071)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.9389%; UK10K: 1.3224%; gnomAD_G_AFR: 0.1838%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 1.9220%; gnomAD_G_NFE: 1.3763%; gnomAD_G_OTH: 1.4344%

INTERGENIC_VARIANT chr2:g.45645045GT>G [0/1] rs58712970 (variation viewer)

Variant score: 0.023

Transcripts:: PRKCE:ENST00000306156.8::

Pathogenicity Data:: Best Score: 0.02343762; CADD: 0.023 (0.103)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45703021T>TCCC [0/1] rs11445755 (variation viewer)

Variant score: 0.014

Transcripts:: PRKCE:ENST00000306156.8:c.348+50573_348+50574insCCC:p.(=)

Pathogenicity Data:: Best Score: 0.037279963; CADD: 0.037 (0.165)

Frequency Data:: gnomAD_G_AFR: 1.5298%; gnomAD_G_AMR: 0.8495%; gnomAD_G_ASJ: 1.7123%; gnomAD_G_EAS: 0.5625%; gnomAD_G_FIN: 0.9490%; gnomAD_G_NFE: 0.6764%; gnomAD_G_OTH: 0.4211%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45884994TATA>T [0|1] rs55862193 (variation viewer)

Variant score: 0.003

Transcripts:: PRKCE:ENST00000306156.8:c.412+41932_412+41934del:p.(=)

Pathogenicity Data:: Best Score: 0.012584388; CADD: 0.013 (0.055)

Frequency Data:: gnomAD_G_AFR: 0.0899%; gnomAD_G_AMR: 1.8987%; gnomAD_G_EAS: 0.2375%; gnomAD_G_FIN: 0.2841%; gnomAD_G_NFE: 0.3148%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45884992TA>T [-/1] rs55654601 (variation viewer)

Variant score: 0.002

Transcripts:: PRKCE:ENST00000306156.8:c.412+41930del:p.(=)

Pathogenicity Data:: Best Score: 0.005510986; CADD: 0.006 (0.024)

Frequency Data:: gnomAD_G_AFR: 0.8514%; gnomAD_G_AMR: 1.7857%; gnomAD_G_EAS: 0.2242%; gnomAD_G_FIN: 0.2674%; gnomAD_G_NFE: 0.4333%; gnomAD_G_OTH: 0.2604%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45884992TA>* [-/1]

Variant score: 0.000

Transcripts:: PRKCE:ENST00000306156.8:c.412+41929_412+41930delTAins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45884995A>* [-/1]

Variant score: 0.000

Transcripts:: PRKCE:ENST00000306156.8:c.412+41932A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.45884997A>* [-/1]

Variant score: 0.000

Transcripts:: PRKCE:ENST00000306156.8:c.412+41934A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.46085754TG>* [-/1]

Variant score: 0.000

Transcripts:: PRKCE:ENST00000306156.8:c.1438-454_1438-453delTGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

KIF5B

Exomiser Score: 0.362

Phenotype Score: 0.507

Variant Score: 0.811

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.115

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.32026437C>CAAA [-/1] rs71027049 (variation viewer)

Variant score: 0.115 CONTRIBUTING VARIANT

Transcripts:: KIF5B:ENST00000302418.5:c.1725+1990_1725+1991insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.11549562; CADD: 0.115 (0.533)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.362

Phenotype Score: 0.507

Variant Score: 0.811

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr10:g.32008067CAAAAAAAAAA>C [1/1] rs573320995 (variation viewer)

Variant score: 0.811 CONTRIBUTING VARIANT

Transcripts:: KIF5B:ENST00000302418.5::; KIF5B:ENST00000415903.1::

Pathogenicity Data:: Best Score: 0.8109834; CADD: 0.811 (7.235)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.32017900A>C [0/1] rs367646014 (variation viewer)

Variant score: 0.843

Transcripts:: KIF5B:ENST00000302418.5:c.2544+152T>G:p.(=)

Pathogenicity Data:: Best Score: 0.9478805; CADD: 0.948 (12.830)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.2501%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0114%; gnomAD_G_AMR: 0.5967%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.2932%

DOWNSTREAM_GENE_VARIANT chr10:g.32008787CA>C [1/1] rs201207711 (variation viewer)

Variant score: 0.194

Transcripts:: KIF5B:ENST00000302418.5::; KIF5B:ENST00000415903.1::

Pathogenicity Data:: Best Score: 0.19369382; CADD: 0.194 (0.935)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.32006436C>CA [1/1] rs58152417 (variation viewer)

Variant score: 0.186

Transcripts:: KIF5B:ENST00000302418.5::; KIF5B:ENST00000415903.1::

Pathogenicity Data:: Best Score: 0.18567085; CADD: 0.186 (0.892)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.32026437C>CAAAAAAA [-/1] rs71027049 (variation viewer)

Variant score: 0.106

Transcripts:: KIF5B:ENST00000302418.5:c.1725+1990_1725+1991insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.106488824; CADD: 0.106 (0.489)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.32027485TTA>* [-/1]

Variant score: 0.000

Transcripts:: KIF5B:ENST00000302418.5:c.1725+941_1725+943delTAAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UGT1A8

Exomiser Score: 0.361

Phenotype Score: 0.505

Variant Score: 0.813

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.113

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.233610159G>A [0/1] rs562442301 (variation viewer)

Variant score: 0.113 CONTRIBUTING VARIANT

Transcripts:: UGT1A8:ENST00000373450.4::

Pathogenicity Data:: Best Score: 0.11386478; CADD: 0.114 (0.525)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0399%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.361

Phenotype Score: 0.505

Variant Score: 0.813

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233632869T>A [0/1] rs185654258 (variation viewer)

Variant score: 0.859 CONTRIBUTING VARIANT

Transcripts:: UGT1A8:ENST00000373450.4:c.855+14307T>A:p.(=)

Pathogenicity Data:: Best Score: 0.9665805; CADD: 0.967 (14.760)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.1035%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1465%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233662942T>C [0/1] rs185178881 (variation viewer)

Variant score: 0.767 CONTRIBUTING VARIANT

Transcripts:: UGT1A8:ENST00000373450.4:c.855+44380T>C:p.(=); UGT1A8:ENST00000344644.9:c.855+25565T>C:p.(=); UGT1A8:ENST00000373445.1:c.855+25565T>C:p.(=)

Pathogenicity Data:: Best Score: 0.86288023; CADD: 0.863 (8.629)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.1035%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2392%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1466%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233646191A>G [0/1] rs569666722 (variation viewer)

Variant score: 0.561

Transcripts:: UGT1A8:ENST00000373450.4:c.855+27629A>G:p.(=); UGT1A8:ENST00000344644.9:c.855+8814A>G:p.(=); UGT1A8:ENST00000373445.1:c.855+8814A>G:p.(=)

Pathogenicity Data:: Best Score: 0.64989364; CADD: 0.650 (4.558)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 0.1234%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1533%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233643108G>A [0/1] rs138858511 (variation viewer)

Variant score: 0.483

Transcripts:: UGT1A8:ENST00000373450.4:c.855+24546G>A:p.(=); UGT1A8:ENST00000344644.9:c.855+5731G>A:p.(=); UGT1A8:ENST00000373445.1:c.855+5731G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5219206; CADD: 0.522 (3.205)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.0996%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1334%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233633682T>C [0/1] rs182376894 (variation viewer)

Variant score: 0.354

Transcripts:: UGT1A8:ENST00000373450.4:c.855+15120T>C:p.(=)

Pathogenicity Data:: Best Score: 0.43921036; CADD: 0.439 (2.512)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0860%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0230%; gnomAD_G_FIN: 0.8903%; gnomAD_G_NFE: 0.2271%; gnomAD_G_OTH: 0.6135%

INTERGENIC_VARIANT chr2:g.233609005GT>G [1/1] rs34433479 (variation viewer)

Variant score: 0.185

Transcripts:: UGT1A8:ENST00000373450.4::

Pathogenicity Data:: Best Score: 0.1852957; CADD: 0.185 (0.890)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233665875C>T [0/1] rs552952595 (variation viewer)

Variant score: 0.123

Transcripts:: UGT1A8:ENST00000373450.4:c.855+47313C>T:p.(=); UGT1A8:ENST00000344644.9:c.855+28498C>T:p.(=); UGT1A8:ENST00000373445.1:c.855+28498C>T:p.(=)

Pathogenicity Data:: Best Score: 0.15238231; CADD: 0.152 (0.718)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0876%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0229%; gnomAD_G_FIN: 0.8877%; gnomAD_G_NFE: 0.2265%; gnomAD_G_OTH: 0.7143%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233626542C>T [0/1] rs145036280 (variation viewer)

Variant score: 0.095

Transcripts:: UGT1A8:ENST00000373450.4:c.855+7980C>T:p.(=)

Pathogenicity Data:: Best Score: 0.11773306; CADD: 0.118 (0.544)

Frequency Data:: 1000Genomes: 0.8786%; TOPMed: 0.1664%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.2067%; gnomAD_G_OTH: 0.3055%

UPSTREAM_GENE_VARIANT chr2:g.233615389G>T [0/1] rs193062305 (variation viewer)

Variant score: 0.095

Transcripts:: UGT1A8:ENST00000373450.4::; UGT1A8:ENST00000456635.1::

Pathogenicity Data:: Best Score: 0.10977453; CADD: 0.110 (0.505)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 0.1187%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1533%; gnomAD_G_OTH: 0.1018%

INTERGENIC_VARIANT chr2:g.233611129T>A [0/1] rs72984444 (variation viewer)

Variant score: 0.071

Transcripts:: UGT1A8:ENST00000373450.4::

Pathogenicity Data:: Best Score: 0.12340295; CADD: 0.123 (0.572)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.5973%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 1.2055%; gnomAD_G_NFE: 0.8932%; gnomAD_G_OTH: 1.4257%

UPSTREAM_GENE_VARIANT chr2:g.233614800C>T [0/1] rs143603790 (variation viewer)

Variant score: 0.036

Transcripts:: UGT1A8:ENST00000373450.4::; UGT1A8:ENST00000456635.1::

Pathogenicity Data:: Best Score: 0.042144477; CADD: 0.042 (0.187)

Frequency Data:: 1000Genomes: 0.7588%; TOPMed: 0.1633%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.2404%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.2067%; gnomAD_G_OTH: 0.1020%

UBL4A

Exomiser Score: 0.359

Phenotype Score: 0.505

Variant Score: 0.812

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.359

Phenotype Score: 0.505

Variant Score: 0.812

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154486446G>T [1/1] rs12392491 (variation viewer)

Variant score: 0.812 CONTRIBUTING VARIANT

Transcripts:: UBL4A:ENST00000369653.8:c.48+91C>A:p.(=); UBL4A:ENST00000369660.9:c.48+91C>A:p.(=); UBL4A:ENST00000630530.1:c.48+91C>A:p.(=)

Pathogenicity Data:: Best Score: 0.81185186; CADD: 0.812 (7.255)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.359

Phenotype Score: 0.505

Variant Score: 0.812

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.154486446G>T [1/1] rs12392491 (variation viewer)

Variant score: 0.812 CONTRIBUTING VARIANT

Transcripts:: UBL4A:ENST00000369653.8:c.48+91C>A:p.(=); UBL4A:ENST00000369660.9:c.48+91C>A:p.(=); UBL4A:ENST00000630530.1:c.48+91C>A:p.(=)

Pathogenicity Data:: Best Score: 0.81185186; CADD: 0.812 (7.255)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr23:g.154480352T>TA [1/1] rs71913278 (variation viewer)

Variant score: 0.239

Transcripts:: UBL4A:ENST00000369660.9::

Pathogenicity Data:: Best Score: 0.23949862; CADD: 0.239 (1.189)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr23:g.154481281C>CA [1/1] rs60920696 (variation viewer)

Variant score: 0.161

Transcripts:: UBL4A:ENST00000369660.9::

Pathogenicity Data:: Best Score: 0.16053998; CADD: 0.161 (0.760)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr23:g.154481910CAA>C [1/1] rs4063129 (variation viewer)

Variant score: 0.157

Transcripts:: UBL4A:ENST00000369660.9::

Pathogenicity Data:: Best Score: 0.15666527; CADD: 0.157 (0.740)

Frequency Data:: No frequency data

LEF1

Exomiser Score: 0.350

Phenotype Score: 0.503

Variant Score: 0.811

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.350

Phenotype Score: 0.503

Variant Score: 0.811

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108086716A>T [0/1]

Variant score: 0.811 CONTRIBUTING VARIANT

Transcripts:: LEF1:ENST00000265165.6:c.547+2409T>A:p.(=); LEF1:ENST00000379951.6:c.547+2409T>A:p.(=); LEF1:ENST00000438313.6:c.547+2409T>A:p.(=); LEF1:ENST00000510624.5:c.343+2409T>A:p.(=); LEF1:ENST00000512172.1:c.343+2409T>A:p.(=)

Pathogenicity Data:: Best Score: 0.81054765; CADD: 0.811 (7.225)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.167

Phenotype Score: 0.503

Variant Score: 0.702

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108086716A>T [0/1]

Variant score: 0.811 CONTRIBUTING VARIANT

Transcripts:: LEF1:ENST00000265165.6:c.547+2409T>A:p.(=); LEF1:ENST00000379951.6:c.547+2409T>A:p.(=); LEF1:ENST00000438313.6:c.547+2409T>A:p.(=); LEF1:ENST00000510624.5:c.343+2409T>A:p.(=); LEF1:ENST00000512172.1:c.343+2409T>A:p.(=)

Pathogenicity Data:: Best Score: 0.81054765; CADD: 0.811 (7.225)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108055469T>C [0/1] rs183595092 (variation viewer)

Variant score: 0.594 CONTRIBUTING VARIANT

Transcripts:: LEF1:ENST00000379951.6:c.1082-6718A>G:p.(=); LEF1:ENST00000265165.6:c.*7-6718A>G:p.(=); LEF1:ENST00000438313.6:c.*7-6718A>G:p.(=); LEF1:ENST00000510624.5:c.*7-6718A>G:p.(=)

Pathogenicity Data:: Best Score: 0.94847715; CADD: 0.948 (12.880)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0948%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0344%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.1466%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108051321G>C [0/1] rs188387236 (variation viewer)

Variant score: 0.571

Transcripts:: LEF1:ENST00000379951.6:c.1082-2570C>G:p.(=); LEF1:ENST00000265165.6:c.*7-2570C>G:p.(=); LEF1:ENST00000438313.6:c.*7-2570C>G:p.(=); LEF1:ENST00000510624.5:c.*7-2570C>G:p.(=)

Pathogenicity Data:: Best Score: 0.91209775; CADD: 0.912 (10.560)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1091%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.1199%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.1154%; gnomAD_G_NFE: 0.1607%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108128187G>C [0/1] rs772921654 (variation viewer)

Variant score: 0.494

Transcripts:: LEF1:ENST00000265165.6:c.414+35381C>G:p.(=); LEF1:ENST00000379951.6:c.414+35381C>G:p.(=); LEF1:ENST00000438313.6:c.414+35381C>G:p.(=); LEF1:ENST00000510624.5:c.210+35381C>G:p.(=); LEF1:ENST00000512172.1:c.210+35381C>G:p.(=)

Pathogenicity Data:: Best Score: 0.50146; CADD: 0.501 (3.023)

Frequency Data:: TOPMed: 0.0319%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0534%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108149458C>CAAAAAAAAAAA [1/1] rs371482539 (variation viewer)

Variant score: 0.291

Transcripts:: LEF1:ENST00000265165.6:c.414+14109_414+14110insTTTTTTTTTTT:p.(=); LEF1:ENST00000379951.6:c.414+14109_414+14110insTTTTTTTTTTT:p.(=); LEF1:ENST00000438313.6:c.414+14109_414+14110insTTTTTTTTTTT:p.(=); LEF1:ENST00000510624.5:c.210+14109_210+14110insTTTTTTTTTTT:p.(=); LEF1:ENST00000512172.1:c.210+14109_210+14110insTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.29058564; CADD: 0.291 (1.491)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108071868A>AAC [0|1] rs1438492227 (variation viewer)

Variant score: 0.160

Transcripts:: LEF1:ENST00000265165.6:c.1009-1099_1009-1098insGT:p.(=); LEF1:ENST00000379951.6:c.925-1099_925-1098insGT:p.(=); LEF1:ENST00000438313.6:c.925-1099_925-1098insGT:p.(=); LEF1:ENST00000510624.5:c.721-1099_721-1098insGT:p.(=)

Pathogenicity Data:: Best Score: 0.1597665; CADD: 0.160 (0.756)

Frequency Data:: gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108113593T>C [0/1] rs138191388 (variation viewer)

Variant score: 0.144

Transcripts:: LEF1:ENST00000265165.6:c.415-24336A>G:p.(=); LEF1:ENST00000379951.6:c.415-24336A>G:p.(=); LEF1:ENST00000438313.6:c.415-24336A>G:p.(=); LEF1:ENST00000510624.5:c.211-24336A>G:p.(=); LEF1:ENST00000512172.1:c.211-24336A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9702833; CADD: 0.970 (15.270)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.3395%; UK10K: 0.5554%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.8300%; gnomAD_G_NFE: 0.8728%; gnomAD_G_OTH: 1.0246%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108086829T>TACACACACACACACACACAC [1/1] rs139231288 (variation viewer)

Variant score: 0.072

Transcripts:: LEF1:ENST00000265165.6:c.547+2295_547+2296insGTGTGTGTGTGTGTGTGTGT:p.(=); LEF1:ENST00000379951.6:c.547+2295_547+2296insGTGTGTGTGTGTGTGTGTGT:p.(=); LEF1:ENST00000438313.6:c.547+2295_547+2296insGTGTGTGTGTGTGTGTGTGT:p.(=); LEF1:ENST00000510624.5:c.343+2295_343+2296insGTGTGTGTGTGTGTGTGTGT:p.(=); LEF1:ENST00000512172.1:c.343+2295_343+2296insGTGTGTGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.071888804; CADD: 0.072 (0.324)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.108088598C>T [0/1] rs756627439 (variation viewer)

Variant score: 0.032

Transcripts:: LEF1:ENST00000265165.6:c.547+527G>A:p.(=); LEF1:ENST00000379951.6:c.547+527G>A:p.(=); LEF1:ENST00000438313.6:c.547+527G>A:p.(=); LEF1:ENST00000510624.5:c.343+527G>A:p.(=); LEF1:ENST00000512172.1:c.343+527G>A:p.(=)

Pathogenicity Data:: Best Score: 0.03194505; CADD: 0.032 (0.141)

Frequency Data:: TOPMed: 0.0143%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0133%

ENTPD4

Exomiser Score: 0.341

Phenotype Score: 0.503

Variant Score: 0.805

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.341

Phenotype Score: 0.503

Variant Score: 0.805

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.23392247C>T [0/1] rs995009316 (variation viewer)

Variant score: 0.805 CONTRIBUTING VARIANT

Transcripts:: ENTPD4:ENST00000356206.10:c.1599-6202G>A:p.(=); ENTPD4:ENST00000389131.8:c.-84+11707G>A:p.(=)

Pathogenicity Data:: Best Score: 0.80782366; CADD: 0.808 (7.163)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.194

Phenotype Score: 0.503

Variant Score: 0.722

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.23392247C>T [0/1] rs995009316 (variation viewer)

Variant score: 0.805 CONTRIBUTING VARIANT

Transcripts:: ENTPD4:ENST00000356206.10:c.1599-6202G>A:p.(=); ENTPD4:ENST00000389131.8:c.-84+11707G>A:p.(=)

Pathogenicity Data:: Best Score: 0.80782366; CADD: 0.808 (7.163)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.23446450A>C [0/1] rs144904026 (variation viewer)

Variant score: 0.639 CONTRIBUTING VARIANT

Transcripts:: ENTPD4:ENST00000356206.10:c.412+1230T>G:p.(=); ENTPD4:ENST00000358689.9:c.412+1230T>G:p.(=); ENTPD4:ENST00000417069.6:c.412+1230T>G:p.(=)

Pathogenicity Data:: Best Score: 0.6675702; CADD: 0.668 (4.783)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1752%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0801%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.1399%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.23433358G>A [0/1] rs145911665 (variation viewer)

Variant score: 0.152

Transcripts:: ENTPD4:ENST00000356206.10:c.1598+959C>T:p.(=); ENTPD4:ENST00000358689.9:c.1623-204C>T:p.(=); ENTPD4:ENST00000417069.6:c.1599-204C>T:p.(=)

Pathogenicity Data:: Best Score: 0.15821731; CADD: 0.158 (0.748)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1776%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1399%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.23388623TCACACA>T [-/1] rs10522826 (variation viewer)

Variant score: 0.098

Transcripts:: ENTPD4:ENST00000356206.10:c.1599-2584_1599-2579del:p.(=); ENTPD4:ENST00000389131.8:c.-84+15325_-84+15330del:p.(=)

Pathogenicity Data:: Best Score: 0.09822124; CADD: 0.098 (0.449)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.23427124CA>C [1/1] rs71548897 (variation viewer)

Variant score: 0.021

Transcripts:: ENTPD4:ENST00000356206.10:c.1598+7192del:p.(=)

Pathogenicity Data:: Best Score: 0.020960987; CADD: 0.021 (0.092)

Frequency Data:: No frequency data

SURF1

Exomiser Score: 0.334

Phenotype Score: 0.504

Variant Score: 0.801

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with SURF1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:220110 Mitochondrial complex IV deficiency, nuclear type 1 - autosomal recessive; OMIM:616684 Charcot-Marie-Tooth disease, type 4K - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:70474 Leigh syndrome with cardiomyopathy

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.334

Phenotype Score: 0.504

Variant Score: 0.801

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.133356366G>GCCCCGCACCCCGCA [1/1] rs3041852 (variation viewer)

ClinVar: BENIGN (criteria_provided,_single_submitter)

Variant score: 0.801 CONTRIBUTING VARIANT

Transcripts:: SURF1:ENST00000371974.8:c.54+33_54+34insTGCGGGGTGCGGGG:p.(=); SURF1:ENST00000615505.4:c.-222+33_-222+34insTGCGGGGTGCGGGG:p.(=)

Pathogenicity Data:: Best Score: 0.8011617; CADD: 0.801 (7.015)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr9:g.133351736G>A [1|1] rs599924 (variation viewer)

Variant score: 0.036

Transcripts:: SURF1:ENST00000371974.8::; SURF1:ENST00000315731.4::

Pathogenicity Data:: Best Score: 0.03594899; CADD: 0.036 (0.159)

Frequency Data:: No frequency data

PIK3CG

Exomiser Score: 0.333

Phenotype Score: 0.507

Variant Score: 0.797

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.132

Phenotype Score: 0.507

Variant Score: 0.668

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr7:g.106862821C>T [0/1] rs1393507219 (variation viewer)

Variant score: 0.668 CONTRIBUTING VARIANT

Transcripts:: PIK3CG:ENST00000440650.6::; PIK3CG:ENST00000516169.1::

Pathogenicity Data:: Best Score: 0.6682583; CADD: 0.668 (4.792)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.333

Phenotype Score: 0.507

Variant Score: 0.797

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.106883715A>G [0/1] rs557406692 (variation viewer)

Variant score: 0.926 CONTRIBUTING VARIANT

Transcripts:: PIK3CG:ENST00000359195.3:c.2761-440A>G:p.(=); PIK3CG:ENST00000440650.6:c.2761-440A>G:p.(=); PIK3CG:ENST00000496166.6:c.2761-440A>G:p.(=)

Pathogenicity Data:: Best Score: 0.978273; CADD: 0.978 (16.630)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0852%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0344%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.2532%; gnomAD_G_OTH: 0.2041%

UPSTREAM_GENE_VARIANT chr7:g.106862821C>T [0/1] rs1393507219 (variation viewer)

Variant score: 0.668 CONTRIBUTING VARIANT

Transcripts:: PIK3CG:ENST00000440650.6::; PIK3CG:ENST00000516169.1::

Pathogenicity Data:: Best Score: 0.6682583; CADD: 0.668 (4.792)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

UGT2A1

Exomiser Score: 0.332

Phenotype Score: 0.504

Variant Score: 0.800

Phenotype matches:

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.081

Phenotype Score: 0.504

Variant Score: 0.611

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.69615682A>C [0/1] rs1220480445 (variation viewer)

Variant score: 0.611 CONTRIBUTING VARIANT

Transcripts:: UGT2A1:ENST00000286604.8:c.848-16288T>G:p.(=); UGT2A1:ENST00000503640.5:c.716-16288T>G:p.(=); UGT2A1:ENST00000512704.5:c.716-16288T>G:p.(=); UGT2A1:ENST00000514019.1:c.1346-16288T>G:p.(=); UGT2A1:ENST00000604021.1:c.743-16288T>G:p.(=); UGT2A1:ENST00000604629.5:c.743-16288T>G:p.(=)

Pathogenicity Data:: Best Score: 0.611492; CADD: 0.611 (4.106)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.332

Phenotype Score: 0.504

Variant Score: 0.800

Variants contributing to score:

SPLICE_REGION_VARIANT chr4:g.69635828CA>C [1|1] rs1191267919 (variation viewer)

Variant score: 0.800 CONTRIBUTING VARIANT

Transcripts:: UGT2A1:ENST00000286604.8:c.716-7del:p.?; UGT2A1:ENST00000503640.5:c.715+11101del:p.(=); UGT2A1:ENST00000512704.5:c.715+11101del:p.(=); UGT2A1:ENST00000514019.1:c.1345+3070del:p.(=); UGT2A1:ENST00000604021.1:c.742+3070del:p.(=); UGT2A1:ENST00000604629.5:c.742+3070del:p.(=)

Pathogenicity Data:: Best Score: 0.12582171; CADD: 0.126 (0.584)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.69603958G>A [0/1] rs545380427 (variation viewer)

Variant score: 0.306

Transcripts:: UGT2A1:ENST00000286604.8:c.848-4564C>T:p.(=); UGT2A1:ENST00000503640.5:c.716-4564C>T:p.(=); UGT2A1:ENST00000512704.5:c.716-4564C>T:p.(=); UGT2A1:ENST00000514019.1:c.1346-4564C>T:p.(=); UGT2A1:ENST00000604021.1:c.743-4564C>T:p.(=); UGT2A1:ENST00000604629.5:c.743-4564C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5330181; CADD: 0.533 (3.307)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.2596%; gnomAD_G_AFR: 0.3155%; gnomAD_G_AMR: 0.1269%; gnomAD_G_FIN: 0.9756%; gnomAD_G_NFE: 1.4241%; gnomAD_G_OTH: 0.7625%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.69593612ATTCAT>A [0/1]

Variant score: 0.000

Transcripts:: UGT2A1:ENST00000286604.8:c.1304+860_1304+864del:p.(=); UGT2A1:ENST00000503640.5:c.1304+860_1304+864del:p.(=); UGT2A1:ENST00000512704.5:c.1172+860_1172+864del:p.(=); UGT2A1:ENST00000514019.1:c.1802+860_1802+864del:p.(=); UGT2A1:ENST00000604021.1:c.1199+860_1199+864del:p.(=); UGT2A1:ENST00000604629.5:c.1331+860_1331+864del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ERBB3

Exomiser Score: 0.326

Phenotype Score: 0.505

Variant Score: 0.796

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:133180 ?Erythroleukemia, familial, susceptibility to (susceptibility); OMIM:607598 ?Lethal congenital contractural syndrome 2 (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.326

Phenotype Score: 0.505

Variant Score: 0.796

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.56083509T>C [0/1]

Variant score: 0.796 CONTRIBUTING VARIANT

Transcripts:: ERBB3:ENST00000267101.7:c.83-242T>C:p.(=); ERBB3:ENST00000411731.6:c.83-242T>C:p.(=); ERBB3:ENST00000415288.6:c.-135T>C:p.(=)

Pathogenicity Data:: Best Score: 0.79620194; CADD: 0.796 (6.908)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.297

Phenotype Score: 0.505

Variant Score: 0.782

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.56083509T>C [0/1]

Variant score: 0.796 CONTRIBUTING VARIANT

Transcripts:: ERBB3:ENST00000267101.7:c.83-242T>C:p.(=); ERBB3:ENST00000411731.6:c.83-242T>C:p.(=); ERBB3:ENST00000415288.6:c.-135T>C:p.(=)

Pathogenicity Data:: Best Score: 0.79620194; CADD: 0.796 (6.908)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.56090462G>A [0/1] rs573486302 (variation viewer)

Variant score: 0.767 CONTRIBUTING VARIANT

Transcripts:: ERBB3:ENST00000267101.7:c.1109+1594G>A:p.(=); ERBB3:ENST00000415288.6:c.932+1594G>A:p.(=)

Pathogenicity Data:: Best Score: 0.76858044; CADD: 0.769 (6.356)

Frequency Data:: TOPMed: 0.0127%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0133%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.56100939CA>C [0/1] rs10536745 (variation viewer)

Variant score: 0.232

Transcripts:: ERBB3:ENST00000267101.7:c.3202-121del:p.(=); ERBB3:ENST00000415288.6:c.3025-121del:p.(=); ERBB3:ENST00000549832.1:c.562-121del:p.(=); ERBB3:ENST00000553131.5:c.925-121del:p.(=)

Pathogenicity Data:: Best Score: 0.23193145; CADD: 0.232 (1.146)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.56097623CTCCCCT>C [0/1] rs577296673 (variation viewer)

Variant score: 0.208

Transcripts:: ERBB3:ENST00000267101.7:c.2461-161_2461-156del:p.(=); ERBB3:ENST00000415288.6:c.2284-161_2284-156del:p.(=); ERBB3:ENST00000553131.5:c.184-161_184-156del:p.(=)

Pathogenicity Data:: Best Score: 0.33242512; CADD: 0.332 (1.755)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2469%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.2733%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.56091334A>ATATATATAAATATAAATATATGTTACAAATATATATTATAAATATAAACATATAAATATATATTATATATAAATATATATATATATGTTTATATTTATAATATATATTTGTAACATATATTTATATTTATATATAAATTTATATATATATAAAATATATATATATT [1/1]

Variant score: 0.000

Transcripts:: ERBB3:ENST00000267101.7:c.1110-1413_1110-1412insTATATATAAATATAAATATATGTTACAAATATATATTATAAATATAAACATATAAATATATATTATATATAAATATATATATATATGTTTATATTTATAATATATATTTGTAACATATATTTATATTTATATATAAATTTATATATATATAAAATATATATATATT:p.(=); ERBB3:ENST00000415288.6:c.933-1413_933-1412insTATATATAAATATAAATATATGTTACAAATATATATTATAAATATAAACATATAAATATATATTATATATAAATATATATATATATGTTTATATTTATAATATATATTTGTAACATATATTTATATTTATATATAAATTTATATATATATAAAATATATATATATT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UGCG

Exomiser Score: 0.319

Phenotype Score: 0.505

Variant Score: 0.792

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.319

Phenotype Score: 0.505

Variant Score: 0.792

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr9:g.111935290G>A [0/1] rs527622752 (variation viewer)

Variant score: 0.792 CONTRIBUTING VARIANT

Transcripts:: UGCG:ENST00000374279.4:c.*2293G>A:p.(=)

Pathogenicity Data:: Best Score: 0.80074924; CADD: 0.801 (7.006)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0581%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0734%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.040

Phenotype Score: 0.505

Variant Score: 0.529

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr9:g.111935290G>A [0/1] rs527622752 (variation viewer)

Variant score: 0.792 CONTRIBUTING VARIANT

Transcripts:: UGCG:ENST00000374279.4:c.*2293G>A:p.(=)

Pathogenicity Data:: Best Score: 0.80074924; CADD: 0.801 (7.006)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0581%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0734%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.111921802A>ATTTTTTTTTTTTTTTT [0/1]

Variant score: 0.266 CONTRIBUTING VARIANT

Transcripts:: UGCG:ENST00000374279.4:c.241-1047_241-1046insTTTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.26582432; CADD: 0.266 (1.342)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr9:g.111947783CAAAAAAA>C [1/1] rs58692107 (variation viewer)

Variant score: 0.223

Transcripts:: UGCG:ENST00000374279.4::

Pathogenicity Data:: Best Score: 0.22321647; CADD: 0.223 (1.097)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.111911905GATATATAT>G [-/1] rs200468304 (variation viewer)

Variant score: 0.199

Transcripts:: UGCG:ENST00000374279.4:c.99-2699_99-2692del:p.(=)

Pathogenicity Data:: Best Score: 0.19850653; CADD: 0.199 (0.961)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.111926861C>CT [1/1] rs56298523 (variation viewer)

Variant score: 0.068

Transcripts:: UGCG:ENST00000374279.4:c.558+365_558+366insT:p.(=)

Pathogenicity Data:: Best Score: 0.067819536; CADD: 0.068 (0.305)

Frequency Data:: No frequency data

AGMO

Exomiser Score: 0.318

Phenotype Score: 0.534

Variant Score: 0.759

Phenotype matches:

Proximity score 0.534 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.318

Phenotype Score: 0.534

Variant Score: 0.759

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15428633T>C [0/1] rs761796283 (variation viewer)

Variant score: 0.759 CONTRIBUTING VARIANT

Transcripts:: AGMO:ENST00000342526.8:c.513+2372A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7622065; CADD: 0.762 (6.238)

Frequency Data:: TOPMed: 0.0191%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0267%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.184

Phenotype Score: 0.534

Variant Score: 0.680

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15428633T>C [0/1] rs761796283 (variation viewer)

Variant score: 0.759 CONTRIBUTING VARIANT

Transcripts:: AGMO:ENST00000342526.8:c.513+2372A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7622065; CADD: 0.762 (6.238)

Frequency Data:: TOPMed: 0.0191%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0267%

DOWNSTREAM_GENE_VARIANT chr7:g.15198250AGAGAGACAGAGACAGAGAGAGAGT>A [0/1] rs1300056474 (variation viewer)

Variant score: 0.601 CONTRIBUTING VARIANT

Transcripts:: AGMO:ENST00000342526.8::; AGMO:ENST00000442645.1::

Pathogenicity Data:: Best Score: 0.6827512; CADD: 0.683 (4.986)

Frequency Data:: gnomAD_G_AFR: 0.2120%; gnomAD_G_AMR: 0.1515%; gnomAD_G_ASJ: 0.3846%; gnomAD_G_EAS: 0.0694%; gnomAD_G_FIN: 0.1705%; gnomAD_G_NFE: 0.6357%; gnomAD_G_OTH: 0.1259%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15542749A>G [0/1] rs143796462 (variation viewer)

Variant score: 0.597

Transcripts:: AGMO:ENST00000342526.8:c.409+2023T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6342368; CADD: 0.634 (4.368)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.0828%; UK10K: 0.0793%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15530511A>ATATATATATTCTATATACGTATTTC [1/1] rs1583652821 (variation viewer)

Variant score: 0.458

Transcripts:: AGMO:ENST00000342526.8:c.409+14260_409+14261insGAAATACGTATATAGAATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.4579991; CADD: 0.458 (2.660)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15259096G>A [0/1] rs190074115 (variation viewer)

Variant score: 0.375

Transcripts:: AGMO:ENST00000342526.8:c.1264-57737C>T:p.(=)

Pathogenicity Data:: Best Score: 0.38127166; CADD: 0.381 (2.085)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0438%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0334%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15409528T>G [0/1]

Variant score: 0.362

Transcripts:: AGMO:ENST00000342526.8:c.609+9030A>C:p.(=)

Pathogenicity Data:: Best Score: 0.36247092; CADD: 0.362 (1.955)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15248179C>CATATATATATATATATAT [-/1]

Variant score: 0.361

Transcripts:: AGMO:ENST00000342526.8:c.1264-46821_1264-46820insATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.3608541; CADD: 0.361 (1.944)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15547267C>T [0/1] rs75747711 (variation viewer)

Variant score: 0.262

Transcripts:: AGMO:ENST00000342526.8:c.258-2344G>A:p.(=)

Pathogenicity Data:: Best Score: 0.33732587; CADD: 0.337 (1.787)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.4707%; UK10K: 0.9786%; gnomAD_G_AFR: 0.1145%; gnomAD_G_FIN: 0.6297%; gnomAD_G_NFE: 0.8129%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15410023T>A [0/1] rs566427153 (variation viewer)

Variant score: 0.246

Transcripts:: AGMO:ENST00000342526.8:c.609+8535A>T:p.(=)

Pathogenicity Data:: Best Score: 0.247338; CADD: 0.247 (1.234)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0239%; gnomAD_G_AFR: 0.0116%; gnomAD_G_NFE: 0.0335%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15232801GCA>G [0/1] rs71004371 (variation viewer)

Variant score: 0.208

Transcripts:: AGMO:ENST00000342526.8:c.1264-31444_1264-31443del:p.(=)

Pathogenicity Data:: Best Score: 0.2080459; CADD: 0.208 (1.013)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15218327A>ATGTG [-/1] rs138890087 (variation viewer)

Variant score: 0.183

Transcripts:: AGMO:ENST00000342526.8:c.1264-16969_1264-16968insCACA:p.(=)

Pathogenicity Data:: Best Score: 0.18285334; CADD: 0.183 (0.877)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15315328C>CT [0/1] rs1178276622 (variation viewer)

Variant score: 0.178

Transcripts:: AGMO:ENST00000342526.8:c.1263+50185_1263+50186insA:p.(=)

Pathogenicity Data:: Best Score: 0.17756802; CADD: 0.178 (0.849)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15218327A>ATGTGTGTGTG [-/1] rs138890087 (variation viewer)

Variant score: 0.164

Transcripts:: AGMO:ENST00000342526.8:c.1264-16969_1264-16968insCACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.16362703; CADD: 0.164 (0.776)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15342172T>TAAAA [0/1] rs775057626 (variation viewer)

Variant score: 0.163

Transcripts:: AGMO:ENST00000342526.8:c.1263+23341_1263+23342insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.16285634; CADD: 0.163 (0.772)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15555292T>TACAC [-/1] rs58173194 (variation viewer)

Variant score: 0.153

Transcripts:: AGMO:ENST00000342526.8:c.257+4848_257+4849insGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.15316266; CADD: 0.153 (0.722)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15220208C>CT [0/1] rs904364065 (variation viewer)

Variant score: 0.139

Transcripts:: AGMO:ENST00000342526.8:c.1264-18850_1264-18849insA:p.(=)

Pathogenicity Data:: Best Score: 0.13940269; CADD: 0.139 (0.652)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15459599T>TGTGTGTGTGTGTG [0|1] rs1554274867 (variation viewer)

Variant score: 0.135

Transcripts:: AGMO:ENST00000342526.8:c.410-28492_410-28491insCACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.1352312; CADD: 0.135 (0.631)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15439005G>C [0/1] rs148034552 (variation viewer)

Variant score: 0.129

Transcripts:: AGMO:ENST00000342526.8:c.410-7897C>G:p.(=)

Pathogenicity Data:: Best Score: 0.15588814; CADD: 0.156 (0.736)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.4165%; UK10K: 0.8199%; gnomAD_G_AFR: 0.1031%; gnomAD_G_FIN: 0.6583%; gnomAD_G_NFE: 0.7866%; gnomAD_G_OTH: 0.8163%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15355504C>CAAAA [-/1] rs56695710 (variation viewer)

Variant score: 0.113

Transcripts:: AGMO:ENST00000342526.8:c.1263+10009_1263+10010insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.11345661; CADD: 0.113 (0.523)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15202458CAAAAAAAAAAAA>C [1/1] rs71004370 (variation viewer)

Variant score: 0.107

Transcripts:: AGMO:ENST00000342526.8:c.1264-1111_1264-1100del:p.(=)

Pathogenicity Data:: Best Score: 0.10731137; CADD: 0.107 (0.493)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15355504CA>C [-/1] rs56695710 (variation viewer)

Variant score: 0.095

Transcripts:: AGMO:ENST00000342526.8:c.1263+10009del:p.(=)

Pathogenicity Data:: Best Score: 0.09510124; CADD: 0.095 (0.434)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15419318T>G [0/1] rs140409911 (variation viewer)

Variant score: 0.095

Transcripts:: AGMO:ENST00000342526.8:c.514-665A>C:p.(=)

Pathogenicity Data:: Best Score: 0.6395874; CADD: 0.640 (4.432)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.5137%; UK10K: 0.7405%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.7617%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15247459C>G [1/1] rs13223031 (variation viewer)

Variant score: 0.052

Transcripts:: AGMO:ENST00000342526.8:c.1264-46100G>C:p.(=)

Pathogenicity Data:: Best Score: 0.05245465; CADD: 0.052 (0.234)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15250957T>A [0|1] rs1014841844 (variation viewer)

Variant score: 0.014

Transcripts:: AGMO:ENST00000342526.8:c.1264-49598A>T:p.(=)

Pathogenicity Data:: Best Score: 0.014401555; CADD: 0.014 (0.063)

Frequency Data:: TOPMed: 0.0311%; gnomAD_G_AFR: 0.0233%; gnomAD_G_NFE: 0.0134%; gnomAD_G_OTH: 0.1037%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.15480250C>T [0/1] rs949440804 (variation viewer)

Variant score: 0.003

Transcripts:: AGMO:ENST00000342526.8:c.410-49142G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0027592778; CADD: 0.003 (0.012)

Frequency Data:: gnomAD_G_AFR: 0.0115%

NPLOC4

Exomiser Score: 0.318

Phenotype Score: 0.507

Variant Score: 0.790

Phenotype matches:

Proximity score 0.507 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.318

Phenotype Score: 0.507

Variant Score: 0.790

Variants contributing to score:

REGULATORY_REGION_VARIANT chr17:g.81344384T>A [0/1] rs892980752 (variation viewer)

Variant score: 0.790 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.7903475; CADD: 0.790 (6.785)

Frequency Data:: TOPMed: 0.0032%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.039

Phenotype Score: 0.507

Variant Score: 0.523

Variants contributing to score:

REGULATORY_REGION_VARIANT chr17:g.81344384T>A [0/1] rs892980752 (variation viewer)

Variant score: 0.790 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.7903475; CADD: 0.790 (6.785)

Frequency Data:: TOPMed: 0.0032%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81585170C>CA [0/1] rs35473939 (variation viewer)

Variant score: 0.256 CONTRIBUTING VARIANT

Transcripts:: NPLOC4:ENST00000331134.11:c.1281+3773_1281+3774insT:p.(=); NPLOC4:ENST00000374747.9:c.1281+3773_1281+3774insT:p.(=)

Pathogenicity Data:: Best Score: 0.2559536; CADD: 0.256 (1.284)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81614275C>CAAAAAAA [0/1] rs535340434 (variation viewer)

Variant score: 0.218

Transcripts:: NPLOC4:ENST00000331134.11:c.210-782_210-781insTTTTTTT:p.(=); NPLOC4:ENST00000374747.9:c.210-782_210-781insTTTTTTT:p.(=); NPLOC4:ENST00000625705.1:c.207-782_207-781insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.21819222; CADD: 0.218 (1.069)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81631436ATTTTTTTTT>A [0|1] rs70938164 (variation viewer)

Variant score: 0.129

Transcripts:: NPLOC4:ENST00000331134.11:c.16-1640_16-1632del:p.(=); NPLOC4:ENST00000374747.9:c.16-1640_16-1632del:p.(=)

Pathogenicity Data:: Best Score: 0.12943739; CADD: 0.129 (0.602)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81578844G>A [0/1] rs150895705 (variation viewer)

Variant score: 0.014

Transcripts:: NPLOC4:ENST00000331134.11:c.1282-6756C>T:p.(=); NPLOC4:ENST00000374747.9:c.1282-6756C>T:p.(=)

Pathogenicity Data:: Best Score: 0.095517874; CADD: 0.096 (0.436)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.6769%; UK10K: 0.7273%; gnomAD_G_AFR: 0.5506%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.6069%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81582745C>T [0/1] rs140287472 (variation viewer)

Variant score: 0.006

Transcripts:: NPLOC4:ENST00000331134.11:c.1281+6199G>A:p.(=); NPLOC4:ENST00000374747.9:c.1281+6199G>A:p.(=)

Pathogenicity Data:: Best Score: 0.04192394; CADD: 0.042 (0.186)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.4508%; UK10K: 0.6348%; gnomAD_G_AFR: 0.1603%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.6064%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81631439T>* [-/1]

Variant score: 0.000

Transcripts:: NPLOC4:ENST00000331134.11:c.16-1634A>:p.(=); NPLOC4:ENST00000374747.9:c.16-1634A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81631441T>* [-/1]

Variant score: 0.000

Transcripts:: NPLOC4:ENST00000331134.11:c.16-1636A>:p.(=); NPLOC4:ENST00000374747.9:c.16-1636A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81631443T>* [-/1]

Variant score: 0.000

Transcripts:: NPLOC4:ENST00000331134.11:c.16-1638A>:p.(=); NPLOC4:ENST00000374747.9:c.16-1638A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81631445T>* [-/1]

Variant score: 0.000

Transcripts:: NPLOC4:ENST00000331134.11:c.16-1640A>:p.(=); NPLOC4:ENST00000374747.9:c.16-1640A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UQCRFS1

Exomiser Score: 0.305

Phenotype Score: 0.514

Variant Score: 0.775

Phenotype matches:

Proximity score 0.514 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618775 Mitochondrial complex III deficiency, nuclear type 10 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.060

Phenotype Score: 0.257

Variant Score: 0.856

Variants contributing to score:

STOP_RETAINED_VARIANT chr19:g.29207548T>C [0/1]

Variant score: 0.856 CONTRIBUTING VARIANT

Transcripts:: UQCRFS1:ENST00000304863.6:c.825A>G:p.(=)

Pathogenicity Data:: Best Score: 0.85572207; CADD: 0.856 (8.408)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.305

Phenotype Score: 0.514

Variant Score: 0.775

Variants contributing to score:

STOP_RETAINED_VARIANT chr19:g.29207548T>C [0/1]

Variant score: 0.856 CONTRIBUTING VARIANT

Transcripts:: UQCRFS1:ENST00000304863.6:c.825A>G:p.(=)

Pathogenicity Data:: Best Score: 0.85572207; CADD: 0.856 (8.408)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr19:g.27241216G>A [0/1] rs79112842 (variation viewer)

Variant score: 0.695 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.69450784; CADD: 0.695 (5.150)

Frequency Data:: No frequency data

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr19:g.29207497C>T [0/1] rs200118580 (variation viewer)

Variant score: 0.552

Transcripts:: UQCRFS1:ENST00000304863.6:c.*51G>A:p.(=)

Pathogenicity Data:: Best Score: 0.63195574; CADD: 0.632 (4.341)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1760%; ESP AA: 0.0228%; ESP EA: 0.3382%; ESP All: 0.2313%; ExAC AFR: 0.0449%; ExAC AMR: 0.0972%; ExAC EAS: 0.0129%; ExAC FIN: 0.0503%; ExAC NFE: 0.2439%; ExAC SAS: 0.1689%; gnomAD_E_AFR: 0.0371%; gnomAD_E_AMR: 0.1550%; gnomAD_E_ASJ: 0.3345%; gnomAD_E_EAS: 0.0068%; gnomAD_E_FIN: 0.1030%; gnomAD_E_NFE: 0.2569%; gnomAD_E_OTH: 0.2350%; gnomAD_E_SAS: 0.1805%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.2532%; gnomAD_G_OTH: 0.1018%

REGULATORY_REGION_VARIANT chr19:g.27242159A>G [0/1] rs8108614 (variation viewer)

Variant score: 0.493

Transcripts:

Pathogenicity Data:: Best Score: 0.49265897; CADD: 0.493 (2.947)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr19:g.27243215T>C [0/1] rs558548866 (variation viewer)

Variant score: 0.436

Transcripts:

Pathogenicity Data:: Best Score: 0.4851271; CADD: 0.485 (2.883)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.5591%

REGULATORY_REGION_VARIANT chr19:g.27741622G>A [0/1] rs112236697 (variation viewer)

Variant score: 0.351

Transcripts:

Pathogenicity Data:: Best Score: 0.5111226; CADD: 0.511 (3.108)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.6315%; UK10K: 0.8860%; gnomAD_G_AFR: 0.1262%; gnomAD_G_AMR: 1.1990%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0630%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 1.0692%; gnomAD_G_OTH: 0.7143%

REGULATORY_REGION_VARIANT chr19:g.27242097C>G [0/1] rs758525415 (variation viewer)

Variant score: 0.306

Transcripts:

Pathogenicity Data:: Best Score: 0.44779545; CADD: 0.448 (2.579)

Frequency Data:: gnomAD_G_AFR: 0.1394%; gnomAD_G_AMR: 0.7267%; gnomAD_G_ASJ: 0.3401%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.2075%; gnomAD_G_NFE: 1.0201%; gnomAD_G_OTH: 0.8734%

INTERGENIC_VARIANT chr19:g.29196856T>TATATATATATACACAC [0/1] rs1203452829 (variation viewer)

Variant score: 0.026

Transcripts:: UQCRFS1:ENST00000304863.6::; UQCRFS1:ENST00000516463.1::

Pathogenicity Data:: Best Score: 0.026356459; CADD: 0.026 (0.116)

Frequency Data:: No frequency data

NDUFV3

Exomiser Score: 0.304

Phenotype Score: 0.504

Variant Score: 0.786

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.304

Phenotype Score: 0.504

Variant Score: 0.786

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr21:g.42891690G>A [0/1] rs1022979517 (variation viewer)

Variant score: 0.786 CONTRIBUTING VARIANT

Transcripts:: NDUFV3:ENST00000340344.4::; NDUFV3:ENST00000398208.3::

Pathogenicity Data:: Best Score: 0.78649896; CADD: 0.786 (6.706)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.042

Phenotype Score: 0.504

Variant Score: 0.535

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr21:g.42891690G>A [0/1] rs1022979517 (variation viewer)

Variant score: 0.786 CONTRIBUTING VARIANT

Transcripts:: NDUFV3:ENST00000340344.4::; NDUFV3:ENST00000398208.3::

Pathogenicity Data:: Best Score: 0.78649896; CADD: 0.786 (6.706)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.42908489C>T [0/1] rs888580808 (variation viewer)

Variant score: 0.283 CONTRIBUTING VARIANT

Transcripts:: NDUFV3:ENST00000340344.4:c.170-375C>T:p.(=); NDUFV3:ENST00000354250.7:c.1265-375C>T:p.(=)

Pathogenicity Data:: Best Score: 0.28369164; CADD: 0.284 (1.449)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

Other passed variants:

UPSTREAM_GENE_VARIANT chr21:g.42889779G>A [0/1] rs184884399 (variation viewer)

Variant score: 0.139

Transcripts:: NDUFV3:ENST00000340344.4::; NDUFV3:ENST00000398208.3::

Pathogenicity Data:: Best Score: 0.1743424; CADD: 0.174 (0.832)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4563%; UK10K: 0.7273%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.5155%; gnomAD_G_NFE: 0.7132%; gnomAD_G_OTH: 0.9165%

STAM

Exomiser Score: 0.295

Phenotype Score: 0.506

Variant Score: 0.780

Phenotype matches:

Proximity score 0.506 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.295

Phenotype Score: 0.506

Variant Score: 0.780

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17657041C>G [0/1] rs1454291605 (variation viewer)

Variant score: 0.780 CONTRIBUTING VARIANT

Transcripts:: STAM:ENST00000377524.8:c.41-3423C>G:p.(=)

Pathogenicity Data:: Best Score: 0.7801128; CADD: 0.780 (6.578)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.058

Phenotype Score: 0.506

Variant Score: 0.572

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17657041C>G [0/1] rs1454291605 (variation viewer)

Variant score: 0.780 CONTRIBUTING VARIANT

Transcripts:: STAM:ENST00000377524.8:c.41-3423C>G:p.(=)

Pathogenicity Data:: Best Score: 0.7801128; CADD: 0.780 (6.578)

Frequency Data:: TOPMed: 0.0016%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17706369C>CTT [-/1] rs59585445 (variation viewer)

Variant score: 0.364 CONTRIBUTING VARIANT

Transcripts:: STAM:ENST00000377524.8:c.1209+628_1209+629insTT:p.(=)

Pathogenicity Data:: Best Score: 0.36379075; CADD: 0.364 (1.964)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17706369C>CTTT [-/1] rs59585445 (variation viewer)

Variant score: 0.358

Transcripts:: STAM:ENST00000377524.8:c.1209+628_1209+629insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.35849506; CADD: 0.358 (1.928)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17669884C>CT [1/1] rs76381388 (variation viewer)

Variant score: 0.263

Transcripts:: STAM:ENST00000377524.8:c.125+9336_125+9337insT:p.(=)

Pathogenicity Data:: Best Score: 0.26345378; CADD: 0.263 (1.328)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17664147C>G [0/1] rs66927489 (variation viewer)

Variant score: 0.142

Transcripts:: STAM:ENST00000377524.8:c.125+3599C>G:p.(=)

Pathogenicity Data:: Best Score: 0.1519919; CADD: 0.152 (0.716)

Frequency Data:: 1000Genomes: 0.2396%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.2071%; gnomAD_G_OTH: 0.4090%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17666387ATT>A [0/1] rs10673746 (variation viewer)

Variant score: 0.139

Transcripts:: STAM:ENST00000377524.8:c.125+5840_125+5841del:p.(=)

Pathogenicity Data:: Best Score: 0.13880795; CADD: 0.139 (0.649)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.17686351T>C [0/1] rs76481764 (variation viewer)

Variant score: 0.082

Transcripts:: STAM:ENST00000377524.8:c.297+1424T>C:p.(=)

Pathogenicity Data:: Best Score: 0.08756906; CADD: 0.088 (0.398)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.1848%; UK10K: 0.2248%; gnomAD_G_AFR: 0.0345%; gnomAD_G_AMR: 0.1205%; gnomAD_G_NFE: 0.2070%; gnomAD_G_OTH: 0.4090%

CREM

Exomiser Score: 0.291

Phenotype Score: 0.504

Variant Score: 0.780

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving CREM.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.291

Phenotype Score: 0.504

Variant Score: 0.780

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.35164317T>C [0/1]

Variant score: 0.780 CONTRIBUTING VARIANT

Transcripts:: CREM:ENST00000337656.8:c.169-14572T>C:p.(=); CREM:ENST00000345491.7:c.169-14572T>C:p.(=); CREM:ENST00000348787.6:c.121-14572T>C:p.(=); CREM:ENST00000354759.7:c.169-14572T>C:p.(=); CREM:ENST00000374721.7:c.121-11536T>C:p.(=); CREM:ENST00000374726.7:c.121-14572T>C:p.(=); CREM:ENST00000374728.7:c.121-14572T>C:p.(=); CREM:ENST00000374734.7:c.169-14572T>C:p.(=); CREM:ENST00000429130.7:c.121-11536T>C:p.(=); CREM:ENST00000439705.5:c.169-14572T>C:p.(=); CREM:ENST00000479070.5:c.169-14572T>C:p.(=); CREM:ENST00000489321.5:c.121-14572T>C:p.(=); CREM:ENST00000460270.5:c.-15+37124T>C:p.(=); CREM:ENST00000474362.5:c.-15+37124T>C:p.(=)

Pathogenicity Data:: Best Score: 0.77965665; CADD: 0.780 (6.569)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.114

Phenotype Score: 0.504

Variant Score: 0.654

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.35164317T>C [0/1]

Variant score: 0.780 CONTRIBUTING VARIANT

Transcripts:: CREM:ENST00000337656.8:c.169-14572T>C:p.(=); CREM:ENST00000345491.7:c.169-14572T>C:p.(=); CREM:ENST00000348787.6:c.121-14572T>C:p.(=); CREM:ENST00000354759.7:c.169-14572T>C:p.(=); CREM:ENST00000374721.7:c.121-11536T>C:p.(=); CREM:ENST00000374726.7:c.121-14572T>C:p.(=); CREM:ENST00000374728.7:c.121-14572T>C:p.(=); CREM:ENST00000374734.7:c.169-14572T>C:p.(=); CREM:ENST00000429130.7:c.121-11536T>C:p.(=); CREM:ENST00000439705.5:c.169-14572T>C:p.(=); CREM:ENST00000479070.5:c.169-14572T>C:p.(=); CREM:ENST00000489321.5:c.121-14572T>C:p.(=); CREM:ENST00000460270.5:c.-15+37124T>C:p.(=); CREM:ENST00000474362.5:c.-15+37124T>C:p.(=)

Pathogenicity Data:: Best Score: 0.77965665; CADD: 0.780 (6.569)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.35148689C>T [0/1] rs146537690 (variation viewer)

Variant score: 0.528 CONTRIBUTING VARIANT

Transcripts:: CREM:ENST00000337656.8:c.168+198C>T:p.(=); CREM:ENST00000345491.7:c.168+198C>T:p.(=); CREM:ENST00000348787.6:c.120+198C>T:p.(=); CREM:ENST00000354759.7:c.168+198C>T:p.(=); CREM:ENST00000374721.7:c.120+198C>T:p.(=); CREM:ENST00000374726.7:c.120+198C>T:p.(=); CREM:ENST00000374728.7:c.120+198C>T:p.(=); CREM:ENST00000374734.7:c.168+198C>T:p.(=); CREM:ENST00000429130.7:c.120+198C>T:p.(=); CREM:ENST00000439705.5:c.168+198C>T:p.(=); CREM:ENST00000469949.6:c.120+198C>T:p.(=); CREM:ENST00000479070.5:c.168+198C>T:p.(=); CREM:ENST00000489321.5:c.120+198C>T:p.(=); CREM:ENST00000460270.5:c.-15+21496C>T:p.(=); CREM:ENST00000474362.5:c.-15+21496C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6147878; CADD: 0.615 (4.143)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.3719%; UK10K: 0.5290%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.4798%; gnomAD_G_OTH: 0.4073%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.35166598G>A [0/1] rs534912412 (variation viewer)

Variant score: 0.154

Transcripts:: CREM:ENST00000337656.8:c.169-12291G>A:p.(=); CREM:ENST00000345491.7:c.169-12291G>A:p.(=); CREM:ENST00000348787.6:c.121-12291G>A:p.(=); CREM:ENST00000354759.7:c.169-12291G>A:p.(=); CREM:ENST00000374721.7:c.121-9255G>A:p.(=); CREM:ENST00000374726.7:c.121-12291G>A:p.(=); CREM:ENST00000374728.7:c.121-12291G>A:p.(=); CREM:ENST00000374734.7:c.169-12291G>A:p.(=); CREM:ENST00000429130.7:c.121-9255G>A:p.(=); CREM:ENST00000439705.5:c.169-12291G>A:p.(=); CREM:ENST00000479070.5:c.169-12291G>A:p.(=); CREM:ENST00000489321.5:c.121-12291G>A:p.(=); CREM:ENST00000460270.5:c.-15+39405G>A:p.(=); CREM:ENST00000474362.5:c.-15+39405G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15491575; CADD: 0.155 (0.731)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0024%; gnomAD_G_NFE: 0.0068%

INTERGENIC_VARIANT chr10:g.35218869GA>G [0/1] rs200950328 (variation viewer)

Variant score: 0.153

Transcripts:: CREM:ENST00000348787.6::; CREM:ENST00000374706.5::

Pathogenicity Data:: Best Score: 0.17775732; CADD: 0.178 (0.850)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.3719%; UK10K: 0.5422%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.4931%; gnomAD_G_OTH: 0.5092%

SPTLC1

Exomiser Score: 0.289

Phenotype Score: 0.531

Variant Score: 0.748

Phenotype matches:

Proximity score 0.531 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:162400 Neuropathy, hereditary sensory and autonomic, type IA - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.289

Phenotype Score: 0.531

Variant Score: 0.748

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92050811A>ATTTTTTTTTTT [0/1] rs370967911 (variation viewer)

Variant score: 0.748 CONTRIBUTING VARIANT

Transcripts:: SPTLC1:ENST00000262554.7:c.781-745_781-744insAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.7480003; CADD: 0.748 (5.986)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.015

Phenotype Score: 0.265

Variant Score: 0.688

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92050811A>ATTTTTTTTTTT [0/1] rs370967911 (variation viewer)

Variant score: 0.748 CONTRIBUTING VARIANT

Transcripts:: SPTLC1:ENST00000262554.7:c.781-745_781-744insAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.7480003; CADD: 0.748 (5.986)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92034125G>A [0/1] rs951127379 (variation viewer)

Variant score: 0.628 CONTRIBUTING VARIANT

Transcripts:: SPTLC1:ENST00000262554.7:c.1328+685C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6283792; CADD: 0.628 (4.299)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92045524T>TA [0/1] rs71362367 (variation viewer)

Variant score: 0.592

Transcripts:: SPTLC1:ENST00000262554.7:c.1136+474_1136+475insT:p.(=)

Pathogenicity Data:: Best Score: 0.59186864; CADD: 0.592 (3.892)

Frequency Data:: No frequency data

UHRF2

Exomiser Score: 0.289

Phenotype Score: 0.503

Variant Score: 0.779

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.289

Phenotype Score: 0.503

Variant Score: 0.779

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.6441175T>G [0/1] rs1006833793 (variation viewer)

Variant score: 0.779 CONTRIBUTING VARIANT

Transcripts:: UHRF2:ENST00000276893.10:c.644+7002T>G:p.(=)

Pathogenicity Data:: Best Score: 0.779352; CADD: 0.779 (6.563)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.184

Phenotype Score: 0.503

Variant Score: 0.715

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.6441175T>G [0/1] rs1006833793 (variation viewer)

Variant score: 0.779 CONTRIBUTING VARIANT

Transcripts:: UHRF2:ENST00000276893.10:c.644+7002T>G:p.(=)

Pathogenicity Data:: Best Score: 0.779352; CADD: 0.779 (6.563)

Frequency Data:: TOPMed: 0.0008%

REGULATORY_REGION_VARIANT chr9:g.6681108G>A [0/1] rs560827314 (variation viewer)

Variant score: 0.651 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.663953; CADD: 0.664 (4.736)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0733%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0666%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.6492832C>CT [0/1] rs34371545 (variation viewer)

Variant score: 0.307

Transcripts:: UHRF2:ENST00000276893.10:c.1498-994_1498-993insT:p.(=)

Pathogenicity Data:: Best Score: 0.30673385; CADD: 0.307 (1.591)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr9:g.6508208A>G [0/1] rs1474337276 (variation viewer)

Variant score: 0.239

Transcripts:: UHRF2:ENST00000276893.10::; UHRF2:ENST00000321612.7::

Pathogenicity Data:: Best Score: 0.23897308; CADD: 0.239 (1.186)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.6445981C>CT [1/1] rs57147850 (variation viewer)

Variant score: 0.226

Transcripts:: UHRF2:ENST00000276893.10:c.644+11808_644+11809insT:p.(=)

Pathogenicity Data:: Best Score: 0.22589475; CADD: 0.226 (1.112)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.6428533CTTTTTTTTTTTTTT>C [1/1] rs1171172143 (variation viewer)

Variant score: 0.189

Transcripts:: UHRF2:ENST00000276893.10:c.385-5380_385-5367del:p.(=)

Pathogenicity Data:: Best Score: 0.18903893; CADD: 0.189 (0.910)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.6484785C>CT [1/1] rs34815980 (variation viewer)

Variant score: 0.148

Transcripts:: UHRF2:ENST00000276893.10:c.1393-2036_1393-2035insT:p.(=)

Pathogenicity Data:: Best Score: 0.14768523; CADD: 0.148 (0.694)

Frequency Data:: No frequency data

SLC25A13

Exomiser Score: 0.282

Phenotype Score: 0.683

Variant Score: 0.572

Phenotype matches:

Phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

Proximity score 0.500 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:603471 Citrullinemia, adult-onset type II - autosomal recessive; OMIM:605814 Citrullinemia, type II, neonatal-onset - autosomal recessive; ORPHA:247585 Citrullinemia type II; ORPHA:247598 Neonatal intrahepatic cholestasis due to citrin deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.082

Phenotype Score: 0.341

Variant Score: 0.797

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96224280A>C [0/1] rs1379443672 (variation viewer)

Variant score: 0.797 CONTRIBUTING VARIANT

Transcripts:: SLC25A13:ENST00000265631.9:c.328+10522T>G:p.(=); SLC25A13:ENST00000416240.6:c.328+10522T>G:p.(=)

Pathogenicity Data:: Best Score: 0.80411553; CADD: 0.804 (7.080)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_EAS: 0.0617%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.282

Phenotype Score: 0.683

Variant Score: 0.572

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96224280A>C [0/1] rs1379443672 (variation viewer)

Variant score: 0.797 CONTRIBUTING VARIANT

Transcripts:: SLC25A13:ENST00000265631.9:c.328+10522T>G:p.(=); SLC25A13:ENST00000416240.6:c.328+10522T>G:p.(=)

Pathogenicity Data:: Best Score: 0.80411553; CADD: 0.804 (7.080)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_EAS: 0.0617%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96128939G>GCTCTCTCT [-/1] rs58984088 (variation viewer)

Variant score: 0.347 CONTRIBUTING VARIANT

Transcripts:: SLC25A13:ENST00000265631.9:c.1591+2803_1591+2804insAGAGAGAG:p.(=); SLC25A13:ENST00000416240.6:c.1594+2803_1594+2804insAGAGAGAG:p.(=)

Pathogenicity Data:: Best Score: 0.3474707; CADD: 0.347 (1.854)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96128939GCT>G [-/1] rs58984088 (variation viewer)

Variant score: 0.343

Transcripts:: SLC25A13:ENST00000265631.9:c.1591+2802_1591+2803del:p.(=); SLC25A13:ENST00000416240.6:c.1594+2802_1594+2803del:p.(=)

Pathogenicity Data:: Best Score: 0.34309888; CADD: 0.343 (1.825)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96319540C>CAAAA [0/1] rs747583933 (variation viewer)

Variant score: 0.195

Transcripts:: SLC25A13:ENST00000265631.9:c.15+2401_15+2402insTTTT:p.(=); SLC25A13:ENST00000416240.6:c.15+2401_15+2402insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.19610375; CADD: 0.196 (0.948)

Frequency Data:: gnomAD_G_NFE: 0.0329%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96194442C>CAAAA [1/1] rs546248549 (variation viewer)

Variant score: 0.113

Transcripts:: SLC25A13:ENST00000265631.9:c.469-1260_469-1259insTTTT:p.(=); SLC25A13:ENST00000416240.6:c.469-1260_469-1259insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.11345661; CADD: 0.113 (0.523)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.96217913C>* [-/1]

Variant score: 0.000

Transcripts:: SLC25A13:ENST00000265631.9:c.329-8936G>:p.(=); SLC25A13:ENST00000416240.6:c.329-8936G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TFDP2

Exomiser Score: 0.264

Phenotype Score: 0.503

Variant Score: 0.766

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.139

Phenotype Score: 0.503

Variant Score: 0.679

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.141997174G>A [0/1] rs1261608776 (variation viewer)

Variant score: 0.679 CONTRIBUTING VARIANT

Transcripts:: TFDP2:ENST00000467072.5:c.4-2033C>T:p.(=); TFDP2:ENST00000479040.5:c.4-2033C>T:p.(=); TFDP2:ENST00000486111.5:c.4-2033C>T:p.(=); TFDP2:ENST00000489671.5:c.187-2033C>T:p.(=); TFDP2:ENST00000495310.5:c.18-3589C>T:p.(=); TFDP2:ENST00000499676.5:c.103-2033C>T:p.(=); TFDP2:ENST00000477292.5:c.-52-18492C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6798157; CADD: 0.680 (4.946)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.264

Phenotype Score: 0.503

Variant Score: 0.766

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.142105371T>C [0/1] rs554345661 (variation viewer)

Variant score: 0.853 CONTRIBUTING VARIANT

Transcripts:: TFDP2:ENST00000467072.5:c.-310-3530A>G:p.(=); TFDP2:ENST00000489671.5:c.-92-3530A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8681743; CADD: 0.868 (8.800)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.0558%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0999%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.141997174G>A [0/1] rs1261608776 (variation viewer)

Variant score: 0.679 CONTRIBUTING VARIANT

Transcripts:: TFDP2:ENST00000467072.5:c.4-2033C>T:p.(=); TFDP2:ENST00000479040.5:c.4-2033C>T:p.(=); TFDP2:ENST00000486111.5:c.4-2033C>T:p.(=); TFDP2:ENST00000489671.5:c.187-2033C>T:p.(=); TFDP2:ENST00000495310.5:c.18-3589C>T:p.(=); TFDP2:ENST00000499676.5:c.103-2033C>T:p.(=); TFDP2:ENST00000477292.5:c.-52-18492C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6798157; CADD: 0.680 (4.946)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr3:g.141940650G>T [0/1] rs1273595388 (variation viewer)

Variant score: 0.670

Transcripts:: TFDP2:ENST00000489671.5::; TFDP2:ENST00000286371.8::

Pathogenicity Data:: Best Score: 0.6709969; CADD: 0.671 (4.828)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.142073457A>ACC [0/1] rs34003718 (variation viewer)

Variant score: 0.309

Transcripts:: TFDP2:ENST00000489671.5:c.82+19603_82+19604insGG:p.(=); TFDP2:ENST00000467072.5:c.-136-19309_-136-19308insGG:p.(=)

Pathogenicity Data:: Best Score: 0.30912417; CADD: 0.309 (1.606)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.142089271G>A [0/1] rs548832841 (variation viewer)

Variant score: 0.280

Transcripts:: TFDP2:ENST00000489671.5:c.82+3790C>T:p.(=); TFDP2:ENST00000467072.5:c.-137+3790C>T:p.(=)

Pathogenicity Data:: Best Score: 0.28616148; CADD: 0.286 (1.464)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1398%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0358%; gnomAD_G_NFE: 0.0910%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.141985519CA>C [0/1] rs61684289 (variation viewer)

Variant score: 0.264

Transcripts:: TFDP2:ENST00000467072.5:c.174-6838del:p.(=); TFDP2:ENST00000479040.5:c.174-6838del:p.(=); TFDP2:ENST00000486111.5:c.174-6838del:p.(=); TFDP2:ENST00000489671.5:c.357-6838del:p.(=); TFDP2:ENST00000495310.5:c.66-6838del:p.(=); TFDP2:ENST00000499676.5:c.273-6838del:p.(=); TFDP2:ENST00000477292.5:c.-52-6838del:p.(=)

Pathogenicity Data:: Best Score: 0.26447064; CADD: 0.264 (1.334)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.142036970A>C [0/1] rs141981362 (variation viewer)

Variant score: 0.188

Transcripts:: TFDP2:ENST00000489671.5:c.83-31426T>G:p.(=); TFDP2:ENST00000467072.5:c.-102+17145T>G:p.(=)

Pathogenicity Data:: Best Score: 0.19202113; CADD: 0.192 (0.926)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.0565%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0933%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.141973123A>ATTTT [0/1] rs761950988 (variation viewer)

Variant score: 0.160

Transcripts:: TFDP2:ENST00000467072.5:c.483+924_483+925insAAAA:p.(=); TFDP2:ENST00000477292.5:c.255+924_255+925insAAAA:p.(=); TFDP2:ENST00000479040.5:c.480+924_480+925insAAAA:p.(=); TFDP2:ENST00000486111.5:c.483+924_483+925insAAAA:p.(=); TFDP2:ENST00000489671.5:c.663+924_663+925insAAAA:p.(=); TFDP2:ENST00000495310.5:c.372+924_372+925insAAAA:p.(=); TFDP2:ENST00000499676.5:c.579+924_579+925insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.1597665; CADD: 0.160 (0.756)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.141974907CT>C [0/1] rs753702830 (variation viewer)

Variant score: 0.103

Transcripts:: TFDP2:ENST00000467072.5:c.337-714del:p.(=); TFDP2:ENST00000477292.5:c.112-717del:p.(=); TFDP2:ENST00000479040.5:c.337-717del:p.(=); TFDP2:ENST00000486111.5:c.337-714del:p.(=); TFDP2:ENST00000489671.5:c.520-717del:p.(=); TFDP2:ENST00000495310.5:c.229-717del:p.(=); TFDP2:ENST00000499676.5:c.436-717del:p.(=)

Pathogenicity Data:: Best Score: 0.10298437; CADD: 0.103 (0.472)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.141969080TA>T [0|1] rs1407800511 (variation viewer)

Variant score: 0.087

Transcripts:: TFDP2:ENST00000467072.5:c.552+992del:p.(=); TFDP2:ENST00000477292.5:c.324+992del:p.(=); TFDP2:ENST00000479040.5:c.549+992del:p.(=); TFDP2:ENST00000486111.5:c.552+992del:p.(=); TFDP2:ENST00000489671.5:c.732+992del:p.(=); TFDP2:ENST00000495310.5:c.441+992del:p.(=); TFDP2:ENST00000499676.5:c.648+992del:p.(=)

Pathogenicity Data:: Best Score: 0.087148786; CADD: 0.087 (0.396)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.142050646C>T [0/1] rs544439423 (variation viewer)

Variant score: 0.027

Transcripts:: TFDP2:ENST00000489671.5:c.82+42415G>A:p.(=); TFDP2:ENST00000467072.5:c.-102+3469G>A:p.(=)

Pathogenicity Data:: Best Score: 0.026804686; CADD: 0.027 (0.118)

Frequency Data:: TOPMed: 0.0032%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0116%

UQCRC1

Exomiser Score: 0.262

Phenotype Score: 0.514

Variant Score: 0.753

Phenotype matches:

Proximity score 0.514 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.262

Phenotype Score: 0.514

Variant Score: 0.753

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr3:g.48610704C>CA [0/1] rs758150793 (variation viewer)

Variant score: 0.753 CONTRIBUTING VARIANT

Transcripts:: UQCRC1:ENST00000203407.6::; UQCRC1:ENST00000330862.4::

Pathogenicity Data:: Best Score: 0.75254285; CADD: 0.753 (6.065)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.226

Phenotype Score: 0.514

Variant Score: 0.731

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr3:g.48610704C>CA [0/1] rs758150793 (variation viewer)

Variant score: 0.753 CONTRIBUTING VARIANT

Transcripts:: UQCRC1:ENST00000203407.6::; UQCRC1:ENST00000330862.4::

Pathogenicity Data:: Best Score: 0.75254285; CADD: 0.753 (6.065)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr3:g.48611907C>G [0/1] rs113892128 (variation viewer)

Variant score: 0.710 CONTRIBUTING VARIANT

Transcripts:: UQCRC1:ENST00000203407.6::; UQCRC1:ENST00000330862.4::

Pathogenicity Data:: Best Score: 0.95574117; CADD: 0.956 (13.540)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.4396%; UK10K: 0.0661%; gnomAD_G_AFR: 1.0660%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0801%; gnomAD_G_OTH: 0.3080%

Other passed variants:

UPSTREAM_GENE_VARIANT chr3:g.48613277T>C [0/1] rs184871825 (variation viewer)

Variant score: 0.261

Transcripts:: UQCRC1:ENST00000203407.6::; UQCRC1:ENST00000330862.4::

Pathogenicity Data:: Best Score: 0.35419708; CADD: 0.354 (1.899)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.4468%; gnomAD_G_AFR: 1.0771%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0809%; gnomAD_G_OTH: 0.4149%

SPATA5

Exomiser Score: 0.262

Phenotype Score: 0.506

Variant Score: 0.761

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616577 Epilepsy, hearing loss, and mental retardation syndrome - autosomal recessive; ORPHA:457351 Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.222

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.122939071CTT>C [0|1] rs201897478 (variation viewer)

Variant score: 0.222 CONTRIBUTING VARIANT

Transcripts:: SPATA5:ENST00000274008.5:c.1458+823_1458+824del:p.(=)

Pathogenicity Data:: Best Score: 0.22214258; CADD: 0.222 (1.091)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.262

Phenotype Score: 0.506

Variant Score: 0.761

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123051640C>CT [1/1] rs61142992 (variation viewer)

Variant score: 0.761 CONTRIBUTING VARIANT

Transcripts:: SPATA5:ENST00000274008.5:c.2080-4747_2080-4746insT:p.(=)

Pathogenicity Data:: Best Score: 0.76143867; CADD: 0.761 (6.224)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123216539T>G [0/1] rs181869014 (variation viewer)

Variant score: 0.523

Transcripts:: SPATA5:ENST00000274008.5:c.2341-39477T>G:p.(=)

Pathogenicity Data:: Best Score: 0.59876394; CADD: 0.599 (3.966)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2684%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1724%; gnomAD_G_NFE: 0.4596%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123074095A>ATTTTTTTT [1/1] rs397995242 (variation viewer)

Variant score: 0.445

Transcripts:: SPATA5:ENST00000274008.5:c.2214-16484_2214-16483insTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.44499105; CADD: 0.445 (2.557)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123007490G>C [0/1] rs573671833 (variation viewer)

Variant score: 0.377

Transcripts:: SPATA5:ENST00000274008.5:c.1870-20696G>C:p.(=)

Pathogenicity Data:: Best Score: 0.43597287; CADD: 0.436 (2.487)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0998%; gnomAD_G_ASJ: 0.6897%; gnomAD_G_NFE: 0.0415%; gnomAD_G_OTH: 0.2160%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123184532C>CTTTT [1/1] rs34331725 (variation viewer)

Variant score: 0.267

Transcripts:: SPATA5:ENST00000274008.5:c.2341-71484_2341-71483insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.26650017; CADD: 0.267 (1.346)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123015976C>T [1|1] rs112520316 (variation viewer)

Variant score: 0.253

Transcripts:: SPATA5:ENST00000274008.5:c.1870-12210C>T:p.(=)

Pathogenicity Data:: Best Score: 0.56508934; CADD: 0.565 (3.616)

Frequency Data:: gnomAD_G_FIN: 1.2821%; gnomAD_G_NFE: 1.6245%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123017414ATTTTTTTTTTTTT>A [1/1] rs55688914 (variation viewer)

Variant score: 0.245

Transcripts:: SPATA5:ENST00000274008.5:c.1870-10771_1870-10759del:p.(=)

Pathogenicity Data:: Best Score: 0.24455994; CADD: 0.245 (1.218)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123166916A>G [0/1] rs142029997 (variation viewer)

Variant score: 0.191

Transcripts:: SPATA5:ENST00000274008.5:c.2340+76211A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4472866; CADD: 0.447 (2.575)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.1951%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.4843%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0292%; gnomAD_G_NFE: 0.2065%; gnomAD_G_OTH: 0.4132%

DOWNSTREAM_GENE_VARIANT chr4:g.123321196CA>C [0/1] rs558399095 (variation viewer)

Variant score: 0.162

Transcripts:: SPATA5:ENST00000274008.5::; SPATA5:ENST00000651917.1::

Pathogenicity Data:: Best Score: 0.22428894; CADD: 0.224 (1.103)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.3594%; gnomAD_G_AFR: 0.0115%; gnomAD_G_EAS: 1.1139%; gnomAD_G_FIN: 0.1271%; gnomAD_G_NFE: 0.1409%; gnomAD_G_OTH: 0.2105%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123232368A>G [0/1] rs182679991 (variation viewer)

Variant score: 0.127

Transcripts:: SPATA5:ENST00000274008.5:c.2341-23648A>G:p.(=)

Pathogenicity Data:: Best Score: 0.14552373; CADD: 0.146 (0.683)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2676%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1719%; gnomAD_G_NFE: 0.4606%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123173340GTTTTT>G [1/1] rs59541277 (variation viewer)

Variant score: 0.106

Transcripts:: SPATA5:ENST00000274008.5:c.2340+82636_2340+82640del:p.(=)

Pathogenicity Data:: Best Score: 0.105665445; CADD: 0.106 (0.485)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.122998839G>T [0/1] rs546037591 (variation viewer)

Variant score: 0.090

Transcripts:: SPATA5:ENST00000274008.5:c.1869+19453G>T:p.(=)

Pathogenicity Data:: Best Score: 0.14394832; CADD: 0.144 (0.675)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.1441%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1599%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123179307CTACTTACT>C [-/1] rs140649085 (variation viewer)

Variant score: 0.079

Transcripts:: SPATA5:ENST00000274008.5:c.2341-76708_2341-76701del:p.(=)

Pathogenicity Data:: Best Score: 0.095309556; CADD: 0.095 (0.435)

Frequency Data:: gnomAD_G_AFR: 0.1758%; gnomAD_G_AMR: 0.2469%; gnomAD_G_ASJ: 0.6849%; gnomAD_G_EAS: 0.1274%; gnomAD_G_FIN: 0.8069%; gnomAD_G_NFE: 0.5353%; gnomAD_G_OTH: 0.6316%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123189809C>CTT [1/1] rs1164117146 (variation viewer)

Variant score: 0.064

Transcripts:: SPATA5:ENST00000274008.5:c.2341-66207_2341-66206insTT:p.(=)

Pathogenicity Data:: Best Score: 0.063516796; CADD: 0.064 (0.285)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.123109809G>A [0/1] rs191474395 (variation viewer)

Variant score: 0.046

Transcripts:: SPATA5:ENST00000274008.5:c.2340+19104G>A:p.(=)

Pathogenicity Data:: Best Score: 0.04676497; CADD: 0.047 (0.208)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0868%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0229%; gnomAD_G_FIN: 0.0861%; gnomAD_G_NFE: 0.1203%; gnomAD_G_OTH: 0.1018%

CACNA1C

Exomiser Score: 0.250

Phenotype Score: 0.506

Variant Score: 0.755

Phenotype matches:

Phenotypic similarity 0.383 to mouse mutant involving CACNA1C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Proximity score 0.506 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:601005 Timothy syndrome - autosomal dominant; OMIM:611875 Brugada syndrome 3 - autosomal dominant; ORPHA:101016 Romano-Ward syndrome; ORPHA:130 Brugada syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.250

Phenotype Score: 0.506

Variant Score: 0.755

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2660196G>A [0/1]

Variant score: 0.755 CONTRIBUTING VARIANT

Transcripts:: CACNA1C:ENST00000327702.12:c.4233-4629G>A:p.(=); CACNA1C:ENST00000335762.9:c.4308-4629G>A:p.(=); CACNA1C:ENST00000344100.7:c.4299-4629G>A:p.(=); CACNA1C:ENST00000347598.9:c.4377-4629G>A:p.(=); CACNA1C:ENST00000399591.5:c.4200-4629G>A:p.(=); CACNA1C:ENST00000399595.5:c.4200-4629G>A:p.(=); CACNA1C:ENST00000399597.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399601.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399603.6:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399606.5:c.4293-4629G>A:p.(=); CACNA1C:ENST00000399617.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399621.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399629.5:c.4284-4629G>A:p.(=); CACNA1C:ENST00000399634.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399637.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399638.5:c.4317-4629G>A:p.(=); CACNA1C:ENST00000399641.6:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399644.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399649.5:c.4194-4629G>A:p.(=); CACNA1C:ENST00000399655.6:c.4233-4629G>A:p.(=); CACNA1C:ENST00000402845.7:c.4233-4629G>A:p.(=); CACNA1C:ENST00000406454.7:c.4233-4629G>A:p.(=); CACNA1C:ENST00000366455.3:n.260G>A:

Pathogenicity Data:: Best Score: 0.7545856; CADD: 0.755 (6.101)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.124

Phenotype Score: 0.506

Variant Score: 0.661

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2660196G>A [0/1]

Variant score: 0.755 CONTRIBUTING VARIANT

Transcripts:: CACNA1C:ENST00000327702.12:c.4233-4629G>A:p.(=); CACNA1C:ENST00000335762.9:c.4308-4629G>A:p.(=); CACNA1C:ENST00000344100.7:c.4299-4629G>A:p.(=); CACNA1C:ENST00000347598.9:c.4377-4629G>A:p.(=); CACNA1C:ENST00000399591.5:c.4200-4629G>A:p.(=); CACNA1C:ENST00000399595.5:c.4200-4629G>A:p.(=); CACNA1C:ENST00000399597.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399601.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399603.6:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399606.5:c.4293-4629G>A:p.(=); CACNA1C:ENST00000399617.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399621.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399629.5:c.4284-4629G>A:p.(=); CACNA1C:ENST00000399634.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399637.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399638.5:c.4317-4629G>A:p.(=); CACNA1C:ENST00000399641.6:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399644.5:c.4233-4629G>A:p.(=); CACNA1C:ENST00000399649.5:c.4194-4629G>A:p.(=); CACNA1C:ENST00000399655.6:c.4233-4629G>A:p.(=); CACNA1C:ENST00000402845.7:c.4233-4629G>A:p.(=); CACNA1C:ENST00000406454.7:c.4233-4629G>A:p.(=); CACNA1C:ENST00000366455.3:n.260G>A:

Pathogenicity Data:: Best Score: 0.7545856; CADD: 0.755 (6.101)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2441803A>G [0/1] rs535721221 (variation viewer)

Variant score: 0.568 CONTRIBUTING VARIANT

Transcripts:: CACNA1C:ENST00000327702.12:c.478-7173A>G:p.(=); CACNA1C:ENST00000335762.9:c.478-7173A>G:p.(=); CACNA1C:ENST00000344100.7:c.478-7173A>G:p.(=); CACNA1C:ENST00000347598.9:c.478-7173A>G:p.(=); CACNA1C:ENST00000399591.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399595.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399597.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399601.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399603.6:c.478-7173A>G:p.(=); CACNA1C:ENST00000399606.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399617.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399621.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399629.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399634.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399637.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399638.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399641.6:c.478-7173A>G:p.(=); CACNA1C:ENST00000399644.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399649.5:c.478-7173A>G:p.(=); CACNA1C:ENST00000399655.6:c.478-7173A>G:p.(=); CACNA1C:ENST00000402845.7:c.478-7173A>G:p.(=); CACNA1C:ENST00000406454.7:c.478-7173A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5677848; CADD: 0.568 (3.643)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2378228A>T [0/1] rs182592937 (variation viewer)

Variant score: 0.557

Transcripts:: CACNA1C:ENST00000327702.12:c.478-70748A>T:p.(=); CACNA1C:ENST00000335762.9:c.478-70748A>T:p.(=); CACNA1C:ENST00000344100.7:c.478-70748A>T:p.(=); CACNA1C:ENST00000347598.9:c.478-70748A>T:p.(=); CACNA1C:ENST00000399591.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399595.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399597.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399601.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399603.6:c.478-70748A>T:p.(=); CACNA1C:ENST00000399606.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399617.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399621.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399629.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399634.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399637.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399638.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399641.6:c.478-70748A>T:p.(=); CACNA1C:ENST00000399644.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399649.5:c.478-70748A>T:p.(=); CACNA1C:ENST00000399655.6:c.478-70748A>T:p.(=); CACNA1C:ENST00000402845.7:c.478-70748A>T:p.(=); CACNA1C:ENST00000406454.7:c.478-70748A>T:p.(=)

Pathogenicity Data:: Best Score: 0.87996715; CADD: 0.880 (9.207)

Frequency Data:: 1000Genomes: 0.9385%; TOPMed: 0.6745%; UK10K: 1.0050%; gnomAD_G_AFR: 0.1950%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.9200%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2280415GACCTCTTGATACCTTGCTGTGCTTCGGTTTA>G [0/1] rs1357924208 (variation viewer)

Variant score: 0.509

Transcripts:: CACNA1C:ENST00000327702.12:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000335762.9:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000344100.7:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000347598.9:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399591.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399595.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399597.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399601.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399603.6:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399606.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399617.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399621.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399629.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399634.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399637.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399638.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399641.6:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399644.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399649.5:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000399655.6:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000402845.7:c.477+159986_477+160016del:p.(=); CACNA1C:ENST00000406454.7:c.477+159986_477+160016del:p.(=)

Pathogenicity Data:: Best Score: 0.50920516; CADD: 0.509 (3.091)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2589783A>T [0/1] rs957448657 (variation viewer)

Variant score: 0.373

Transcripts:: CACNA1C:ENST00000327702.12:c.2531-3430A>T:p.(=); CACNA1C:ENST00000335762.9:c.2606-3430A>T:p.(=); CACNA1C:ENST00000344100.7:c.2531-3430A>T:p.(=); CACNA1C:ENST00000347598.9:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399591.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399595.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399597.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399601.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399603.6:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399606.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399617.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399621.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399629.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399634.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399637.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399638.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399641.6:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399644.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399649.5:c.2531-3430A>T:p.(=); CACNA1C:ENST00000399655.6:c.2531-3430A>T:p.(=); CACNA1C:ENST00000402845.7:c.2531-3430A>T:p.(=); CACNA1C:ENST00000406454.7:c.2531-3430A>T:p.(=)

Pathogenicity Data:: Best Score: 0.37338614; CADD: 0.373 (2.030)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_NFE: 0.0072%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2497969T>TCACACACACACACACA [-/1] rs3058710 (variation viewer)

Variant score: 0.341

Transcripts:: CACNA1C:ENST00000327702.12:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000335762.9:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000344100.7:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000347598.9:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399591.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399595.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399597.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399601.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399603.6:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399606.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399617.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399621.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399629.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399634.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399637.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399638.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399641.6:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399644.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399649.5:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000399655.6:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000402845.7:c.1113+4583_1113+4584insCACACACACACACACA:p.(=); CACNA1C:ENST00000406454.7:c.1113+4583_1113+4584insCACACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.34052247; CADD: 0.341 (1.808)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2668479A>G [0/1] rs116896129 (variation viewer)

Variant score: 0.323

Transcripts:: CACNA1C:ENST00000327702.12:c.4624-454A>G:p.(=); CACNA1C:ENST00000335762.9:c.4699-454A>G:p.(=); CACNA1C:ENST00000344100.7:c.4690-454A>G:p.(=); CACNA1C:ENST00000347598.9:c.4768-454A>G:p.(=); CACNA1C:ENST00000399591.5:c.4591-454A>G:p.(=); CACNA1C:ENST00000399595.5:c.4591-454A>G:p.(=); CACNA1C:ENST00000399597.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399601.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399603.6:c.4624-454A>G:p.(=); CACNA1C:ENST00000399606.5:c.4684-454A>G:p.(=); CACNA1C:ENST00000399617.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399621.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399629.5:c.4675-454A>G:p.(=); CACNA1C:ENST00000399634.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399637.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399638.5:c.4708-454A>G:p.(=); CACNA1C:ENST00000399641.6:c.4624-454A>G:p.(=); CACNA1C:ENST00000399644.5:c.4624-454A>G:p.(=); CACNA1C:ENST00000399649.5:c.4585-454A>G:p.(=); CACNA1C:ENST00000399655.6:c.4624-454A>G:p.(=); CACNA1C:ENST00000402845.7:c.4624-454A>G:p.(=); CACNA1C:ENST00000406454.7:c.4624-454A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5988563; CADD: 0.599 (3.967)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.7773%; UK10K: 1.4811%; gnomAD_G_AFR: 0.3668%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.6594%; gnomAD_G_NFE: 1.3218%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2639218G>A [0/1] rs746518126 (variation viewer)

Variant score: 0.315

Transcripts:: CACNA1C:ENST00000327702.12:c.3912+4838G>A:p.(=); CACNA1C:ENST00000335762.9:c.3987+4838G>A:p.(=); CACNA1C:ENST00000344100.7:c.3912+4838G>A:p.(=); CACNA1C:ENST00000347598.9:c.4056+4838G>A:p.(=); CACNA1C:ENST00000399591.5:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399595.5:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399597.5:c.3912+5506G>A:p.(=); CACNA1C:ENST00000399601.5:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399603.6:c.3912+5506G>A:p.(=); CACNA1C:ENST00000399606.5:c.3972+4838G>A:p.(=); CACNA1C:ENST00000399617.5:c.3912+5506G>A:p.(=); CACNA1C:ENST00000399621.5:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399629.5:c.3996+4838G>A:p.(=); CACNA1C:ENST00000399634.5:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399637.5:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399638.5:c.3996+4838G>A:p.(=); CACNA1C:ENST00000399641.6:c.3912+4838G>A:p.(=); CACNA1C:ENST00000399644.5:c.3912+5506G>A:p.(=); CACNA1C:ENST00000399649.5:c.3906+4844G>A:p.(=); CACNA1C:ENST00000399655.6:c.3912+4838G>A:p.(=); CACNA1C:ENST00000402845.7:c.3912+5506G>A:p.(=); CACNA1C:ENST00000406454.7:c.3912+5506G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3209527; CADD: 0.321 (1.681)

Frequency Data:: TOPMed: 0.0366%; UK10K: 0.0132%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0133%

INTERGENIC_VARIANT chr12:g.2041270C>CTT [-/1] rs58922699 (variation viewer)

Variant score: 0.313

Transcripts:: CACNA1C:ENST00000327702.12::

Pathogenicity Data:: Best Score: 0.31308973; CADD: 0.313 (1.631)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr12:g.2041270C>CTTT [-/1] rs58922699 (variation viewer)

Variant score: 0.308

Transcripts:: CACNA1C:ENST00000327702.12::

Pathogenicity Data:: Best Score: 0.308169; CADD: 0.308 (1.600)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2229751C>T [0/1] rs117504042 (variation viewer)

Variant score: 0.298

Transcripts:: CACNA1C:ENST00000327702.12:c.477+109321C>T:p.(=); CACNA1C:ENST00000335762.9:c.477+109321C>T:p.(=); CACNA1C:ENST00000344100.7:c.477+109321C>T:p.(=); CACNA1C:ENST00000347598.9:c.477+109321C>T:p.(=); CACNA1C:ENST00000399591.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399595.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399597.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399601.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399603.6:c.477+109321C>T:p.(=); CACNA1C:ENST00000399606.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399617.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399621.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399629.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399634.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399637.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399638.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399641.6:c.477+109321C>T:p.(=); CACNA1C:ENST00000399644.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399649.5:c.477+109321C>T:p.(=); CACNA1C:ENST00000399655.6:c.477+109321C>T:p.(=); CACNA1C:ENST00000402845.7:c.477+109321C>T:p.(=); CACNA1C:ENST00000406454.7:c.477+109321C>T:p.(=)

Pathogenicity Data:: Best Score: 0.35016966; CADD: 0.350 (1.872)

Frequency Data:: 1000Genomes: 0.7388%; TOPMed: 0.4953%; UK10K: 0.7009%; gnomAD_G_AFR: 0.1604%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1717%; gnomAD_G_NFE: 0.7337%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2321714T>C [0/1] rs187423074 (variation viewer)

Variant score: 0.242

Transcripts:: CACNA1C:ENST00000327702.12:c.478-127262T>C:p.(=); CACNA1C:ENST00000335762.9:c.478-127262T>C:p.(=); CACNA1C:ENST00000344100.7:c.478-127262T>C:p.(=); CACNA1C:ENST00000347598.9:c.478-127262T>C:p.(=); CACNA1C:ENST00000399591.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399595.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399597.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399601.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399603.6:c.478-127262T>C:p.(=); CACNA1C:ENST00000399606.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399617.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399621.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399629.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399634.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399637.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399638.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399641.6:c.478-127262T>C:p.(=); CACNA1C:ENST00000399644.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399649.5:c.478-127262T>C:p.(=); CACNA1C:ENST00000399655.6:c.478-127262T>C:p.(=); CACNA1C:ENST00000402845.7:c.478-127262T>C:p.(=); CACNA1C:ENST00000406454.7:c.478-127262T>C:p.(=)

Pathogenicity Data:: Best Score: 0.3140381; CADD: 0.314 (1.637)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.5423%; UK10K: 0.7934%; gnomAD_G_AFR: 0.1032%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.4293%; gnomAD_G_NFE: 0.6537%; gnomAD_G_OTH: 0.6160%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2071172C>CCCTGCCTG [1/1] rs767264073 (variation viewer)

Variant score: 0.211

Transcripts:: CACNA1C:ENST00000327702.12:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000335762.9:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000344100.7:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000347598.9:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399591.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399595.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399597.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399601.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399603.6:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399606.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399617.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399621.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399629.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399634.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399637.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399638.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399641.6:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399644.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399649.5:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000399655.6:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000402845.7:c.49+17561_49+17562insCCTGCCTG:p.(=); CACNA1C:ENST00000406454.7:c.49+17561_49+17562insCCTGCCTG:p.(=)

Pathogenicity Data:: Best Score: 0.21059477; CADD: 0.211 (1.027)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2611057G>A [0/1] rs216002 (variation viewer)

Variant score: 0.204

Transcripts:: CACNA1C:ENST00000327702.12:c.3717+358G>A:p.(=); CACNA1C:ENST00000335762.9:c.3792+358G>A:p.(=); CACNA1C:ENST00000344100.7:c.3717+358G>A:p.(=); CACNA1C:ENST00000347598.9:c.3777+358G>A:p.(=); CACNA1C:ENST00000399591.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399595.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399597.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399601.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399603.6:c.3717+358G>A:p.(=); CACNA1C:ENST00000399606.5:c.3777+358G>A:p.(=); CACNA1C:ENST00000399617.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399621.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399629.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399634.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399637.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399638.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399641.6:c.3717+358G>A:p.(=); CACNA1C:ENST00000399644.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399649.5:c.3717+358G>A:p.(=); CACNA1C:ENST00000399655.6:c.3717+358G>A:p.(=); CACNA1C:ENST00000402845.7:c.3717+358G>A:p.(=); CACNA1C:ENST00000406454.7:c.3717+358G>A:p.(=)

Pathogenicity Data:: Best Score: 0.21602899; CADD: 0.216 (1.057)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1198%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0251%; gnomAD_G_AMR: 0.1425%; gnomAD_G_FIN: 0.1020%; gnomAD_G_NFE: 0.0658%; gnomAD_G_OTH: 0.3480%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2090310C>CT [1/1] rs145675982 (variation viewer)

Variant score: 0.186

Transcripts:: CACNA1C:ENST00000327702.12:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000335762.9:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000344100.7:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000347598.9:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399591.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399595.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399597.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399601.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399603.6:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399606.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399617.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399621.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399629.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399634.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399637.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399638.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399641.6:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399644.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399649.5:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000399655.6:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000402845.7:c.50-24914_50-24913insT:p.(=); CACNA1C:ENST00000406454.7:c.50-24914_50-24913insT:p.(=)

Pathogenicity Data:: Best Score: 0.1862331; CADD: 0.186 (0.895)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2369981G>A [0/1] rs574631518 (variation viewer)

Variant score: 0.179

Transcripts:: CACNA1C:ENST00000327702.12:c.478-78995G>A:p.(=); CACNA1C:ENST00000335762.9:c.478-78995G>A:p.(=); CACNA1C:ENST00000344100.7:c.478-78995G>A:p.(=); CACNA1C:ENST00000347598.9:c.478-78995G>A:p.(=); CACNA1C:ENST00000399591.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399595.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399597.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399601.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399603.6:c.478-78995G>A:p.(=); CACNA1C:ENST00000399606.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399617.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399621.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399629.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399634.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399637.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399638.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399641.6:c.478-78995G>A:p.(=); CACNA1C:ENST00000399644.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399649.5:c.478-78995G>A:p.(=); CACNA1C:ENST00000399655.6:c.478-78995G>A:p.(=); CACNA1C:ENST00000402845.7:c.478-78995G>A:p.(=); CACNA1C:ENST00000406454.7:c.478-78995G>A:p.(=)

Pathogenicity Data:: Best Score: 0.23193145; CADD: 0.232 (1.146)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1943%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1666%; gnomAD_G_OTH: 0.3067%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2244661A>G [0/1] rs141158311 (variation viewer)

Variant score: 0.155

Transcripts:: CACNA1C:ENST00000327702.12:c.477+124231A>G:p.(=); CACNA1C:ENST00000335762.9:c.477+124231A>G:p.(=); CACNA1C:ENST00000344100.7:c.477+124231A>G:p.(=); CACNA1C:ENST00000347598.9:c.477+124231A>G:p.(=); CACNA1C:ENST00000399591.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399595.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399597.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399601.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399603.6:c.477+124231A>G:p.(=); CACNA1C:ENST00000399606.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399617.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399621.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399629.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399634.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399637.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399638.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399641.6:c.477+124231A>G:p.(=); CACNA1C:ENST00000399644.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399649.5:c.477+124231A>G:p.(=); CACNA1C:ENST00000399655.6:c.477+124231A>G:p.(=); CACNA1C:ENST00000402845.7:c.477+124231A>G:p.(=); CACNA1C:ENST00000406454.7:c.477+124231A>G:p.(=)

Pathogenicity Data:: Best Score: 0.18341762; CADD: 0.183 (0.880)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.4818%; UK10K: 0.7538%; gnomAD_G_AFR: 0.1374%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1718%; gnomAD_G_NFE: 0.6868%; gnomAD_G_OTH: 0.5092%

INTERGENIC_VARIANT chr12:g.2710890T>TTC [0/1] rs200256699 (variation viewer)

Variant score: 0.082

Transcripts:: CACNA1C:ENST00000399655.6::; CACNA1C:ENST00000637219.1::

Pathogenicity Data:: Best Score: 0.26852417; CADD: 0.269 (1.358)

Frequency Data:: 1000Genomes: 0.3395%; UK10K: 1.1373%; gnomAD_G_AFR: 0.2292%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.5204%; gnomAD_G_NFE: 1.8126%; gnomAD_G_OTH: 1.4286%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2310352A>AAAAATAT [0/1] rs201363709 (variation viewer)

Variant score: 0.081

Transcripts:: CACNA1C:ENST00000327702.12:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000335762.9:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000344100.7:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000347598.9:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399591.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399595.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399597.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399601.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399603.6:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399606.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399617.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399621.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399629.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399634.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399637.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399638.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399641.6:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399644.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399649.5:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000399655.6:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000402845.7:c.478-138624_478-138623insAAAATAT:p.(=); CACNA1C:ENST00000406454.7:c.478-138624_478-138623insAAAATAT:p.(=)

Pathogenicity Data:: Best Score: 0.08103281; CADD: 0.081 (0.367)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2602442G>A [0/1] rs190310977 (variation viewer)

Variant score: 0.080

Transcripts:: CACNA1C:ENST00000327702.12:c.2960+482G>A:p.(=); CACNA1C:ENST00000335762.9:c.3035+482G>A:p.(=); CACNA1C:ENST00000344100.7:c.2960+482G>A:p.(=); CACNA1C:ENST00000347598.9:c.3020+482G>A:p.(=); CACNA1C:ENST00000399591.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399595.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399597.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399601.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399603.6:c.2960+482G>A:p.(=); CACNA1C:ENST00000399606.5:c.3020+482G>A:p.(=); CACNA1C:ENST00000399617.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399621.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399629.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399634.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399637.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399638.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399641.6:c.2960+482G>A:p.(=); CACNA1C:ENST00000399644.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399649.5:c.2960+482G>A:p.(=); CACNA1C:ENST00000399655.6:c.2960+482G>A:p.(=); CACNA1C:ENST00000402845.7:c.2960+482G>A:p.(=); CACNA1C:ENST00000406454.7:c.2960+482G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0806095; CADD: 0.081 (0.365)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0183%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2067481T>TGTGC [-/1] rs3085990 (variation viewer)

Variant score: 0.065

Transcripts:: CACNA1C:ENST00000327702.12:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000335762.9:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000344100.7:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000347598.9:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399591.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399595.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399597.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399601.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399603.6:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399606.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399617.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399621.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399629.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399634.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399637.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399638.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399641.6:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399644.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399649.5:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000399655.6:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000402845.7:c.49+13870_49+13871insGTGC:p.(=); CACNA1C:ENST00000406454.7:c.49+13870_49+13871insGTGC:p.(=)

Pathogenicity Data:: Best Score: 0.06459433; CADD: 0.065 (0.290)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2274744T>C [0/1] rs142589706 (variation viewer)

Variant score: 0.039

Transcripts:: CACNA1C:ENST00000327702.12:c.477+154314T>C:p.(=); CACNA1C:ENST00000335762.9:c.477+154314T>C:p.(=); CACNA1C:ENST00000344100.7:c.477+154314T>C:p.(=); CACNA1C:ENST00000347598.9:c.477+154314T>C:p.(=); CACNA1C:ENST00000399591.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399595.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399597.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399601.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399603.6:c.477+154314T>C:p.(=); CACNA1C:ENST00000399606.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399617.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399621.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399629.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399634.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399637.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399638.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399641.6:c.477+154314T>C:p.(=); CACNA1C:ENST00000399644.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399649.5:c.477+154314T>C:p.(=); CACNA1C:ENST00000399655.6:c.477+154314T>C:p.(=); CACNA1C:ENST00000402845.7:c.477+154314T>C:p.(=); CACNA1C:ENST00000406454.7:c.477+154314T>C:p.(=)

Pathogenicity Data:: Best Score: 0.05005163; CADD: 0.050 (0.223)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.5423%; UK10K: 0.7934%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.4007%; gnomAD_G_NFE: 0.6331%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2284956A>C [0/1] rs1391389969 (variation viewer)

Variant score: 0.037

Transcripts:: CACNA1C:ENST00000327702.12:c.478-164020A>C:p.(=); CACNA1C:ENST00000335762.9:c.478-164020A>C:p.(=); CACNA1C:ENST00000344100.7:c.478-164020A>C:p.(=); CACNA1C:ENST00000347598.9:c.478-164020A>C:p.(=); CACNA1C:ENST00000399591.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399595.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399597.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399601.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399603.6:c.478-164020A>C:p.(=); CACNA1C:ENST00000399606.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399617.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399621.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399629.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399634.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399637.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399638.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399641.6:c.478-164020A>C:p.(=); CACNA1C:ENST00000399644.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399649.5:c.478-164020A>C:p.(=); CACNA1C:ENST00000399655.6:c.478-164020A>C:p.(=); CACNA1C:ENST00000402845.7:c.478-164020A>C:p.(=); CACNA1C:ENST00000406454.7:c.478-164020A>C:p.(=)

Pathogenicity Data:: Best Score: 0.036836565; CADD: 0.037 (0.163)

Frequency Data:: gnomAD_G_FIN: 0.0287%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2314712A>G [0/1] rs146763423 (variation viewer)

Variant score: 0.025

Transcripts:: CACNA1C:ENST00000327702.12:c.478-134264A>G:p.(=); CACNA1C:ENST00000335762.9:c.478-134264A>G:p.(=); CACNA1C:ENST00000344100.7:c.478-134264A>G:p.(=); CACNA1C:ENST00000347598.9:c.478-134264A>G:p.(=); CACNA1C:ENST00000399591.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399595.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399597.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399601.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399603.6:c.478-134264A>G:p.(=); CACNA1C:ENST00000399606.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399617.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399621.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399629.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399634.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399637.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399638.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399641.6:c.478-134264A>G:p.(=); CACNA1C:ENST00000399644.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399649.5:c.478-134264A>G:p.(=); CACNA1C:ENST00000399655.6:c.478-134264A>G:p.(=); CACNA1C:ENST00000402845.7:c.478-134264A>G:p.(=); CACNA1C:ENST00000406454.7:c.478-134264A>G:p.(=)

Pathogenicity Data:: Best Score: 0.032390773; CADD: 0.032 (0.143)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.5447%; UK10K: 0.7934%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.4293%; gnomAD_G_NFE: 0.6528%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2207835C>CAAA [0|1] rs755189577 (variation viewer)

Variant score: 0.009

Transcripts:: CACNA1C:ENST00000327702.12:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000335762.9:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000344100.7:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000347598.9:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399591.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399595.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399597.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399601.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399603.6:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399606.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399617.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399621.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399629.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399634.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399637.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399638.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399641.6:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399644.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399649.5:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000399655.6:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000402845.7:c.477+87405_477+87406insAAA:p.(=); CACNA1C:ENST00000406454.7:c.477+87405_477+87406insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.035060704; CADD: 0.035 (0.155)

Frequency Data:: UK10K: 1.8646%; gnomAD_G_AFR: 0.3153%; gnomAD_G_AMR: 1.0283%; gnomAD_G_ASJ: 0.6849%; gnomAD_G_FIN: 0.3427%; gnomAD_G_NFE: 0.8937%; gnomAD_G_OTH: 0.9534%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2345059G>A [0/1] rs148654637 (variation viewer)

Variant score: 0.003

Transcripts:: CACNA1C:ENST00000327702.12:c.478-103917G>A:p.(=); CACNA1C:ENST00000335762.9:c.478-103917G>A:p.(=); CACNA1C:ENST00000344100.7:c.478-103917G>A:p.(=); CACNA1C:ENST00000347598.9:c.478-103917G>A:p.(=); CACNA1C:ENST00000399591.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399595.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399597.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399601.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399603.6:c.478-103917G>A:p.(=); CACNA1C:ENST00000399606.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399617.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399621.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399629.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399634.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399637.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399638.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399641.6:c.478-103917G>A:p.(=); CACNA1C:ENST00000399644.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399649.5:c.478-103917G>A:p.(=); CACNA1C:ENST00000399655.6:c.478-103917G>A:p.(=); CACNA1C:ENST00000402845.7:c.478-103917G>A:p.(=); CACNA1C:ENST00000406454.7:c.478-103917G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0036773682; CADD: 0.004 (0.016)

Frequency Data:: 1000Genomes: 0.7987%; TOPMed: 0.3767%; UK10K: 0.1058%; gnomAD_G_AFR: 0.7827%; gnomAD_G_AMR: 0.5981%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1483%; gnomAD_G_OTH: 0.2075%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2292812A>G [0/1] rs372161962 (variation viewer)

Variant score: 0.001

Transcripts:: CACNA1C:ENST00000327702.12:c.478-156164A>G:p.(=); CACNA1C:ENST00000335762.9:c.478-156164A>G:p.(=); CACNA1C:ENST00000344100.7:c.478-156164A>G:p.(=); CACNA1C:ENST00000347598.9:c.478-156164A>G:p.(=); CACNA1C:ENST00000399591.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399595.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399597.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399601.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399603.6:c.478-156164A>G:p.(=); CACNA1C:ENST00000399606.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399617.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399621.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399629.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399634.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399637.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399638.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399641.6:c.478-156164A>G:p.(=); CACNA1C:ENST00000399644.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399649.5:c.478-156164A>G:p.(=); CACNA1C:ENST00000399655.6:c.478-156164A>G:p.(=); CACNA1C:ENST00000402845.7:c.478-156164A>G:p.(=); CACNA1C:ENST00000406454.7:c.478-156164A>G:p.(=)

Pathogenicity Data:: Best Score: 0.0016105175; CADD: 0.002 (0.007)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.1290%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1735%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.2277362GACACACACACAC>* [-/1]

Variant score: 0.000

Transcripts:: CACNA1C:ENST00000327702.12:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000335762.9:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000344100.7:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000347598.9:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399591.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399595.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399597.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399601.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399603.6:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399606.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399617.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399621.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399629.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399634.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399637.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399638.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399641.6:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399644.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399649.5:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000399655.6:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000402845.7:c.477+156932_477+156944delGACACACACACACins*:p.(=); CACNA1C:ENST00000406454.7:c.477+156932_477+156944delGACACACACACACins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PMPCB

Exomiser Score: 0.250

Phenotype Score: 0.503

Variant Score: 0.758

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO1 and phenotypic similarity 0.864 to MELAS associated with MT-CO1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617954 Multiple mitochondrial dysfunctions syndrome 6 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.111

Phenotype Score: 0.252

Variant Score: 0.935

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.103305284A>C [0/1] rs916742682 (variation viewer)

Variant score: 0.935 CONTRIBUTING VARIANT

Transcripts:: PMPCB:ENST00000249269.9:c.736+794A>C:p.(=); PMPCB:ENST00000428154.5:c.736+794A>C:p.(=)

Pathogenicity Data:: Best Score: 0.9361736; CADD: 0.936 (11.950)

Frequency Data:: TOPMed: 0.0064%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.250

Phenotype Score: 0.503

Variant Score: 0.758

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.103305284A>C [0/1] rs916742682 (variation viewer)

Variant score: 0.935 CONTRIBUTING VARIANT

Transcripts:: PMPCB:ENST00000249269.9:c.736+794A>C:p.(=); PMPCB:ENST00000428154.5:c.736+794A>C:p.(=)

Pathogenicity Data:: Best Score: 0.9361736; CADD: 0.936 (11.950)

Frequency Data:: TOPMed: 0.0064%

INTERGENIC_VARIANT chr7:g.103285825G>A [0/1] rs1174741973 (variation viewer)

Variant score: 0.580 CONTRIBUTING VARIANT

Transcripts:: PMPCB:ENST00000428154.5::; PMPCB:ENST00000312132.8::

Pathogenicity Data:: Best Score: 0.58033764; CADD: 0.580 (3.771)

Frequency Data:: TOPMed: 0.0064%

Other passed variants:

NDUFB6

Exomiser Score: 0.249

Phenotype Score: 0.504

Variant Score: 0.756

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.249

Phenotype Score: 0.504

Variant Score: 0.756

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.32566006T>G [0/1]

Variant score: 0.756 CONTRIBUTING VARIANT

Transcripts:: NDUFB6:ENST00000350021.2:c.273+4954A>C:p.(=); NDUFB6:ENST00000366466.5:c.180+6875A>C:p.(=); NDUFB6:ENST00000379847.8:c.273+4954A>C:p.(=); NDUFB6:ENST00000451672.2:c.46-385T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7559381; CADD: 0.756 (6.125)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.239

Phenotype Score: 0.504

Variant Score: 0.750

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.32566006T>G [0/1]

Variant score: 0.756 CONTRIBUTING VARIANT

Transcripts:: NDUFB6:ENST00000350021.2:c.273+4954A>C:p.(=); NDUFB6:ENST00000366466.5:c.180+6875A>C:p.(=); NDUFB6:ENST00000379847.8:c.273+4954A>C:p.(=); NDUFB6:ENST00000451672.2:c.46-385T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7559381; CADD: 0.756 (6.125)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.32572157G>GTATT [0/1] rs569555997 (variation viewer)

Variant score: 0.743 CONTRIBUTING VARIANT

Transcripts:: NDUFB6:ENST00000350021.2:c.180+723_180+724insAATA:p.(=); NDUFB6:ENST00000366466.5:c.180+723_180+724insAATA:p.(=); NDUFB6:ENST00000379847.8:c.180+723_180+724insAATA:p.(=)

Pathogenicity Data:: Best Score: 0.7771565; CADD: 0.777 (6.520)

Frequency Data:: TOPMed: 0.0964%; UK10K: 0.2777%; gnomAD_G_FIN: 0.1717%; gnomAD_G_NFE: 0.1533%; gnomAD_G_OTH: 0.1020%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.32571311T>G [0/1] rs562817698 (variation viewer)

Variant score: 0.103

Transcripts:: NDUFB6:ENST00000350021.2:c.181-259A>C:p.(=); NDUFB6:ENST00000366466.5:c.180+1570A>C:p.(=); NDUFB6:ENST00000379847.8:c.181-259A>C:p.(=)

Pathogenicity Data:: Best Score: 0.1079278; CADD: 0.108 (0.496)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1035%; UK10K: 0.2777%; gnomAD_G_FIN: 0.1719%; gnomAD_G_NFE: 0.1534%; gnomAD_G_OTH: 0.1018%

ADH5

Exomiser Score: 0.245

Phenotype Score: 0.505

Variant Score: 0.753

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.245

Phenotype Score: 0.505

Variant Score: 0.753

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086902T>C [0|1]

Variant score: 0.753 CONTRIBUTING VARIANT

Transcripts:: ADH5:ENST00000296412.13:c.13-1686A>G:p.(=); ADH5:ENST00000626055.2:c.13-1686A>G:p.(=)

Pathogenicity Data:: Best Score: 0.75277066; CADD: 0.753 (6.069)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.154

Phenotype Score: 0.505

Variant Score: 0.690

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086902T>C [0|1]

Variant score: 0.753 CONTRIBUTING VARIANT

Transcripts:: ADH5:ENST00000296412.13:c.13-1686A>G:p.(=); ADH5:ENST00000626055.2:c.13-1686A>G:p.(=)

Pathogenicity Data:: Best Score: 0.75277066; CADD: 0.753 (6.069)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086918T>C [0|1]

Variant score: 0.626 CONTRIBUTING VARIANT

Transcripts:: ADH5:ENST00000296412.13:c.13-1702A>G:p.(=); ADH5:ENST00000626055.2:c.13-1702A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6264919; CADD: 0.626 (4.277)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086927A>G [0|1]

Variant score: 0.617

Transcripts:: ADH5:ENST00000296412.13:c.13-1711T>C:p.(=); ADH5:ENST00000626055.2:c.13-1711T>C:p.(=)

Pathogenicity Data:: Best Score: 0.61735153; CADD: 0.617 (4.172)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086934C>T [0|1] rs1247249817 (variation viewer)

Variant score: 0.371

Transcripts:: ADH5:ENST00000296412.13:c.13-1718G>A:p.(=); ADH5:ENST00000626055.2:c.13-1718G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3707837; CADD: 0.371 (2.012)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086933G>C [0|1] rs1200650142 (variation viewer)

Variant score: 0.272

Transcripts:: ADH5:ENST00000296412.13:c.13-1717C>G:p.(=); ADH5:ENST00000626055.2:c.13-1717C>G:p.(=)

Pathogenicity Data:: Best Score: 0.27188498; CADD: 0.272 (1.378)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99086894C>T [0|1] rs532491186 (variation viewer)

Variant score: 0.152

Transcripts:: ADH5:ENST00000296412.13:c.13-1678G>A:p.(=); ADH5:ENST00000626055.2:c.13-1678G>A:p.(=)

Pathogenicity Data:: Best Score: 0.24716467; CADD: 0.247 (1.233)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.3195%; gnomAD_G_AFR: 1.3431%

UPSTREAM_GENE_VARIANT chr4:g.99089439CTTTCTTTG>* [-/1]

Variant score: 0.000

Transcripts:: ADH5:ENST00000626055.2::; ADH5:ENST00000508393.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MYO7A

Exomiser Score: 0.241

Phenotype Score: 0.514

Variant Score: 0.740

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 2 associated with MYO7A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Phenotypic similarity 0.436 to mouse mutant involving MYO7A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.514 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.514 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:276900 Usher syndrome, type 1B - autosomal recessive; OMIM:600060 Deafness, autosomal recessive 2 - autosomal recessive; OMIM:601317 Deafness, autosomal dominant 11 - autosomal dominant; ORPHA:231169 Usher syndrome type 1; ORPHA:231178 Usher syndrome type 2

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.241

Phenotype Score: 0.514

Variant Score: 0.740

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.77179378GATT>G [0/1] rs1355621312 (variation viewer)

Variant score: 0.740 CONTRIBUTING VARIANT

Transcripts:: MYO7A:ENST00000409619.6:c.2334+250_2334+252del:p.(=); MYO7A:ENST00000409709.9:c.2367+250_2367+252del:p.(=); MYO7A:ENST00000458637.6:c.2367+250_2367+252del:p.(=); MYO7A:ENST00000620575.4:c.2367+250_2367+252del:p.(=)

Pathogenicity Data:: Best Score: 0.7407612; CADD: 0.741 (5.863)

Frequency Data:: TOPMed: 0.0048%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.514

Variant Score: 0.392

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.77179378GATT>G [0/1] rs1355621312 (variation viewer)

Variant score: 0.740 CONTRIBUTING VARIANT

Transcripts:: MYO7A:ENST00000409619.6:c.2334+250_2334+252del:p.(=); MYO7A:ENST00000409709.9:c.2367+250_2367+252del:p.(=); MYO7A:ENST00000458637.6:c.2367+250_2367+252del:p.(=); MYO7A:ENST00000620575.4:c.2367+250_2367+252del:p.(=)

Pathogenicity Data:: Best Score: 0.7407612; CADD: 0.741 (5.863)

Frequency Data:: TOPMed: 0.0048%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.77164507A>G [0/1] rs116968703 (variation viewer)

Variant score: 0.044 CONTRIBUTING VARIANT

Transcripts:: MYO7A:ENST00000409619.6:c.1657+1519A>G:p.(=); MYO7A:ENST00000409709.9:c.1690+1519A>G:p.(=); MYO7A:ENST00000458637.6:c.1690+1519A>G:p.(=); MYO7A:ENST00000620575.4:c.1690+1519A>G:p.(=)

Pathogenicity Data:: Best Score: 0.054198503; CADD: 0.054 (0.242)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4802%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.6395%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.77178274CACT>C [1|1] rs1555081421 (variation viewer)

Variant score: 0.060

Transcripts:: MYO7A:ENST00000409619.6:c.2249+632_2249+634del:p.(=); MYO7A:ENST00000409709.9:c.2282+632_2282+634del:p.(=); MYO7A:ENST00000458637.6:c.2282+632_2282+634del:p.(=); MYO7A:ENST00000620575.4:c.2282+632_2282+634del:p.(=)

Pathogenicity Data:: Best Score: 0.126023; CADD: 0.126 (0.585)

Frequency Data:: gnomAD_G_AFR: 1.3777%; gnomAD_G_AMR: 0.8537%; gnomAD_G_ASJ: 0.6897%; gnomAD_G_EAS: 1.4085%; gnomAD_G_FIN: 1.5878%; gnomAD_G_NFE: 1.2348%; gnomAD_G_OTH: 0.7415%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.77174118A>G [0/1] rs180906734 (variation viewer)

Variant score: 0.017

Transcripts:: MYO7A:ENST00000409619.6:c.1903-638A>G:p.(=); MYO7A:ENST00000409709.9:c.1936-638A>G:p.(=); MYO7A:ENST00000458637.6:c.1936-638A>G:p.(=); MYO7A:ENST00000620575.4:c.1936-638A>G:p.(=)

Pathogenicity Data:: Best Score: 0.06696057; CADD: 0.067 (0.301)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 1.0280%; UK10K: 1.8778%; gnomAD_G_AFR: 0.2761%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.7172%; gnomAD_G_NFE: 1.2470%; gnomAD_G_OTH: 0.8197%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.77178271AG>A [1|1] rs1555081417 (variation viewer)

Variant score: 0.007

Transcripts:: MYO7A:ENST00000409619.6:c.2249+629del:p.(=); MYO7A:ENST00000409709.9:c.2282+629del:p.(=); MYO7A:ENST00000458637.6:c.2282+629del:p.(=); MYO7A:ENST00000620575.4:c.2282+629del:p.(=)

Pathogenicity Data:: Best Score: 0.016215444; CADD: 0.016 (0.071)

Frequency Data:: gnomAD_G_AFR: 1.4898%; gnomAD_G_AMR: 0.8621%; gnomAD_G_ASJ: 0.7143%; gnomAD_G_EAS: 1.5504%; gnomAD_G_FIN: 1.6241%; gnomAD_G_NFE: 1.2702%; gnomAD_G_OTH: 0.8658%

KLHL1

Exomiser Score: 0.237

Phenotype Score: 0.513

Variant Score: 0.739

Phenotype matches:

Proximity score 0.513 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.237

Phenotype Score: 0.513

Variant Score: 0.739

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69818219C>CT [0/1] rs1316398623 (variation viewer)

Variant score: 0.739 CONTRIBUTING VARIANT

Transcripts:: KLHL1:ENST00000377844.9:c.1414+20756_1414+20757insA:p.(=); KLHL1:ENST00000545028.2:c.1231+20756_1231+20757insA:p.(=)

Pathogenicity Data:: Best Score: 0.7389642; CADD: 0.739 (5.833)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.146

Phenotype Score: 0.513

Variant Score: 0.674

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69818219C>CT [0/1] rs1316398623 (variation viewer)

Variant score: 0.739 CONTRIBUTING VARIANT

Transcripts:: KLHL1:ENST00000377844.9:c.1414+20756_1414+20757insA:p.(=); KLHL1:ENST00000545028.2:c.1231+20756_1231+20757insA:p.(=)

Pathogenicity Data:: Best Score: 0.7389642; CADD: 0.739 (5.833)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69782725C>A [0/1] rs570144942 (variation viewer)

Variant score: 0.609 CONTRIBUTING VARIANT

Transcripts:: KLHL1:ENST00000377844.9:c.1639+14013G>T:p.(=); KLHL1:ENST00000545028.2:c.1456+14013G>T:p.(=)

Pathogenicity Data:: Best Score: 0.69800484; CADD: 0.698 (5.200)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3369%; gnomAD_G_AFR: 0.1489%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.4067%; gnomAD_G_OTH: 0.4082%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69734025G>C [0/1] rs143142986 (variation viewer)

Variant score: 0.426

Transcripts:: KLHL1:ENST00000377844.9:c.1802+6369C>G:p.(=); KLHL1:ENST00000545028.2:c.1619+6369C>G:p.(=)

Pathogenicity Data:: Best Score: 0.5013452; CADD: 0.501 (3.022)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3799%; UK10K: 0.6480%; gnomAD_G_AFR: 0.1147%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.7470%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70074860GTAGA>G [0/1] rs375949010 (variation viewer)

Variant score: 0.322

Transcripts:: KLHL1:ENST00000377844.9:c.497+32339_497+32342del:p.(=); KLHL1:ENST00000545028.2:c.497+32339_497+32342del:p.(=)

Pathogenicity Data:: Best Score: 0.39841086; CADD: 0.398 (2.207)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.4667%; UK10K: 0.6744%; gnomAD_G_AFR: 0.1493%; gnomAD_G_AMR: 0.2392%; gnomAD_G_FIN: 0.0579%; gnomAD_G_NFE: 0.8800%; gnomAD_G_OTH: 0.5112%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69796223A>G [0/1] rs544429927 (variation viewer)

Variant score: 0.291

Transcripts:: KLHL1:ENST00000377844.9:c.1639+515T>C:p.(=); KLHL1:ENST00000545028.2:c.1456+515T>C:p.(=)

Pathogenicity Data:: Best Score: 0.3336537; CADD: 0.334 (1.763)

Frequency Data:: TOPMed: 0.0199%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69809147A>C [0/1]

Variant score: 0.272

Transcripts:: KLHL1:ENST00000377844.9:c.1415-12185T>G:p.(=); KLHL1:ENST00000545028.2:c.1232-12185T>G:p.(=)

Pathogenicity Data:: Best Score: 0.2720526; CADD: 0.272 (1.379)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69740360C>T [0/1] rs148930007 (variation viewer)

Variant score: 0.226

Transcripts:: KLHL1:ENST00000377844.9:c.1802+34G>A:p.(=); KLHL1:ENST00000545028.2:c.1619+34G>A:p.(=)

Pathogenicity Data:: Best Score: 0.25971323; CADD: 0.260 (1.306)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.3225%; UK10K: 0.3042%; ESP AA: 0.0230%; ESP EA: 0.1521%; ESP All: 0.1086%; ExAC AFR: 0.0600%; ExAC AMR: 0.2994%; ExAC FIN: 0.1167%; ExAC NFE: 0.6395%; ExAC OTH: 0.4149%; ExAC SAS: 0.3845%; gnomAD_E_AFR: 0.0527%; gnomAD_E_AMR: 0.2947%; gnomAD_E_ASJ: 0.4120%; gnomAD_E_FIN: 0.1718%; gnomAD_E_NFE: 0.4203%; gnomAD_E_OTH: 0.2893%; gnomAD_E_SAS: 0.2044%; gnomAD_G_AFR: 0.1505%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.1195%; gnomAD_G_NFE: 0.3853%; gnomAD_G_OTH: 0.4141%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69939378T>TATATAC [0/1] rs1200160699 (variation viewer)

Variant score: 0.177

Transcripts:: KLHL1:ENST00000377844.9:c.1014+661_1014+662insGTATAT:p.(=); KLHL1:ENST00000545028.2:c.831+661_831+662insGTATAT:p.(=)

Pathogenicity Data:: Best Score: 0.17681015; CADD: 0.177 (0.845)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70084622CTTTT>C [1/1] rs71116988 (variation viewer)

Variant score: 0.172

Transcripts:: KLHL1:ENST00000377844.9:c.497+22577_497+22580del:p.(=); KLHL1:ENST00000545028.2:c.497+22577_497+22580del:p.(=)

Pathogenicity Data:: Best Score: 0.17224842; CADD: 0.172 (0.821)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70033604CTT>C [1/1] rs71116981 (variation viewer)

Variant score: 0.141

Transcripts:: KLHL1:ENST00000377844.9:c.498-57804_498-57803del:p.(=); KLHL1:ENST00000545028.2:c.498-72162_498-72161del:p.(=)

Pathogenicity Data:: Best Score: 0.14138198; CADD: 0.141 (0.662)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69891254C>A [0/1] rs143160366 (variation viewer)

Variant score: 0.139

Transcripts:: KLHL1:ENST00000377844.9:c.1015-8759G>T:p.(=); KLHL1:ENST00000545028.2:c.832-8759G>T:p.(=)

Pathogenicity Data:: Best Score: 0.15899223; CADD: 0.159 (0.752)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.2509%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0802%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.2271%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69882117C>T [0/1] rs142894988 (variation viewer)

Variant score: 0.138

Transcripts:: KLHL1:ENST00000377844.9:c.1227+166G>A:p.(=); KLHL1:ENST00000545028.2:c.1044+166G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15782952; CADD: 0.158 (0.746)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.2349%; UK10K: 0.2248%; gnomAD_G_AFR: 0.0801%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.2399%; gnomAD_G_OTH: 0.4090%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69757957CA>C [0/1] rs59302694 (variation viewer)

Variant score: 0.130

Transcripts:: KLHL1:ENST00000377844.9:c.1640-17402del:p.(=); KLHL1:ENST00000545028.2:c.1457-17402del:p.(=)

Pathogenicity Data:: Best Score: 0.12983823; CADD: 0.130 (0.604)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69752434A>T [0/1] rs192469654 (variation viewer)

Variant score: 0.127

Transcripts:: KLHL1:ENST00000377844.9:c.1640-11878T>A:p.(=); KLHL1:ENST00000545028.2:c.1457-11878T>A:p.(=)

Pathogenicity Data:: Best Score: 0.14572048; CADD: 0.146 (0.684)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.3241%; UK10K: 0.2909%; gnomAD_G_AFR: 0.1489%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3931%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70010031GA>G [0/1] rs531992455 (variation viewer)

Variant score: 0.126

Transcripts:: KLHL1:ENST00000377844.9:c.498-34230del:p.(=); KLHL1:ENST00000545028.2:c.498-48588del:p.(=)

Pathogenicity Data:: Best Score: 0.16208494; CADD: 0.162 (0.768)

Frequency Data:: TOPMed: 0.4205%; gnomAD_G_AFR: 0.0898%; gnomAD_G_AMR: 0.1534%; gnomAD_G_ASJ: 0.3788%; gnomAD_G_FIN: 0.8899%; gnomAD_G_NFE: 0.7356%; gnomAD_G_OTH: 0.9642%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69753731T>A [0/1] rs141139691 (variation viewer)

Variant score: 0.113

Transcripts:: KLHL1:ENST00000377844.9:c.1640-13175A>T:p.(=); KLHL1:ENST00000545028.2:c.1457-13175A>T:p.(=)

Pathogenicity Data:: Best Score: 0.43467265; CADD: 0.435 (2.477)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.9111%; UK10K: 0.2909%; gnomAD_G_AFR: 1.8676%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3864%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69745317T>C [0/1] rs139604873 (variation viewer)

Variant score: 0.110

Transcripts:: KLHL1:ENST00000377844.9:c.1640-4761A>G:p.(=); KLHL1:ENST00000545028.2:c.1457-4761A>G:p.(=)

Pathogenicity Data:: Best Score: 0.13023889; CADD: 0.130 (0.606)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3854%; UK10K: 0.6744%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.1205%; gnomAD_G_NFE: 0.7604%; gnomAD_G_OTH: 0.3080%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69728649C>CAAAAAAAAAA [0/1] rs536317353 (variation viewer)

Variant score: 0.109

Transcripts:: KLHL1:ENST00000377844.9:c.1803-9069_1803-9068insTTTTTTTTTT:p.(=); KLHL1:ENST00000545028.2:c.1620-9069_1620-9068insTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.18510813; CADD: 0.185 (0.889)

Frequency Data:: gnomAD_G_AFR: 0.3592%; gnomAD_G_AMR: 0.1961%; gnomAD_G_ASJ: 1.2397%; gnomAD_G_FIN: 0.3882%; gnomAD_G_NFE: 1.2201%; gnomAD_G_OTH: 1.3975%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70027649G>GTTTTTTTTTTT [0/1] rs1185282462 (variation viewer)

Variant score: 0.088

Transcripts:: KLHL1:ENST00000377844.9:c.498-51848_498-51847insAAAAAAAAAAA:p.(=); KLHL1:ENST00000545028.2:c.498-66206_498-66205insAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.08819914; CADD: 0.088 (0.401)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70075569G>GTATATATATATATATA [-/1] rs1555295388 (variation viewer)

Variant score: 0.087

Transcripts:: KLHL1:ENST00000377844.9:c.497+31633_497+31634insTATATATATATATATA:p.(=); KLHL1:ENST00000545028.2:c.497+31633_497+31634insTATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.08651799; CADD: 0.087 (0.393)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70019944A>G [0/1] rs150864774 (variation viewer)

Variant score: 0.084

Transcripts:: KLHL1:ENST00000377844.9:c.498-44142T>C:p.(=); KLHL1:ENST00000545028.2:c.498-58500T>C:p.(=)

Pathogenicity Data:: Best Score: 0.097390294; CADD: 0.097 (0.445)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.4197%; UK10K: 0.5686%; gnomAD_G_AFR: 0.0573%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.3150%; gnomAD_G_NFE: 0.6272%; gnomAD_G_OTH: 0.7143%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70075569G>GTATATATATATATATATA [-/1] rs1555295388 (variation viewer)

Variant score: 0.083

Transcripts:: KLHL1:ENST00000377844.9:c.497+31633_497+31634insTATATATATATATATATA:p.(=); KLHL1:ENST00000545028.2:c.497+31633_497+31634insTATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.08314639; CADD: 0.083 (0.377)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69939340C>CATATATAT [0/1] rs34074889 (variation viewer)

Variant score: 0.080

Transcripts:: KLHL1:ENST00000377844.9:c.1014+699_1014+700insATATATAT:p.(=); KLHL1:ENST00000545028.2:c.831+699_831+700insATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.08018601; CADD: 0.080 (0.363)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70067634G>GACAACAACA [-/1] rs141632976 (variation viewer)

Variant score: 0.074

Transcripts:: KLHL1:ENST00000377844.9:c.497+39568_497+39569insTGTTGTTGT:p.(=); KLHL1:ENST00000545028.2:c.497+39568_497+39569insTGTTGTTGT:p.(=)

Pathogenicity Data:: Best Score: 0.08588678; CADD: 0.086 (0.390)

Frequency Data:: gnomAD_G_AFR: 0.3363%; gnomAD_G_ASJ: 0.3356%; gnomAD_G_FIN: 0.3187%; gnomAD_G_NFE: 0.6952%; gnomAD_G_OTH: 0.7202%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69745657C>T [0/1] rs145209433 (variation viewer)

Variant score: 0.055

Transcripts:: KLHL1:ENST00000377844.9:c.1640-5101G>A:p.(=); KLHL1:ENST00000545028.2:c.1457-5101G>A:p.(=)

Pathogenicity Data:: Best Score: 0.06265384; CADD: 0.063 (0.281)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.3241%; gnomAD_G_AFR: 0.1493%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1159%; gnomAD_G_NFE: 0.3817%; gnomAD_G_OTH: 0.5123%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69908132G>A [0/1]

Variant score: 0.052

Transcripts:: KLHL1:ENST00000377844.9:c.1015-25637C>T:p.(=); KLHL1:ENST00000545028.2:c.832-25637C>T:p.(=)

Pathogenicity Data:: Best Score: 0.052236438; CADD: 0.052 (0.233)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69781119G>C [0/1] rs1016651822 (variation viewer)

Variant score: 0.034

Transcripts:: KLHL1:ENST00000377844.9:c.1639+15619C>G:p.(=); KLHL1:ENST00000545028.2:c.1456+15619C>G:p.(=)

Pathogenicity Data:: Best Score: 0.034616232; CADD: 0.035 (0.153)

Frequency Data:: TOPMed: 0.0191%; gnomAD_G_AFR: 0.0574%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70047764G>A [0/1] rs117563009 (variation viewer)

Variant score: 0.000

Transcripts:: KLHL1:ENST00000377844.9:c.497+59439C>T:p.(=); KLHL1:ENST00000545028.2:c.497+59439C>T:p.(=)

Pathogenicity Data:: Best Score: 0.001840353; CADD: 0.002 (0.008)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 1.0110%; UK10K: 1.6001%; gnomAD_G_AFR: 0.2753%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.4590%; gnomAD_G_NFE: 1.7423%; gnomAD_G_OTH: 1.2220%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.69721062G>GATATATATATATATATACAAATTCCTTGTAAGGGAGGTACATAGCTTTATATATATATATATATATATATATATATATATATATATATATATAT [1/1]

Variant score: 0.000

Transcripts:: KLHL1:ENST00000377844.9:c.1803-1482_1803-1481insATATATATATATATATATATATATATATATATATATATATATATATAAAGCTATGTACCTCCCTTACAAGGAATTTGTATATATATATATATAT:p.(=); KLHL1:ENST00000545028.2:c.1620-1482_1620-1481insATATATATATATATATATATATATATATATATATATATATATATATAAAGCTATGTACCTCCCTTACAAGGAATTTGTATATATATATATATAT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70022281T>* [-/1]

Variant score: 0.000

Transcripts:: KLHL1:ENST00000377844.9:c.498-46479A>:p.(=); KLHL1:ENST00000545028.2:c.498-60837A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.70026705TGTGTGTGTG>* [-/1]

Variant score: 0.000

Transcripts:: KLHL1:ENST00000377844.9:c.498-50912_498-50903delCACACACACAins:p.(=); KLHL1:ENST00000545028.2:c.498-65270_498-65261delCACACACACAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DNAH8

Exomiser Score: 0.232

Phenotype Score: 0.507

Variant Score: 0.742

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.232

Phenotype Score: 0.507

Variant Score: 0.742

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38917218G>A [0|1] rs761065489 (variation viewer)

Variant score: 0.742 CONTRIBUTING VARIANT

Transcripts:: DNAH8:ENST00000327475.11:c.10141-21G>A:p.(=); DNAH8:ENST00000359357.7:c.9490-21G>A:p.(=); DNAH8:ENST00000449981.6:c.10141-21G>A:p.(=)

Pathogenicity Data:: Best Score: 0.742842; CADD: 0.743 (5.898)

Frequency Data:: TOPMed: 0.0008%; ExAC NFE: 0.0034%; gnomAD_E_NFE: 0.0034%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.066

Phenotype Score: 0.507

Variant Score: 0.583

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38917218G>A [0|1] rs761065489 (variation viewer)

Variant score: 0.742 CONTRIBUTING VARIANT

Transcripts:: DNAH8:ENST00000327475.11:c.10141-21G>A:p.(=); DNAH8:ENST00000359357.7:c.9490-21G>A:p.(=); DNAH8:ENST00000449981.6:c.10141-21G>A:p.(=)

Pathogenicity Data:: Best Score: 0.742842; CADD: 0.743 (5.898)

Frequency Data:: TOPMed: 0.0008%; ExAC NFE: 0.0034%; gnomAD_E_NFE: 0.0034%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38766135T>TTGTGTGTGTGTGTGTGTGTGTGTGTG [0|1] rs774448668 (variation viewer)

Variant score: 0.424 CONTRIBUTING VARIANT

Transcripts:: DNAH8:ENST00000327475.11:c.1618-4278_1618-4277insTGTGTGTGTGTGTGTGTGTGTGTGTG:p.(=); DNAH8:ENST00000359357.7:c.967-4278_967-4277insTGTGTGTGTGTGTGTGTGTGTGTGTG:p.(=); DNAH8:ENST00000449981.6:c.1618-4278_1618-4277insTGTGTGTGTGTGTGTGTGTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.42402983; CADD: 0.424 (2.396)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38942805A>G [0/1] rs74886488 (variation viewer)

Variant score: 0.361

Transcripts:: DNAH8:ENST00000327475.11:c.12008-2662A>G:p.(=); DNAH8:ENST00000359357.7:c.11357-2662A>G:p.(=); DNAH8:ENST00000449981.6:c.12008-2662A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6996; CADD: 0.700 (5.223)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.9780%; UK10K: 1.5208%; gnomAD_G_AFR: 0.2635%; gnomAD_G_AMR: 0.5981%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.3723%; gnomAD_G_NFE: 1.2939%; gnomAD_G_OTH: 1.1224%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38978285G>T [0/1]

Variant score: 0.314

Transcripts:: DNAH8:ENST00000327475.11:c.12834+3756G>T:p.(=); DNAH8:ENST00000359357.7:c.12183+3756G>T:p.(=)

Pathogenicity Data:: Best Score: 0.31372213; CADD: 0.314 (1.635)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.39018932G>A [0/1] rs181667613 (variation viewer)

Variant score: 0.239

Transcripts:: DNAH8:ENST00000327475.11:c.13714+6295G>A:p.(=); DNAH8:ENST00000359357.7:c.13063+6295G>A:p.(=)

Pathogenicity Data:: Best Score: 0.38736755; CADD: 0.387 (2.128)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2381%; UK10K: 0.4761%; gnomAD_G_AFR: 0.0801%; gnomAD_G_FIN: 1.3452%; gnomAD_G_NFE: 0.3531%; gnomAD_G_OTH: 0.8163%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38818537C>CAAA [-/1] rs70981590 (variation viewer)

Variant score: 0.194

Transcripts:: DNAH8:ENST00000327475.11:c.3523+2880_3523+2881insAAA:p.(=); DNAH8:ENST00000359357.7:c.2872+2880_2872+2881insAAA:p.(=); DNAH8:ENST00000449981.6:c.3523+2880_3523+2881insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.19443607; CADD: 0.194 (0.939)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38747384CT>C [1/1] rs55729629 (variation viewer)

Variant score: 0.184

Transcripts:: DNAH8:ENST00000327475.11:c.1294-3091del:p.(=); DNAH8:ENST00000359357.7:c.643-3091del:p.(=); DNAH8:ENST00000449981.6:c.1294-3091del:p.(=)

Pathogenicity Data:: Best Score: 0.18435723; CADD: 0.184 (0.885)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38818537C>CAAAAAAA [-/1] rs70981590 (variation viewer)

Variant score: 0.181

Transcripts:: DNAH8:ENST00000327475.11:c.3523+2880_3523+2881insAAAAAAA:p.(=); DNAH8:ENST00000359357.7:c.2872+2880_2872+2881insAAAAAAA:p.(=); DNAH8:ENST00000449981.6:c.3523+2880_3523+2881insAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.18059236; CADD: 0.181 (0.865)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38932183A>AACACACACACAC [1/1] rs70981599 (variation viewer)

Variant score: 0.149

Transcripts:: DNAH8:ENST00000327475.11:c.11457+190_11457+191insACACACACACAC:p.(=); DNAH8:ENST00000359357.7:c.10806+190_10806+191insACACACACACAC:p.(=); DNAH8:ENST00000449981.6:c.11457+190_11457+191insACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.1494497; CADD: 0.149 (0.703)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38957866C>CA [0/1] rs1209427701 (variation viewer)

Variant score: 0.136

Transcripts:: DNAH8:ENST00000327475.11:c.12451+6346_12451+6347insA:p.(=); DNAH8:ENST00000359357.7:c.11800+6346_11800+6347insA:p.(=); DNAH8:ENST00000449981.6:c.12451+6346_12451+6347insA:p.(=)

Pathogenicity Data:: Best Score: 0.13642514; CADD: 0.136 (0.637)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38772971CTTTTTTT>C [-/1] rs58784448 (variation viewer)

Variant score: 0.131

Transcripts:: DNAH8:ENST00000327475.11:c.1764+2413_1764+2419del:p.(=); DNAH8:ENST00000359357.7:c.1113+2413_1113+2419del:p.(=); DNAH8:ENST00000449981.6:c.1764+2413_1764+2419del:p.(=)

Pathogenicity Data:: Best Score: 0.13083947; CADD: 0.131 (0.609)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38830634CA>C [1/1] rs56761180 (variation viewer)

Variant score: 0.056

Transcripts:: DNAH8:ENST00000327475.11:c.4189-1687del:p.(=); DNAH8:ENST00000359357.7:c.3538-1687del:p.(=); DNAH8:ENST00000449981.6:c.4189-1687del:p.(=)

Pathogenicity Data:: Best Score: 0.056373775; CADD: 0.056 (0.252)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.38914392CT>C [0/1] rs66765653 (variation viewer)

Variant score: 0.043

Transcripts:: DNAH8:ENST00000327475.11:c.9963+441del:p.(=); DNAH8:ENST00000359357.7:c.9312+441del:p.(=); DNAH8:ENST00000449981.6:c.9963+441del:p.(=)

Pathogenicity Data:: Best Score: 0.04280591; CADD: 0.043 (0.190)

Frequency Data:: No frequency data

SMPD3

Exomiser Score: 0.231

Phenotype Score: 0.505

Variant Score: 0.744

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.231

Phenotype Score: 0.505

Variant Score: 0.744

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr16:g.68360139A>G [0/1] rs536546716 (variation viewer)

Variant score: 0.778 CONTRIBUTING VARIANT

Transcripts:: SMPD3:ENST00000219334.10:c.*1067T>C:p.(=)

Pathogenicity Data:: Best Score: 0.89073026; CADD: 0.891 (9.615)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3106%; UK10K: 0.4496%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.2865%; gnomAD_G_NFE: 0.4470%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68364314G>C [0/1] rs571305390 (variation viewer)

Variant score: 0.710 CONTRIBUTING VARIANT

Transcripts:: SMPD3:ENST00000219334.10:c.1555+437C>G:p.(=); SMPD3:ENST00000563226.1:c.1555+437C>G:p.(=); SMPD3:ENST00000568373.5:c.1555+437C>G:p.(=)

Pathogenicity Data:: Best Score: 0.74961984; CADD: 0.750 (6.014)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0430%; UK10K: 0.0264%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0334%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr16:g.68435523C>A [0/1] rs182750442 (variation viewer)

Variant score: 0.488

Transcripts:: SMPD3:ENST00000219334.10:c.-269+12830G>T:p.(=)

Pathogenicity Data:: Best Score: 0.51549304; CADD: 0.515 (3.147)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.0613%; UK10K: 0.0264%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0534%; gnomAD_G_OTH: 0.3061%

CLCN4

Exomiser Score: 0.229

Phenotype Score: 0.864

Variant Score: 0.337

Phenotype matches:

Phenotypic similarity 0.864 to Raynaud-Claes syndrome associated with CLCN4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases:: OMIM:300114 Raynaud-Claes syndrome - X-linked dominant; ORPHA:777 X-linked non-syndromic intellectual disability

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.046

Phenotype Score: 0.432

Variant Score: 0.628

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.10228905C>T [1/1] rs143909677 (variation viewer)

Variant score: 0.628 CONTRIBUTING VARIANT

Transcripts:: CLCN4:ENST00000380829.5:c.2100-4589C>T:p.(=); CLCN4:ENST00000380833.9:c.2193-4589C>T:p.(=); CLCN4:ENST00000421085.6:c.1911-4589C>T:p.(=)

Pathogenicity Data:: Best Score: 0.72779256; CADD: 0.728 (5.651)

Frequency Data:: 1000Genomes: 0.0795%; TOPMed: 0.2763%; UK10K: 0.6973%; gnomAD_G_AFR: 0.0342%; gnomAD_G_FIN: 0.1501%; gnomAD_G_NFE: 0.5913%; gnomAD_G_OTH: 0.1383%

X_DOMINANT

Exomiser Score: 0.229

Phenotype Score: 0.864

Variant Score: 0.337

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.10224293CGTGTGT>C [1/1] rs772983564 (variation viewer)

Variant score: 0.337 CONTRIBUTING VARIANT

Transcripts:: CLCN4:ENST00000380829.5:c.2099+3417_2099+3422del:p.(=); CLCN4:ENST00000380833.9:c.2192+3417_2192+3422del:p.(=); CLCN4:ENST00000421085.6:c.1910+3417_1910+3422del:p.(=)

Pathogenicity Data:: Best Score: 0.33671528; CADD: 0.337 (1.783)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.10191692A>AT [1/1] rs760315418 (variation viewer)

Variant score: 0.154

Transcripts:: CLCN4:ENST00000380829.5:c.245-3219_245-3218insT:p.(=); CLCN4:ENST00000380833.9:c.245-3219_245-3218insT:p.(=); CLCN4:ENST00000421085.6:c.-38-3219_-38-3218insT:p.(=)

Pathogenicity Data:: Best Score: 0.15413707; CADD: 0.154 (0.727)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.10191117G>A [1/1] rs1039522109 (variation viewer)

Variant score: 0.137

Transcripts:: CLCN4:ENST00000380829.5:c.244+3503G>A:p.(=); CLCN4:ENST00000380833.9:c.244+3503G>A:p.(=); CLCN4:ENST00000421085.6:c.-38-3794G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13662392; CADD: 0.137 (0.638)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.10216918TAC>T [1/1]

Variant score: 0.093

Transcripts:: CLCN4:ENST00000380829.5:c.1882+2840_1882+2841del:p.(=); CLCN4:ENST00000380833.9:c.1975+2840_1975+2841del:p.(=); CLCN4:ENST00000421085.6:c.1693+2840_1693+2841del:p.(=)

Pathogenicity Data:: Best Score: 0.093015194; CADD: 0.093 (0.424)

Frequency Data:: No frequency data

PPARA

Exomiser Score: 0.222

Phenotype Score: 0.503

Variant Score: 0.741

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.222

Phenotype Score: 0.503

Variant Score: 0.741

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr22:g.46149669TC>T [0/1] rs748326336 (variation viewer)

Variant score: 0.741 CONTRIBUTING VARIANT

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.7448474; CADD: 0.745 (5.932)

Frequency Data:: TOPMed: 0.0159%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0267%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.080

Phenotype Score: 0.503

Variant Score: 0.612

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr22:g.46149669TC>T [0/1] rs748326336 (variation viewer)

Variant score: 0.741 CONTRIBUTING VARIANT

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.7448474; CADD: 0.745 (5.932)

Frequency Data:: TOPMed: 0.0159%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0267%

THREE_PRIME_UTR_EXON_VARIANT chr22:g.46236958G>A [0/1]

Variant score: 0.483 CONTRIBUTING VARIANT

Transcripts:: PPARA:ENST00000262735.9:c.*1578G>A:p.(=); PPARA:ENST00000407236.5:c.*1578G>A:p.(=)

Pathogenicity Data:: Best Score: 0.48334575; CADD: 0.483 (2.868)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr22:g.46139067ACGGGC>A [1|1] rs201003839 (variation viewer)

Variant score: 0.486

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.48595637; CADD: 0.486 (2.890)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.46157923A>AC [0/1] rs781916704 (variation viewer)

Variant score: 0.387

Transcripts:: PPARA:ENST00000262735.9:c.-43+5953_-43+5954insC:p.(=); PPARA:ENST00000407236.5:c.-127+5953_-127+5954insC:p.(=)

Pathogenicity Data:: Best Score: 0.38722646; CADD: 0.387 (2.127)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.46144361A>AT [1/1] rs135558 (variation viewer)

Variant score: 0.267

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.26650017; CADD: 0.267 (1.346)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.46139074T>TCA [1|1] rs1555924323 (variation viewer)

Variant score: 0.251

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.25114113; CADD: 0.251 (1.256)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.46170402AT>A [1/1] rs935185946 (variation viewer)

Variant score: 0.181

Transcripts:: PPARA:ENST00000262735.9:c.-43+18433del:p.(=); PPARA:ENST00000407236.5:c.-126-6350del:p.(=)

Pathogenicity Data:: Best Score: 0.18115819; CADD: 0.181 (0.868)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46217819CTTTTTTTTT>C [0/1] rs60894989 (variation viewer)

Variant score: 0.177

Transcripts:: PPARA:ENST00000262735.9:c.370-443_370-435del:p.(=); PPARA:ENST00000402126.1:c.370-443_370-435del:p.(=); PPARA:ENST00000407236.5:c.370-443_370-435del:p.(=)

Pathogenicity Data:: Best Score: 0.17681015; CADD: 0.177 (0.845)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.46139001AAAC>A [1|1] rs782513352 (variation viewer)

Variant score: 0.166

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.16631883; CADD: 0.166 (0.790)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.46172318TAA>T [0/1] rs35328780 (variation viewer)

Variant score: 0.154

Transcripts:: PPARA:ENST00000262735.9:c.-43+20349_-43+20350del:p.(=); PPARA:ENST00000407236.5:c.-126-4434_-126-4433del:p.(=)

Pathogenicity Data:: Best Score: 0.15394229; CADD: 0.154 (0.726)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46207679T>TA [0/1]

Variant score: 0.129

Transcripts:: PPARA:ENST00000262735.9:c.209-7494_209-7493insA:p.(=); PPARA:ENST00000402126.1:c.209-7494_209-7493insA:p.(=); PPARA:ENST00000407236.5:c.209-7494_209-7493insA:p.(=)

Pathogenicity Data:: Best Score: 0.12883586; CADD: 0.129 (0.599)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.46153163CT>C [0/1] rs996863467 (variation viewer)

Variant score: 0.113

Transcripts:: PPARA:ENST00000262735.9:c.-43+1194del:p.(=); PPARA:ENST00000407236.5:c.-127+1194del:p.(=)

Pathogenicity Data:: Best Score: 0.112639666; CADD: 0.113 (0.519)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.46139010A>C [1|1] rs4823857 (variation viewer)

Variant score: 0.110

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.11038929; CADD: 0.110 (0.508)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46207680T>TTA [0/1] rs8140236 (variation viewer)

Variant score: 0.107

Transcripts:: PPARA:ENST00000262735.9:c.209-7493_209-7492insTA:p.(=); PPARA:ENST00000402126.1:c.209-7493_209-7492insTA:p.(=); PPARA:ENST00000407236.5:c.209-7493_209-7492insTA:p.(=)

Pathogenicity Data:: Best Score: 0.11100358; CADD: 0.111 (0.511)

Frequency Data:: gnomAD_G_AFR: 0.1721%; gnomAD_G_NFE: 0.1280%; gnomAD_G_OTH: 0.2551%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46200985G>A [0/1] rs944291366 (variation viewer)

Variant score: 0.092

Transcripts:: PPARA:ENST00000262735.9:c.208+2394G>A:p.(=); PPARA:ENST00000402126.1:c.208+2394G>A:p.(=); PPARA:ENST00000407236.5:c.208+2394G>A:p.(=)

Pathogenicity Data:: Best Score: 0.091970444; CADD: 0.092 (0.419)

Frequency Data:: gnomAD_G_AFR: 0.0117%; gnomAD_G_NFE: 0.0344%

INTERGENIC_VARIANT chr22:g.46142034A>T [1/1] rs11704748 (variation viewer)

Variant score: 0.041

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.041041076; CADD: 0.041 (0.182)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr22:g.46142036A>T [1/1] rs11704750 (variation viewer)

Variant score: 0.040

Transcripts:: PPARA:ENST00000262735.9::; PPARA:ENST00000339464.9::

Pathogenicity Data:: Best Score: 0.04037845; CADD: 0.040 (0.179)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.46196634C>A [0/1] rs562238469 (variation viewer)

Variant score: 0.015

Transcripts:: PPARA:ENST00000262735.9:c.-42-1708C>A:p.(=); PPARA:ENST00000402126.1:c.-39-1711C>A:p.(=); PPARA:ENST00000407236.5:c.-42-1708C>A:p.(=)

Pathogenicity Data:: Best Score: 0.014855385; CADD: 0.015 (0.065)

Frequency Data:: TOPMed: 0.0319%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0114%; gnomAD_G_NFE: 0.0466%

COG3

Exomiser Score: 0.217

Phenotype Score: 0.503

Variant Score: 0.738

Phenotype matches:

Proximity score 0.503 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.170

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45525634G>GTTTTTTTT [0/1] rs59577529 (variation viewer)

Variant score: 0.170 CONTRIBUTING VARIANT

Transcripts:: COG3:ENST00000349995.10:c.2230+583_2230+584insTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.1703403; CADD: 0.170 (0.811)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.217

Phenotype Score: 0.503

Variant Score: 0.738

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45489262C>CAAA [1/1] rs377551623 (variation viewer)

Variant score: 0.738 CONTRIBUTING VARIANT

Transcripts:: COG3:ENST00000349995.10:c.925-1653_925-1652insAAA:p.(=); COG3:ENST00000617493.1:c.925-1653_925-1652insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.73794043; CADD: 0.738 (5.816)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45485560T>C [1/1] rs1191777797 (variation viewer)

Variant score: 0.725

Transcripts:: COG3:ENST00000349995.10:c.844-935T>C:p.(=); COG3:ENST00000617493.1:c.844-935T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7245137; CADD: 0.725 (5.599)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45485136G>GC [0/1] rs201569836 (variation viewer)

Variant score: 0.193

Transcripts:: COG3:ENST00000349995.10:c.844-1359_844-1358insC:p.(=); COG3:ENST00000617493.1:c.844-1359_844-1358insC:p.(=)

Pathogenicity Data:: Best Score: 0.1964739; CADD: 0.196 (0.950)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1198%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45526076A>AT [0/1] rs386379016 (variation viewer)

Variant score: 0.125

Transcripts:: COG3:ENST00000349995.10:c.2230+1025_2230+1026insT:p.(=)

Pathogenicity Data:: Best Score: 0.124613166; CADD: 0.125 (0.578)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45507937CA>C [0|1]

Variant score: 0.000

Transcripts:: COG3:ENST00000349995.10:c.1595-1754del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.45507941A>AC [0|1]

Variant score: 0.000

Transcripts:: COG3:ENST00000349995.10:c.1595-1751_1595-1750insC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UBE4B

Exomiser Score: 0.212

Phenotype Score: 0.506

Variant Score: 0.732

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.078

Phenotype Score: 0.506

Variant Score: 0.605

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10101498CT>C [0/1] rs34066776 (variation viewer)

Variant score: 0.605 CONTRIBUTING VARIANT

Transcripts:: UBE4B:ENST00000253251.12:c.435+304del:p.(=); UBE4B:ENST00000343090.11:c.435+304del:p.(=); UBE4B:ENST00000672724.1:c.435+304del:p.(=)

Pathogenicity Data:: Best Score: 0.605361; CADD: 0.605 (4.038)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.212

Phenotype Score: 0.506

Variant Score: 0.732

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr1:g.10029907C>T [0/1] rs555011232 (variation viewer)

Variant score: 0.858 CONTRIBUTING VARIANT

Transcripts:: UBE4B:ENST00000253251.12::; UBE4B:ENST00000294435.8::

Pathogenicity Data:: Best Score: 0.8733515; CADD: 0.873 (8.974)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.0342%; gnomAD_G_AFR: 0.1034%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10101498CT>C [0/1] rs34066776 (variation viewer)

Variant score: 0.605 CONTRIBUTING VARIANT

Transcripts:: UBE4B:ENST00000253251.12:c.435+304del:p.(=); UBE4B:ENST00000343090.11:c.435+304del:p.(=); UBE4B:ENST00000672724.1:c.435+304del:p.(=)

Pathogenicity Data:: Best Score: 0.605361; CADD: 0.605 (4.038)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr1:g.10187708T>A [1/1] rs926467628 (variation viewer)

Variant score: 0.547

Transcripts:: UBE4B:ENST00000343090.11::

Pathogenicity Data:: Best Score: 0.54699814; CADD: 0.547 (3.439)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10048500T>A [0/1] rs570921318 (variation viewer)

Variant score: 0.475

Transcripts:: UBE4B:ENST00000253251.12:c.24+14806T>A:p.(=); UBE4B:ENST00000343090.11:c.24+14806T>A:p.(=); UBE4B:ENST00000377153.5:c.24+14806T>A:p.(=); UBE4B:ENST00000672724.1:c.24+14806T>A:p.(=)

Pathogenicity Data:: Best Score: 0.50146; CADD: 0.501 (3.023)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0143%; UK10K: 0.0132%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10095296TTTA>T [0/1] rs201933475 (variation viewer)

Variant score: 0.444

Transcripts:: UBE4B:ENST00000253251.12:c.212-164_212-162del:p.(=); UBE4B:ENST00000343090.11:c.212-164_212-162del:p.(=); UBE4B:ENST00000672724.1:c.212-164_212-162del:p.(=)

Pathogenicity Data:: Best Score: 0.81032944; CADD: 0.810 (7.220)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.9947%; UK10K: 1.4679%; gnomAD_G_AFR: 0.3666%; gnomAD_G_AMR: 0.8353%; gnomAD_G_FIN: 0.4007%; gnomAD_G_NFE: 1.2193%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10144401C>T [0/1] rs114159428 (variation viewer)

Variant score: 0.327

Transcripts:: UBE4B:ENST00000253251.12:c.1977-539C>T:p.(=); UBE4B:ENST00000343090.11:c.2364-539C>T:p.(=); UBE4B:ENST00000672724.1:c.2517-539C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4782049; CADD: 0.478 (2.825)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.8609%; UK10K: 1.2034%; gnomAD_G_AFR: 0.2985%; gnomAD_G_AMR: 0.8353%; gnomAD_G_FIN: 0.3165%; gnomAD_G_NFE: 1.0965%; gnomAD_G_OTH: 0.8197%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10035907C>T [0/1] rs193062848 (variation viewer)

Variant score: 0.273

Transcripts:: UBE4B:ENST00000253251.12:c.24+2213C>T:p.(=); UBE4B:ENST00000343090.11:c.24+2213C>T:p.(=); UBE4B:ENST00000377153.5:c.24+2213C>T:p.(=); UBE4B:ENST00000672724.1:c.24+2213C>T:p.(=)

Pathogenicity Data:: Best Score: 0.46407998; CADD: 0.464 (2.709)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 1.1210%; UK10K: 1.3092%; gnomAD_G_AFR: 0.3780%; gnomAD_G_AMR: 1.1139%; gnomAD_G_FIN: 0.4357%; gnomAD_G_NFE: 1.3953%; gnomAD_G_OTH: 1.0730%

DOWNSTREAM_GENE_VARIANT chr1:g.10183224A>G [0/1] rs544263478 (variation viewer)

Variant score: 0.196

Transcripts:: UBE4B:ENST00000343090.11::; UBE4B:ENST00000377093.8::

Pathogenicity Data:: Best Score: 0.22660744; CADD: 0.227 (1.116)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.2716%; gnomAD_G_AFR: 0.0733%; gnomAD_G_AMR: 0.5063%; gnomAD_G_ASJ: 0.6944%; gnomAD_G_FIN: 0.0984%; gnomAD_G_NFE: 0.3781%; gnomAD_G_OTH: 0.1106%

REGULATORY_REGION_VARIANT chr1:g.9829797CTT>C [1/1] rs35897686 (variation viewer)

Variant score: 0.112

Transcripts:

Pathogenicity Data:: Best Score: 0.11202651; CADD: 0.112 (0.516)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.10131999G>A [0/1] rs191232752 (variation viewer)

Variant score: 0.095

Transcripts:: UBE4B:ENST00000253251.12:c.1525-370G>A:p.(=); UBE4B:ENST00000343090.11:c.1912-370G>A:p.(=); UBE4B:ENST00000672724.1:c.2065-370G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12340295; CADD: 0.123 (0.572)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.2740%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0692%; gnomAD_G_AMR: 0.4819%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0590%; gnomAD_G_NFE: 0.3658%; gnomAD_G_OTH: 0.2079%

INTERGENIC_VARIANT chr1:g.10024986G>C [0/1] rs148086467 (variation viewer)

Variant score: 0.087

Transcripts:: UBE4B:ENST00000253251.12::; UBE4B:ENST00000294435.8::

Pathogenicity Data:: Best Score: 0.113048255; CADD: 0.113 (0.521)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.2771%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.3743%; gnomAD_G_OTH: 0.2058%

INTERGENIC_VARIANT chr1:g.10194473TGA>T [0/1] rs12139170 (variation viewer)

Variant score: 0.024

Transcripts:: UBE4B:ENST00000343090.11::

Pathogenicity Data:: Best Score: 0.037723243; CADD: 0.038 (0.167)

Frequency Data:: gnomAD_G_AFR: 0.2782%; gnomAD_G_AMR: 1.2931%; gnomAD_G_EAS: 0.0651%; gnomAD_G_FIN: 0.7021%; gnomAD_G_NFE: 0.7769%; gnomAD_G_OTH: 0.8255%

NDUFA1

Exomiser Score: 0.211

Phenotype Score: 0.504

Variant Score: 0.732

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:301020 Mitochondrial complex I deficiency, nuclear type 12 - X-linked recessive; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.211

Phenotype Score: 0.504

Variant Score: 0.732

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.119872478G>A [1|1]

Variant score: 0.732 CONTRIBUTING VARIANT

Transcripts:: NDUFA1:ENST00000371437.5:c.102+465G>A:p.(=)

Pathogenicity Data:: Best Score: 0.73214483; CADD: 0.732 (5.721)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.019

Phenotype Score: 0.252

Variant Score: 0.732

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.119872478G>A [1|1]

Variant score: 0.732 CONTRIBUTING VARIANT

Transcripts:: NDUFA1:ENST00000371437.5:c.102+465G>A:p.(=)

Pathogenicity Data:: Best Score: 0.73214483; CADD: 0.732 (5.721)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.119872471G>C [1|1]

Variant score: 0.497

Transcripts:: NDUFA1:ENST00000371437.5:c.102+458G>C:p.(=)

Pathogenicity Data:: Best Score: 0.49731028; CADD: 0.497 (2.987)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr23:g.119883582GC>G [1/1] rs200924431 (variation viewer)

Variant score: 0.126

Transcripts:: NDUFA1:ENST00000371437.5::; NDUFA1:ENST00000371425.8::

Pathogenicity Data:: Best Score: 0.12963784; CADD: 0.130 (0.603)

Frequency Data:: gnomAD_G_AMR: 0.1661%; gnomAD_G_NFE: 0.0198%

INTERGENIC_VARIANT chr23:g.119881940C>CAAAAAAAAAAAAAAAAAA [1/1] rs58872514 (variation viewer)

Variant score: 0.087

Transcripts:: NDUFA1:ENST00000371437.5::; NDUFA1:ENST00000371425.8::

Pathogenicity Data:: Best Score: 0.087148786; CADD: 0.087 (0.396)

Frequency Data:: No frequency data

MARK3

Exomiser Score: 0.207

Phenotype Score: 0.501

Variant Score: 0.733

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618283 ?Visual impairment and progressive phthisis bulbi (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.024

Phenotype Score: 0.251

Variant Score: 0.760

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103494544C>CAAA [-/1] rs35133138 (variation viewer)

Variant score: 0.760 CONTRIBUTING VARIANT

Transcripts:: MARK3:ENST00000216288.11:c.1796+2510_1796+2511insAAA:p.(=); MARK3:ENST00000303622.13:c.1844+2510_1844+2511insAAA:p.(=); MARK3:ENST00000335102.9:c.1913+2510_1913+2511insAAA:p.(=); MARK3:ENST00000416682.6:c.1913+2510_1913+2511insAAA:p.(=); MARK3:ENST00000429436.7:c.1844+2510_1844+2511insAAA:p.(=); MARK3:ENST00000440884.7:c.1607+2510_1607+2511insAAA:p.(=); MARK3:ENST00000553942.5:c.1844+2510_1844+2511insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.76033753; CADD: 0.760 (6.204)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.207

Phenotype Score: 0.501

Variant Score: 0.733

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103494544C>CAAA [-/1] rs35133138 (variation viewer)

Variant score: 0.760 CONTRIBUTING VARIANT

Transcripts:: MARK3:ENST00000216288.11:c.1796+2510_1796+2511insAAA:p.(=); MARK3:ENST00000303622.13:c.1844+2510_1844+2511insAAA:p.(=); MARK3:ENST00000335102.9:c.1913+2510_1913+2511insAAA:p.(=); MARK3:ENST00000416682.6:c.1913+2510_1913+2511insAAA:p.(=); MARK3:ENST00000429436.7:c.1844+2510_1844+2511insAAA:p.(=); MARK3:ENST00000440884.7:c.1607+2510_1607+2511insAAA:p.(=); MARK3:ENST00000553942.5:c.1844+2510_1844+2511insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.76033753; CADD: 0.760 (6.204)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103494544CA>C [-/1] rs35133138 (variation viewer)

Variant score: 0.706 CONTRIBUTING VARIANT

Transcripts:: MARK3:ENST00000216288.11:c.1796+2511del:p.(=); MARK3:ENST00000303622.13:c.1844+2511del:p.(=); MARK3:ENST00000335102.9:c.1913+2511del:p.(=); MARK3:ENST00000416682.6:c.1913+2511del:p.(=); MARK3:ENST00000429436.7:c.1844+2511del:p.(=); MARK3:ENST00000440884.7:c.1607+2511del:p.(=); MARK3:ENST00000553942.5:c.1844+2511del:p.(=)

Pathogenicity Data:: Best Score: 0.7060997; CADD: 0.706 (5.318)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103423200C>CTTTTTTTTTTTTT [1/1] rs10529756 (variation viewer)

Variant score: 0.650

Transcripts:: MARK3:ENST00000216288.11:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000303622.13:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000335102.9:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000416682.6:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000429436.7:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000440884.7:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000553942.5:c.244-5187_244-5186insTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.64957106; CADD: 0.650 (4.554)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103407152C>T [0/1] rs193238120 (variation viewer)

Variant score: 0.609

Transcripts:: MARK3:ENST00000216288.11:c.243+1885C>T:p.(=); MARK3:ENST00000303622.13:c.243+1885C>T:p.(=); MARK3:ENST00000335102.9:c.243+1885C>T:p.(=); MARK3:ENST00000416682.6:c.243+1885C>T:p.(=); MARK3:ENST00000429436.7:c.243+1885C>T:p.(=); MARK3:ENST00000440884.7:c.243+1885C>T:p.(=); MARK3:ENST00000553942.5:c.243+1885C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6822394; CADD: 0.682 (4.979)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2381%; UK10K: 0.5819%; gnomAD_G_AFR: 0.0916%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.3067%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103447606G>T [0/1] rs117391474 (variation viewer)

Variant score: 0.542

Transcripts:: MARK3:ENST00000216288.11:c.298-1313G>T:p.(=); MARK3:ENST00000303622.13:c.298-1313G>T:p.(=); MARK3:ENST00000335102.9:c.298-1313G>T:p.(=); MARK3:ENST00000416682.6:c.298-1313G>T:p.(=); MARK3:ENST00000429436.7:c.298-1313G>T:p.(=); MARK3:ENST00000440884.7:c.298-1313G>T:p.(=); MARK3:ENST00000553942.5:c.298-1313G>T:p.(=)

Pathogenicity Data:: Best Score: 0.7707021; CADD: 0.771 (6.396)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.8298%; UK10K: 1.1108%; gnomAD_G_AFR: 0.2405%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2583%; gnomAD_G_NFE: 1.1605%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103389528C>CAAAAAAAAA [0/1] rs67737305 (variation viewer)

Variant score: 0.508

Transcripts:: MARK3:ENST00000216288.11:c.51+3448_51+3449insAAAAAAAAA:p.(=); MARK3:ENST00000303622.13:c.51+3448_51+3449insAAAAAAAAA:p.(=); MARK3:ENST00000335102.9:c.51+3448_51+3449insAAAAAAAAA:p.(=); MARK3:ENST00000416682.6:c.51+3448_51+3449insAAAAAAAAA:p.(=); MARK3:ENST00000429436.7:c.51+3448_51+3449insAAAAAAAAA:p.(=); MARK3:ENST00000440884.7:c.51+3448_51+3449insAAAAAAAAA:p.(=); MARK3:ENST00000553942.5:c.51+3448_51+3449insAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.5078472; CADD: 0.508 (3.079)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103460073CTTTTTT>C [1/1] rs571611660 (variation viewer)

Variant score: 0.454

Transcripts:: MARK3:ENST00000216288.11:c.484-2331_484-2326del:p.(=); MARK3:ENST00000303622.13:c.484-2331_484-2326del:p.(=); MARK3:ENST00000335102.9:c.552+1279_552+1284del:p.(=); MARK3:ENST00000416682.6:c.552+1279_552+1284del:p.(=); MARK3:ENST00000429436.7:c.484-2331_484-2326del:p.(=); MARK3:ENST00000440884.7:c.484-2331_484-2326del:p.(=); MARK3:ENST00000553942.5:c.484-2331_484-2326del:p.(=)

Pathogenicity Data:: Best Score: 0.45373923; CADD: 0.454 (2.626)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103478819G>A [0/1] rs568837047 (variation viewer)

Variant score: 0.418

Transcripts:: MARK3:ENST00000216288.11:c.1435-1568G>A:p.(=); MARK3:ENST00000303622.13:c.1483-1568G>A:p.(=); MARK3:ENST00000335102.9:c.1552-1568G>A:p.(=); MARK3:ENST00000416682.6:c.1552-1568G>A:p.(=); MARK3:ENST00000429436.7:c.1483-1568G>A:p.(=); MARK3:ENST00000440884.7:c.1246-1568G>A:p.(=); MARK3:ENST00000553942.5:c.1483-1568G>A:p.(=)

Pathogenicity Data:: Best Score: 0.45949465; CADD: 0.459 (2.672)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.2851%; UK10K: 0.5157%; gnomAD_G_AFR: 0.2177%; gnomAD_G_FIN: 0.1434%; gnomAD_G_NFE: 0.3068%; gnomAD_G_OTH: 0.1022%

DOWNSTREAM_GENE_VARIANT chr14:g.103506033G>A [0|1] rs573221390 (variation viewer)

Variant score: 0.352

Transcripts:: MARK3:ENST00000303622.13::; MARK3:ENST00000348956.7::

Pathogenicity Data:: Best Score: 0.56136835; CADD: 0.561 (3.579)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.5272%; gnomAD_G_AFR: 0.1400%; gnomAD_G_AMR: 0.1214%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 0.2656%; gnomAD_G_NFE: 0.5407%; gnomAD_G_OTH: 0.4193%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103501557C>G [0/1] rs76665290 (variation viewer)

Variant score: 0.343

Transcripts:: MARK3:ENST00000216288.11:c.1797-1325C>G:p.(=); MARK3:ENST00000303622.13:c.1845-1325C>G:p.(=); MARK3:ENST00000335102.9:c.1986-1325C>G:p.(=); MARK3:ENST00000416682.6:c.1914-1325C>G:p.(=); MARK3:ENST00000429436.7:c.1917-1325C>G:p.(=); MARK3:ENST00000440884.7:c.1635-1325C>G:p.(=); MARK3:ENST00000553942.5:c.1890-1325C>G:p.(=)

Pathogenicity Data:: Best Score: 0.4948737; CADD: 0.495 (2.966)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.9134%; UK10K: 1.1373%; gnomAD_G_AFR: 0.2750%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2576%; gnomAD_G_NFE: 1.1860%; gnomAD_G_OTH: 1.0225%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103409435TAA>T [1|1] rs61200962 (variation viewer)

Variant score: 0.262

Transcripts:: MARK3:ENST00000216288.11:c.243+4169_243+4170del:p.(=); MARK3:ENST00000303622.13:c.243+4169_243+4170del:p.(=); MARK3:ENST00000335102.9:c.243+4169_243+4170del:p.(=); MARK3:ENST00000416682.6:c.243+4169_243+4170del:p.(=); MARK3:ENST00000429436.7:c.243+4169_243+4170del:p.(=); MARK3:ENST00000440884.7:c.243+4169_243+4170del:p.(=); MARK3:ENST00000553942.5:c.243+4169_243+4170del:p.(=)

Pathogenicity Data:: Best Score: 0.26175588; CADD: 0.262 (1.318)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr14:g.103514534CTTTTTTTTT>C [-/1] rs60261722 (variation viewer)

Variant score: 0.226

Transcripts:: MARK3:ENST00000303622.13::; MARK3:ENST00000348956.7::

Pathogenicity Data:: Best Score: 0.22642934; CADD: 0.226 (1.115)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103427497C>CAA [-/1] rs71126021 (variation viewer)

Variant score: 0.179

Transcripts:: MARK3:ENST00000216288.11:c.244-890_244-889insAA:p.(=); MARK3:ENST00000303622.13:c.244-890_244-889insAA:p.(=); MARK3:ENST00000335102.9:c.244-890_244-889insAA:p.(=); MARK3:ENST00000416682.6:c.244-890_244-889insAA:p.(=); MARK3:ENST00000429436.7:c.244-890_244-889insAA:p.(=); MARK3:ENST00000440884.7:c.244-890_244-889insAA:p.(=); MARK3:ENST00000553942.5:c.244-890_244-889insAA:p.(=)

Pathogenicity Data:: Best Score: 0.17927057; CADD: 0.179 (0.858)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr14:g.103512224C>CTTT [1/1] rs1195252085 (variation viewer)

Variant score: 0.175

Transcripts:: MARK3:ENST00000303622.13::; MARK3:ENST00000348956.7::

Pathogenicity Data:: Best Score: 0.1747225; CADD: 0.175 (0.834)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103427497C>CAAAAA [-/1] rs71126021 (variation viewer)

Variant score: 0.170

Transcripts:: MARK3:ENST00000216288.11:c.244-890_244-889insAAAAA:p.(=); MARK3:ENST00000303622.13:c.244-890_244-889insAAAAA:p.(=); MARK3:ENST00000335102.9:c.244-890_244-889insAAAAA:p.(=); MARK3:ENST00000416682.6:c.244-890_244-889insAAAAA:p.(=); MARK3:ENST00000429436.7:c.244-890_244-889insAAAAA:p.(=); MARK3:ENST00000440884.7:c.244-890_244-889insAAAAA:p.(=); MARK3:ENST00000553942.5:c.244-890_244-889insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.16957581; CADD: 0.170 (0.807)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103485063C>CAAAAAAA [1/1] rs34312214 (variation viewer)

Variant score: 0.135

Transcripts:: MARK3:ENST00000216288.11:c.1538+4573_1538+4574insAAAAAAA:p.(=); MARK3:ENST00000303622.13:c.1586+4573_1586+4574insAAAAAAA:p.(=); MARK3:ENST00000335102.9:c.1655+4573_1655+4574insAAAAAAA:p.(=); MARK3:ENST00000416682.6:c.1655+4573_1655+4574insAAAAAAA:p.(=); MARK3:ENST00000429436.7:c.1586+4573_1586+4574insAAAAAAA:p.(=); MARK3:ENST00000440884.7:c.1349+4573_1349+4574insAAAAAAA:p.(=); MARK3:ENST00000553942.5:c.1586+4573_1586+4574insAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.13543034; CADD: 0.135 (0.632)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr14:g.103514534C>CTTTT [-/1] rs60261722 (variation viewer)

Variant score: 0.114

Transcripts:: MARK3:ENST00000303622.13::; MARK3:ENST00000348956.7::

Pathogenicity Data:: Best Score: 0.11386478; CADD: 0.114 (0.525)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103458454C>CAA [1/1] rs36020485 (variation viewer)

Variant score: 0.109

Transcripts:: MARK3:ENST00000216288.11:c.483+1242_483+1243insAA:p.(=); MARK3:ENST00000303622.13:c.483+1242_483+1243insAA:p.(=); MARK3:ENST00000335102.9:c.484-273_484-272insAA:p.(=); MARK3:ENST00000416682.6:c.484-273_484-272insAA:p.(=); MARK3:ENST00000429436.7:c.483+1242_483+1243insAA:p.(=); MARK3:ENST00000440884.7:c.483+1242_483+1243insAA:p.(=); MARK3:ENST00000553942.5:c.483+1242_483+1243insAA:p.(=)

Pathogenicity Data:: Best Score: 0.10915941; CADD: 0.109 (0.502)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103446710C>CT [-/1] rs746523547 (variation viewer)

Variant score: 0.090

Transcripts:: MARK3:ENST00000216288.11:c.298-2209_298-2208insT:p.(=); MARK3:ENST00000303622.13:c.298-2209_298-2208insT:p.(=); MARK3:ENST00000335102.9:c.298-2209_298-2208insT:p.(=); MARK3:ENST00000416682.6:c.298-2209_298-2208insT:p.(=); MARK3:ENST00000429436.7:c.298-2209_298-2208insT:p.(=); MARK3:ENST00000440884.7:c.298-2209_298-2208insT:p.(=); MARK3:ENST00000553942.5:c.298-2209_298-2208insT:p.(=)

Pathogenicity Data:: Best Score: 0.08966762; CADD: 0.090 (0.408)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103407554C>CTTTT [0/1] rs71460673 (variation viewer)

Variant score: 0.087

Transcripts:: MARK3:ENST00000216288.11:c.243+2287_243+2288insTTTT:p.(=); MARK3:ENST00000303622.13:c.243+2287_243+2288insTTTT:p.(=); MARK3:ENST00000335102.9:c.243+2287_243+2288insTTTT:p.(=); MARK3:ENST00000416682.6:c.243+2287_243+2288insTTTT:p.(=); MARK3:ENST00000429436.7:c.243+2287_243+2288insTTTT:p.(=); MARK3:ENST00000440884.7:c.243+2287_243+2288insTTTT:p.(=); MARK3:ENST00000553942.5:c.243+2287_243+2288insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.08735895; CADD: 0.087 (0.397)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103444086C>CT [-/1] rs10676381 (variation viewer)

Variant score: 0.075

Transcripts:: MARK3:ENST00000216288.11:c.298-4833_298-4832insT:p.(=); MARK3:ENST00000303622.13:c.298-4833_298-4832insT:p.(=); MARK3:ENST00000335102.9:c.298-4833_298-4832insT:p.(=); MARK3:ENST00000416682.6:c.298-4833_298-4832insT:p.(=); MARK3:ENST00000429436.7:c.298-4833_298-4832insT:p.(=); MARK3:ENST00000440884.7:c.298-4833_298-4832insT:p.(=); MARK3:ENST00000553942.5:c.298-4833_298-4832insT:p.(=)

Pathogenicity Data:: Best Score: 0.07508886; CADD: 0.075 (0.339)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr14:g.103378195G>A [0/1] rs763949763 (variation viewer)

Variant score: 0.067

Transcripts:: MARK3:ENST00000440884.7::

Pathogenicity Data:: Best Score: 0.067390144; CADD: 0.067 (0.303)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103464289CTTT>C [1/1] rs143005949 (variation viewer)

Variant score: 0.050

Transcripts:: MARK3:ENST00000216288.11:c.541-1267_541-1265del:p.(=); MARK3:ENST00000303622.13:c.541-1267_541-1265del:p.(=); MARK3:ENST00000335102.9:c.610-1267_610-1265del:p.(=); MARK3:ENST00000416682.6:c.610-1267_610-1265del:p.(=); MARK3:ENST00000429436.7:c.541-1267_541-1265del:p.(=); MARK3:ENST00000440884.7:c.541-1682_541-1680del:p.(=); MARK3:ENST00000553942.5:c.541-1267_541-1265del:p.(=)

Pathogenicity Data:: Best Score: 0.04983288; CADD: 0.050 (0.222)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.103470455A>ATTTTTTTTTTTTT [1/1] rs6145477 (variation viewer)

Variant score: 0.050

Transcripts:: MARK3:ENST00000216288.11:c.1216+2269_1216+2270insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000303622.13:c.1264+2269_1264+2270insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000335102.9:c.1333+2269_1333+2270insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000416682.6:c.1333+2269_1333+2270insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000429436.7:c.1264+2269_1264+2270insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000440884.7:c.1027+2269_1027+2270insTTTTTTTTTTTTT:p.(=); MARK3:ENST00000553942.5:c.1264+2269_1264+2270insTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.04961407; CADD: 0.050 (0.221)

Frequency Data:: No frequency data

DNMT3A

Exomiser Score: 0.199

Phenotype Score: 0.906

Variant Score: 0.270

Phenotype matches:

Phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Known diseases:: OMIM:601626 Acute myeloid leukemia, somatic - autosomal dominant; OMIM:615879 Tatton-Brown-Rahman syndrome - autosomal dominant; OMIM:618724 Heyn-Sproul-Jackson syndrome - autosomal dominant; ORPHA:404443 Tall stature-intellectual disability-facial dysmorphism syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.199

Phenotype Score: 0.906

Variant Score: 0.270

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.25304462C>T [0/1] rs938900178 (variation viewer)

Variant score: 0.270 CONTRIBUTING VARIANT

Transcripts:: DNMT3A:ENST00000264709.7:c.73-4219G>A:p.(=); DNMT3A:ENST00000321117.9:c.73-4219G>A:p.(=); DNMT3A:ENST00000406659.3:c.73-4219G>A:p.(=)

Pathogenicity Data:: Best Score: 0.27071047; CADD: 0.271 (1.371)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.041

Phenotype Score: 0.453

Variant Score: 0.591

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.25278042C>CAAACAG [1/1] rs59654713 (variation viewer)

Variant score: 0.591 CONTRIBUTING VARIANT

Transcripts:: DNMT3A:ENST00000264709.7:c.449-2500_449-2499insCTGTTT:p.(=); DNMT3A:ENST00000321117.9:c.449-2500_449-2499insCTGTTT:p.(=)

Pathogenicity Data:: Best Score: 0.59111613; CADD: 0.591 (3.884)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.25272977A>AT [0/1] rs70947875 (variation viewer)

Variant score: 0.147

Transcripts:: DNMT3A:ENST00000264709.7:c.639+1963_639+1964insA:p.(=); DNMT3A:ENST00000321117.9:c.639+1963_639+1964insA:p.(=)

Pathogenicity Data:: Best Score: 0.14689988; CADD: 0.147 (0.690)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.25300712AATATAT>A [-/1] rs3039391 (variation viewer)

Variant score: 0.095

Transcripts:: DNMT3A:ENST00000264709.7:c.73-475_73-470del:p.(=); DNMT3A:ENST00000321117.9:c.73-475_73-470del:p.(=); DNMT3A:ENST00000406659.3:c.73-475_73-470del:p.(=)

Pathogenicity Data:: Best Score: 0.09510124; CADD: 0.095 (0.434)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.25300712AAT>A [-/1] rs3039391 (variation viewer)

Variant score: 0.078

Transcripts:: DNMT3A:ENST00000264709.7:c.73-471_73-470del:p.(=); DNMT3A:ENST00000321117.9:c.73-471_73-470del:p.(=); DNMT3A:ENST00000406659.3:c.73-471_73-470del:p.(=)

Pathogenicity Data:: Best Score: 0.078065634; CADD: 0.078 (0.353)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr2:g.25224726TTA>* [-/1]

Variant score: 0.000

Transcripts:: DNMT3A:ENST00000264709.7::; DNMT3A:ENST00000405623.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CTNNA3

Exomiser Score: 0.196

Phenotype Score: 0.508

Variant Score: 0.718

Phenotype matches:

Proximity score 0.508 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615616 Arrhythmogenic right ventricular dysplasia, familial, 13 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.196

Phenotype Score: 0.508

Variant Score: 0.718

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67575940G>A [0/1] rs776028392 (variation viewer)

Variant score: 0.718 CONTRIBUTING VARIANT

Transcripts:: CTNNA3:ENST00000433211.7:c.292+30917C>T:p.(=)

Pathogenicity Data:: Best Score: 0.71977943; CADD: 0.720 (5.525)

Frequency Data:: UK10K: 0.0132%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.060

Phenotype Score: 0.254

Variant Score: 0.860

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66362096AT>A [1/1] rs569047811 (variation viewer)

Variant score: 0.860 CONTRIBUTING VARIANT

Transcripts:: CTNNA3:ENST00000433211.7:c.1732+17055del:p.(=)

Pathogenicity Data:: Best Score: 0.8596863; CADD: 0.860 (8.529)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66071386A>AAAACAACTAACACATATATGACAGACACTCTTCTTGAAACCATGAAC [1/1] rs6143957 (variation viewer)

Variant score: 0.792

Transcripts:: CTNNA3:ENST00000433211.7:c.1978-1898_1978-1897insGTTCATGGTTTCAAGAAGAGTGTCTGTCATATATGTGTTAGTTGTTT:p.(=)

Pathogenicity Data:: Best Score: 0.7923653; CADD: 0.792 (6.827)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66724351G>A [0/1] rs75809426 (variation viewer)

Variant score: 0.745

Transcripts:: CTNNA3:ENST00000433211.7:c.1281+41913C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7684206; CADD: 0.768 (6.353)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0701%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1600%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67267997T>C [0/1] rs577327199 (variation viewer)

Variant score: 0.738

Transcripts:: CTNNA3:ENST00000433211.7:c.580-48127A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7753533; CADD: 0.775 (6.485)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1171%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.2266%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67477757A>C [0/1] rs570262293 (variation viewer)

Variant score: 0.709

Transcripts:: CTNNA3:ENST00000433211.7:c.579+44085T>G:p.(=)

Pathogenicity Data:: Best Score: 0.9712922; CADD: 0.971 (15.420)

Frequency Data:: 1000Genomes: 1.0980%; TOPMed: 0.2907%; UK10K: 0.2116%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.3863%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67368603A>C [0/1] rs559202038 (variation viewer)

Variant score: 0.692

Transcripts:: CTNNA3:ENST00000433211.7:c.580-148733T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7269137; CADD: 0.727 (5.637)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0876%; UK10K: 0.1058%; gnomAD_G_NFE: 0.2066%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66437873G>A [0/1] rs553919322 (variation viewer)

Variant score: 0.685

Transcripts:: CTNNA3:ENST00000433211.7:c.1532-58521C>T:p.(=)

Pathogenicity Data:: Best Score: 0.70042884; CADD: 0.700 (5.235)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0597%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0459%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1533%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66691574A>T [0/1] rs534375677 (variation viewer)

Variant score: 0.648

Transcripts:: CTNNA3:ENST00000433211.7:c.1282-69790T>A:p.(=)

Pathogenicity Data:: Best Score: 0.66818196; CADD: 0.668 (4.791)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0693%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1600%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66952294C>T [0/1] rs117122351 (variation viewer)

Variant score: 0.615

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-176770G>A:p.(=); CTNNA3:ENST00000361320.5:c.1536+23842C>T:p.(=)

Pathogenicity Data:: Best Score: 0.69189405; CADD: 0.692 (5.113)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2190%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.2467%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66282104A>G [0/1] rs548423858 (variation viewer)

Variant score: 0.583

Transcripts:: CTNNA3:ENST00000433211.7:c.1733-1483T>C:p.(=)

Pathogenicity Data:: Best Score: 0.58495045; CADD: 0.585 (3.819)

Frequency Data:: TOPMed: 0.0135%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66451679A>AT [0/1] rs759133429 (variation viewer)

Variant score: 0.578

Transcripts:: CTNNA3:ENST00000433211.7:c.1531+68937_1531+68938insA:p.(=)

Pathogenicity Data:: Best Score: 0.5913985; CADD: 0.591 (3.887)

Frequency Data:: TOPMed: 0.0597%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0458%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1534%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67647146T>TTATATATATATA [-/1] rs67324505 (variation viewer)

Variant score: 0.576

Transcripts:: CTNNA3:ENST00000433211.7:c.99+268_99+269insTATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.57567364; CADD: 0.576 (3.723)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66840323A>ATC [1/1] rs71035189 (variation viewer)

Variant score: 0.570

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-64800_1048-64799insGA:p.(=)

Pathogenicity Data:: Best Score: 0.5697707; CADD: 0.570 (3.663)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66478364A>G [0/1] rs563032478 (variation viewer)

Variant score: 0.564

Transcripts:: CTNNA3:ENST00000433211.7:c.1531+42253T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5791765; CADD: 0.579 (3.759)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0558%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0458%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1403%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67583491A>G [0|1] rs543508653 (variation viewer)

Variant score: 0.554

Transcripts:: CTNNA3:ENST00000433211.7:c.292+23366T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7486378; CADD: 0.749 (5.997)

Frequency Data:: 1000Genomes: 0.3794%; gnomAD_G_AFR: 0.0699%; gnomAD_G_AMR: 0.5115%; gnomAD_G_ASJ: 1.0714%; gnomAD_G_FIN: 0.6514%; gnomAD_G_NFE: 0.3413%; gnomAD_G_OTH: 0.5423%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66039363T>A [0/1] rs969605068 (variation viewer)

Variant score: 0.550

Transcripts:: CTNNA3:ENST00000433211.7:c.2159+29945A>T:p.(=)

Pathogenicity Data:: Best Score: 0.55053073; CADD: 0.551 (3.473)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66524186C>CTGTCCCATTCCCTATACCCAGCAAATTGAATTTTCTCCTTTG [0/1] rs71466886 (variation viewer)

Variant score: 0.510

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-3414_1375-3413insCAAAGGAGAAAATTCAATTTGCTGGGTATAGGGAATGGGACA:p.(=)

Pathogenicity Data:: Best Score: 0.5095441; CADD: 0.510 (3.094)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67430820T>TACACACACACACAC [-/1] rs371146065 (variation viewer)

Variant score: 0.498

Transcripts:: CTNNA3:ENST00000433211.7:c.579+91021_579+91022insGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.49846643; CADD: 0.498 (2.997)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67554683A>C [0/1] rs550350727 (variation viewer)

Variant score: 0.497

Transcripts:: CTNNA3:ENST00000433211.7:c.293-15014T>G:p.(=)

Pathogenicity Data:: Best Score: 0.5223608; CADD: 0.522 (3.209)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0852%; UK10K: 0.0661%; gnomAD_G_NFE: 0.2070%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67408882C>CAA [1/1] rs766212790 (variation viewer)

Variant score: 0.494

Transcripts:: CTNNA3:ENST00000433211.7:c.579+112959_579+112960insTT:p.(=)

Pathogenicity Data:: Best Score: 0.49359262; CADD: 0.494 (2.955)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66147608GTT>G [0/1] rs34193216 (variation viewer)

Variant score: 0.487

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-44361_1885-44360del:p.(=)

Pathogenicity Data:: Best Score: 0.48654783; CADD: 0.487 (2.895)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67228098T>C [0/1] rs561277684 (variation viewer)

Variant score: 0.464

Transcripts:: CTNNA3:ENST00000433211.7:c.580-8228A>G:p.(=)

Pathogenicity Data:: Best Score: 0.48761076; CADD: 0.488 (2.904)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0980%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.2067%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67199592A>G [0/1] rs180931651 (variation viewer)

Variant score: 0.382

Transcripts:: CTNNA3:ENST00000433211.7:c.844-19072T>C:p.(=); CTNNA3:ENST00000545309.2:c.268-19072T>C:p.(=)

Pathogenicity Data:: Best Score: 0.4221701; CADD: 0.422 (2.382)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.2063%; UK10K: 0.5290%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.2937%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67060666GTCTCTCTC>G [0/1] rs141445121 (variation viewer)

Variant score: 0.379

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+119643_1047+119650del:p.(=); CTNNA3:ENST00000361320.5:c.1537-36920_1537-36913del:p.(=)

Pathogenicity Data:: Best Score: 0.4129163; CADD: 0.413 (2.313)

Frequency Data:: 1000Genomes: 0.2852%; TOPMed: 0.2852%; gnomAD_G_AFR: 0.0703%; gnomAD_G_NFE: 0.4752%; gnomAD_G_OTH: 0.4435%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67081579C>G [0/1] rs79448097 (variation viewer)

Variant score: 0.345

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+98738G>C:p.(=); CTNNA3:ENST00000361320.5:c.1537-16008C>G:p.(=)

Pathogenicity Data:: Best Score: 0.3816989; CADD: 0.382 (2.088)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.3002%; UK10K: 0.2645%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.5330%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66046453G>A [0|1] rs569393872 (variation viewer)

Variant score: 0.339

Transcripts:: CTNNA3:ENST00000433211.7:c.2159+22855C>T:p.(=)

Pathogenicity Data:: Best Score: 0.34686947; CADD: 0.347 (1.850)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0725%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.1533%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67249416C>T [0/1] rs539540094 (variation viewer)

Variant score: 0.326

Transcripts:: CTNNA3:ENST00000433211.7:c.580-29546G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3429476; CADD: 0.343 (1.824)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0972%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.2066%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66743974C>CAA [0/1] rs536825430 (variation viewer)

Variant score: 0.320

Transcripts:: CTNNA3:ENST00000433211.7:c.1281+22289_1281+22290insTT:p.(=)

Pathogenicity Data:: Best Score: 0.32017052; CADD: 0.320 (1.676)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67524395CAAAAAAAA>C [0/1] rs200850487 (variation viewer)

Variant score: 0.307

Transcripts:: CTNNA3:ENST00000433211.7:c.460-2442_460-2435del:p.(=)

Pathogenicity Data:: Best Score: 0.30689347; CADD: 0.307 (1.592)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67560903A>G [0/1] rs570326677 (variation viewer)

Variant score: 0.305

Transcripts:: CTNNA3:ENST00000433211.7:c.293-21234T>C:p.(=)

Pathogenicity Data:: Best Score: 0.4187004; CADD: 0.419 (2.356)

Frequency Data:: 1000Genomes: 1.0980%; TOPMed: 0.2923%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.3931%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66753403C>G [0/1] rs536645960 (variation viewer)

Variant score: 0.302

Transcripts:: CTNNA3:ENST00000433211.7:c.1281+12861G>C:p.(=)

Pathogenicity Data:: Best Score: 0.31182325; CADD: 0.312 (1.623)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0788%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1600%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66447210T>C [0/1] rs551741274 (variation viewer)

Variant score: 0.286

Transcripts:: CTNNA3:ENST00000433211.7:c.1532-67858A>G:p.(=)

Pathogenicity Data:: Best Score: 0.45624906; CADD: 0.456 (2.646)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2365%; gnomAD_G_AFR: 0.0229%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.7441%; gnomAD_G_NFE: 1.1332%; gnomAD_G_OTH: 1.3238%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66018187T>TACACACACACACACACACAC [-/1] rs59373779 (variation viewer)

Variant score: 0.275

Transcripts:: CTNNA3:ENST00000433211.7:c.2160-29391_2160-29390insGTGTGTGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.27523035; CADD: 0.275 (1.398)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67390498C>A [0/1]

Variant score: 0.245

Transcripts:: CTNNA3:ENST00000433211.7:c.579+131344G>T:p.(=)

Pathogenicity Data:: Best Score: 0.24455994; CADD: 0.245 (1.218)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67583489A>C [0|1] rs1273626521 (variation viewer)

Variant score: 0.242

Transcripts:: CTNNA3:ENST00000433211.7:c.292+23368T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7165999; CADD: 0.717 (5.476)

Frequency Data:: gnomAD_G_AFR: 0.1049%; gnomAD_G_AMR: 0.6410%; gnomAD_G_ASJ: 1.7730%; gnomAD_G_FIN: 0.6546%; gnomAD_G_NFE: 0.3936%; gnomAD_G_OTH: 0.6522%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67419937C>T [0/1] rs559074632 (variation viewer)

Variant score: 0.232

Transcripts:: CTNNA3:ENST00000433211.7:c.579+101905G>A:p.(=)

Pathogenicity Data:: Best Score: 0.24421197; CADD: 0.244 (1.216)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0908%; UK10K: 0.0793%; gnomAD_G_NFE: 0.2068%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66024085A>ATTTTT [0/1] rs71474007 (variation viewer)

Variant score: 0.190

Transcripts:: CTNNA3:ENST00000433211.7:c.2160-35289_2160-35288insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.18978554; CADD: 0.190 (0.914)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67526773C>A [0/1] rs1014250344 (variation viewer)

Variant score: 0.183

Transcripts:: CTNNA3:ENST00000433211.7:c.460-4812G>T:p.(=)

Pathogenicity Data:: Best Score: 0.18266517; CADD: 0.183 (0.876)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66949563T>TA [-/1] rs5785805 (variation viewer)

Variant score: 0.172

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-174040_1048-174039insT:p.(=); CTNNA3:ENST00000361320.5:c.1536+21111_1536+21112insA:p.(=)

Pathogenicity Data:: Best Score: 0.19610375; CADD: 0.196 (0.948)

Frequency Data:: gnomAD_G_AFR: 0.1510%; gnomAD_G_AMR: 0.6369%; gnomAD_G_ASJ: 0.3937%; gnomAD_G_FIN: 0.3839%; gnomAD_G_NFE: 0.2646%; gnomAD_G_OTH: 0.5168%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67368104G>A [0/1] rs35840945 (variation viewer)

Variant score: 0.170

Transcripts:: CTNNA3:ENST00000433211.7:c.580-148234C>T:p.(=)

Pathogenicity Data:: Best Score: 0.36247092; CADD: 0.362 (1.955)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 1.0660%; UK10K: 1.5604%; gnomAD_G_AFR: 0.2407%; gnomAD_G_AMR: 0.9547%; gnomAD_G_FIN: 1.1461%; gnomAD_G_NFE: 1.5944%; gnomAD_G_OTH: 1.3265%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66154719C>CATATATATATATATATATATATATAT [-/1] rs569694429 (variation viewer)

Variant score: 0.169

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-51471_1885-51470insATATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.16861916; CADD: 0.169 (0.802)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66136059G>A [0/1] rs550982510 (variation viewer)

Variant score: 0.156

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-32810C>T:p.(=)

Pathogenicity Data:: Best Score: 0.15957296; CADD: 0.160 (0.755)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0613%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0345%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.1403%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66401518AACACACACACACAC>A [-/1] rs140986771 (variation viewer)

Variant score: 0.151

Transcripts:: CTNNA3:ENST00000433211.7:c.1532-22180_1532-22167del:p.(=)

Pathogenicity Data:: Best Score: 0.15062398; CADD: 0.151 (0.709)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66341575T>C [0/1] rs185886397 (variation viewer)

Variant score: 0.144

Transcripts:: CTNNA3:ENST00000433211.7:c.1732+37577A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9668105; CADD: 0.967 (14.790)

Frequency Data:: 1000Genomes: 0.8187%; TOPMed: 1.2240%; UK10K: 1.9175%; gnomAD_G_AFR: 0.4010%; gnomAD_G_AMR: 1.0766%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.8028%; gnomAD_G_NFE: 1.7864%; gnomAD_G_OTH: 0.9221%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66102238T>A [0/1] rs565886777 (variation viewer)

Variant score: 0.140

Transcripts:: CTNNA3:ENST00000433211.7:c.1977+919A>T:p.(=)

Pathogenicity Data:: Best Score: 0.14296216; CADD: 0.143 (0.670)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0741%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0860%; gnomAD_G_NFE: 0.1465%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66328911C>CAT [-/1] rs1554935009 (variation viewer)

Variant score: 0.139

Transcripts:: CTNNA3:ENST00000433211.7:c.1733-48291_1733-48290insAT:p.(=)

Pathogenicity Data:: Best Score: 0.13940269; CADD: 0.139 (0.652)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67389029CATA>C [0/1] rs1231680516 (variation viewer)

Variant score: 0.139

Transcripts:: CTNNA3:ENST00000433211.7:c.579+132810_579+132812del:p.(=)

Pathogenicity Data:: Best Score: 0.14157963; CADD: 0.142 (0.663)

Frequency Data:: gnomAD_G_AFR: 0.0124%; gnomAD_G_FIN: 0.0323%; gnomAD_G_OTH: 0.1190%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66398724C>T [0/1]

Variant score: 0.131

Transcripts:: CTNNA3:ENST00000433211.7:c.1532-19372G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13083947; CADD: 0.131 (0.609)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66597511C>CATAT [-/1] rs369390875 (variation viewer)

Variant score: 0.128

Transcripts:: CTNNA3:ENST00000433211.7:c.1374+24180_1374+24181insATAT:p.(=)

Pathogenicity Data:: Best Score: 0.1280331; CADD: 0.128 (0.595)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66548979AT>A [0|1] rs1165318505 (variation viewer)

Variant score: 0.126

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-28207del:p.(=)

Pathogenicity Data:: Best Score: 0.126023; CADD: 0.126 (0.585)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66547343C>CTT [-/1] rs1246714246 (variation viewer)

Variant score: 0.124

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-26571_1375-26570insAA:p.(=)

Pathogenicity Data:: Best Score: 0.123806536; CADD: 0.124 (0.574)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66189617T>TATATATAC [-/1] rs151078010 (variation viewer)

Variant score: 0.122

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-86369_1885-86368insGTATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.12198889; CADD: 0.122 (0.565)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66979252G>C [0/1] rs61866214 (variation viewer)

Variant score: 0.115

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+201065C>G:p.(=); CTNNA3:ENST00000361320.5:c.1536+50800G>C:p.(=)

Pathogenicity Data:: Best Score: 0.14236993; CADD: 0.142 (0.667)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.4181%; UK10K: 0.5290%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.8944%; gnomAD_G_NFE: 0.8085%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66845703CAAAAAAA>C [1/1] rs61085873 (variation viewer)

Variant score: 0.113

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-70186_1048-70180del:p.(=)

Pathogenicity Data:: Best Score: 0.11284399; CADD: 0.113 (0.520)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66024011T>C [0/1] rs538864089 (variation viewer)

Variant score: 0.112

Transcripts:: CTNNA3:ENST00000433211.7:c.2160-35214A>G:p.(=)

Pathogenicity Data:: Best Score: 0.11468053; CADD: 0.115 (0.529)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0605%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0584%; gnomAD_G_NFE: 0.1334%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66732800C>CT [0/1] rs532459216 (variation viewer)

Variant score: 0.109

Transcripts:: CTNNA3:ENST00000433211.7:c.1281+33463_1281+33464insA:p.(=)

Pathogenicity Data:: Best Score: 0.13940269; CADD: 0.139 (0.652)

Frequency Data:: gnomAD_G_AFR: 0.2359%; gnomAD_G_AMR: 0.6831%; gnomAD_G_FIN: 0.5575%; gnomAD_G_NFE: 0.9684%; gnomAD_G_OTH: 0.8753%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66547343C>CTTTTTTTTT [-/1] rs1246714246 (variation viewer)

Variant score: 0.108

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-26571_1375-26570insAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.1077224; CADD: 0.108 (0.495)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66978552A>T [1/1] rs201227773 (variation viewer)

Variant score: 0.107

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+201765T>A:p.(=); CTNNA3:ENST00000361320.5:c.1536+50100A>T:p.(=)

Pathogenicity Data:: Best Score: 0.10710579; CADD: 0.107 (0.492)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.65921272G>A [0/1] rs1027802742 (variation viewer)

Variant score: 0.107

Transcripts:: CTNNA3:ENST00000433211.7:c.2401-655C>T:p.(=)

Pathogenicity Data:: Best Score: 0.106900156; CADD: 0.107 (0.491)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66356122GTT>G [0/1] rs59366031 (variation viewer)

Variant score: 0.105

Transcripts:: CTNNA3:ENST00000433211.7:c.1732+23028_1732+23029del:p.(=)

Pathogenicity Data:: Best Score: 0.10545951; CADD: 0.105 (0.484)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66318276A>ATATATGTG [-/1] rs33943741 (variation viewer)

Variant score: 0.104

Transcripts:: CTNNA3:ENST00000433211.7:c.1733-37656_1733-37655insCACATATA:p.(=)

Pathogenicity Data:: Best Score: 0.10401654; CADD: 0.104 (0.477)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.67690845G>A [0/1] rs187993537 (variation viewer)

Variant score: 0.096

Transcripts:: CTNNA3:ENST00000433211.7:c.-6+5155C>T:p.(=)

Pathogenicity Data:: Best Score: 0.22803074; CADD: 0.228 (1.124)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.7860%; UK10K: 1.3092%; gnomAD_G_AFR: 0.2500%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 1.6667%; gnomAD_G_FIN: 0.2597%; gnomAD_G_NFE: 0.9825%; gnomAD_G_OTH: 0.7187%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66328911C>CATATATATATATATATATATAT [-/1] rs1554935009 (variation viewer)

Variant score: 0.094

Transcripts:: CTNNA3:ENST00000433211.7:c.1733-48291_1733-48290insATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.093850195; CADD: 0.094 (0.428)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67417663A>AAATTTAAATCCAATTTAAATTGGTTTAAATCC [0/1] rs1245612241 (variation viewer)

Variant score: 0.092

Transcripts:: CTNNA3:ENST00000433211.7:c.579+104178_579+104179insGGATTTAAACCAATTTAAATTGGATTTAAATT:p.(=)

Pathogenicity Data:: Best Score: 0.09676659; CADD: 0.097 (0.442)

Frequency Data:: gnomAD_G_AFR: 0.0348%; gnomAD_G_NFE: 0.2069%; gnomAD_G_OTH: 0.3067%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67564677GTATATATATATATATATATATA>G [0/1] rs71006151 (variation viewer)

Variant score: 0.092

Transcripts:: CTNNA3:ENST00000433211.7:c.293-25030_293-25009del:p.(=)

Pathogenicity Data:: Best Score: 0.09155214; CADD: 0.092 (0.417)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66831844G>A [0/1] rs142782205 (variation viewer)

Variant score: 0.088

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-56320C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12702864; CADD: 0.127 (0.590)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.6275%; UK10K: 0.9654%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.8394%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66996649C>CAAA [0/1] rs57025097 (variation viewer)

Variant score: 0.087

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+183667_1047+183668insTTT:p.(=); CTNNA3:ENST00000361320.5:c.1536+68197_1536+68198insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.08651799; CADD: 0.087 (0.393)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66543907GTGTGTA>G [-/1] rs1473078207 (variation viewer)

Variant score: 0.086

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-23140_1375-23135del:p.(=)

Pathogenicity Data:: Best Score: 0.08588678; CADD: 0.086 (0.390)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66520245CT>C [0/1] rs543882241 (variation viewer)

Variant score: 0.084

Transcripts:: CTNNA3:ENST00000433211.7:c.1531+371del:p.(=)

Pathogenicity Data:: Best Score: 0.08441222; CADD: 0.084 (0.383)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66738115A>G [0/1] rs190631095 (variation viewer)

Variant score: 0.083

Transcripts:: CTNNA3:ENST00000433211.7:c.1281+28149T>C:p.(=)

Pathogenicity Data:: Best Score: 0.55832785; CADD: 0.558 (3.549)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.4277%; UK10K: 0.4232%; gnomAD_G_AFR: 0.1145%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.1431%; gnomAD_G_NFE: 0.5798%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67620923G>GTGTATA [-/1] rs1402402526 (variation viewer)

Variant score: 0.082

Transcripts:: CTNNA3:ENST00000433211.7:c.100-13875_100-13874insTATACA:p.(=)

Pathogenicity Data:: Best Score: 0.08166742; CADD: 0.082 (0.370)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66978550A>AT [0/1] rs200198620 (variation viewer)

Variant score: 0.074

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+201766_1047+201767insA:p.(=); CTNNA3:ENST00000361320.5:c.1536+50098_1536+50099insT:p.(=)

Pathogenicity Data:: Best Score: 0.083779514; CADD: 0.084 (0.380)

Frequency Data:: gnomAD_G_AFR: 0.4561%; gnomAD_G_EAS: 0.3472%; gnomAD_G_NFE: 0.1444%; gnomAD_G_OTH: 0.6410%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66516100G>T [0/1] rs187297228 (variation viewer)

Variant score: 0.073

Transcripts:: CTNNA3:ENST00000433211.7:c.1531+4517C>A:p.(=)

Pathogenicity Data:: Best Score: 0.1368227; CADD: 0.137 (0.639)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.5153%; gnomAD_G_AFR: 0.1451%; gnomAD_G_AMR: 0.1706%; gnomAD_G_FIN: 1.1551%; gnomAD_G_NFE: 0.7658%; gnomAD_G_OTH: 1.4908%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66170241C>CT [-/1] rs57644952 (variation viewer)

Variant score: 0.071

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-66993_1885-66992insA:p.(=)

Pathogenicity Data:: Best Score: 0.070819676; CADD: 0.071 (0.319)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67620923G>GTGTATATATATATATA [-/1] rs1402402526 (variation viewer)

Variant score: 0.067

Transcripts:: CTNNA3:ENST00000433211.7:c.100-13875_100-13874insTATATATATATATACA:p.(=)

Pathogenicity Data:: Best Score: 0.06696057; CADD: 0.067 (0.301)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66170241C>CTTTT [-/1] rs57644952 (variation viewer)

Variant score: 0.066

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-66993_1885-66992insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.06631583; CADD: 0.066 (0.298)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67621532G>A [0/1] rs151176683 (variation viewer)

Variant score: 0.062

Transcripts:: CTNNA3:ENST00000433211.7:c.100-14483C>T:p.(=)

Pathogenicity Data:: Best Score: 0.067819536; CADD: 0.068 (0.305)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.2206%; UK10K: 0.5157%; gnomAD_G_AFR: 0.1033%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.2943%; gnomAD_G_OTH: 0.1025%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66211983GT>G [1/1] rs61453326 (variation viewer)

Variant score: 0.061

Transcripts:: CTNNA3:ENST00000433211.7:c.1884+68486del:p.(=)

Pathogenicity Data:: Best Score: 0.061357975; CADD: 0.061 (0.275)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66178399GTATA>G [0/1] rs71035113 (variation viewer)

Variant score: 0.059

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-75154_1885-75151del:p.(=)

Pathogenicity Data:: Best Score: 0.05941075; CADD: 0.059 (0.266)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66055649C>T [0/1] rs554211117 (variation viewer)

Variant score: 0.052

Transcripts:: CTNNA3:ENST00000433211.7:c.2159+13659G>A:p.(=)

Pathogenicity Data:: Best Score: 0.052890897; CADD: 0.053 (0.236)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0589%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.0580%; gnomAD_G_NFE: 0.1336%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66749202CA>C [1/1] rs35568730 (variation viewer)

Variant score: 0.042

Transcripts:: CTNNA3:ENST00000433211.7:c.1281+17061del:p.(=)

Pathogenicity Data:: Best Score: 0.041703284; CADD: 0.042 (0.185)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66971408C>G [0/1] rs61866211 (variation viewer)

Variant score: 0.030

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-195884G>C:p.(=); CTNNA3:ENST00000361320.5:c.1536+42956C>G:p.(=)

Pathogenicity Data:: Best Score: 0.041482627; CADD: 0.041 (0.184)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.4285%; UK10K: 0.4761%; gnomAD_G_AFR: 0.1287%; gnomAD_G_AMR: 0.5435%; gnomAD_G_ASJ: 0.3521%; gnomAD_G_FIN: 1.1027%; gnomAD_G_NFE: 0.9815%; gnomAD_G_OTH: 0.7576%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67267427C>T [0/1] rs963784553 (variation viewer)

Variant score: 0.029

Transcripts:: CTNNA3:ENST00000433211.7:c.580-47557G>A:p.(=)

Pathogenicity Data:: Best Score: 0.029266536; CADD: 0.029 (0.129)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66007740A>ACCTTCCTTTCCTCCTCCCTTCCTTCCTCTCTCCCAC [0/1] rs796809708 (variation viewer)

Variant score: 0.027

Transcripts:: CTNNA3:ENST00000433211.7:c.2160-18944_2160-18943insGTGGGAGAGAGGAAGGAAGGGAGGAGGAAAGGAAGG:p.(=)

Pathogenicity Data:: Best Score: 0.027476728; CADD: 0.027 (0.121)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67548782G>A [0/1] rs71496048 (variation viewer)

Variant score: 0.026

Transcripts:: CTNNA3:ENST00000433211.7:c.293-9113C>T:p.(=)

Pathogenicity Data:: Best Score: 0.058110416; CADD: 0.058 (0.260)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 1.0630%; UK10K: 1.5075%; gnomAD_G_AFR: 0.2089%; gnomAD_G_AMR: 1.1139%; gnomAD_G_FIN: 0.8023%; gnomAD_G_NFE: 1.6182%; gnomAD_G_OTH: 1.3655%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66633658C>A [0/1] rs149210472 (variation viewer)

Variant score: 0.024

Transcripts:: CTNNA3:ENST00000433211.7:c.1282-11874G>T:p.(=)

Pathogenicity Data:: Best Score: 0.15860486; CADD: 0.159 (0.750)

Frequency Data:: 1000Genomes: 0.7987%; TOPMed: 1.2570%; UK10K: 1.5075%; gnomAD_G_AFR: 0.3913%; gnomAD_G_AMR: 0.9569%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.5187%; gnomAD_G_NFE: 1.9458%; gnomAD_G_OTH: 1.4344%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66806756ATG>A [-/1] rs57749652 (variation viewer)

Variant score: 0.022

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-31234_1048-31233del:p.(=)

Pathogenicity Data:: Best Score: 0.021862268; CADD: 0.022 (0.096)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67243254G>A [0/1] rs71496036 (variation viewer)

Variant score: 0.017

Transcripts:: CTNNA3:ENST00000433211.7:c.580-23384C>T:p.(=)

Pathogenicity Data:: Best Score: 0.033726633; CADD: 0.034 (0.149)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 1.0230%; UK10K: 1.4414%; gnomAD_G_AFR: 0.1948%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.0888%; gnomAD_G_NFE: 1.5406%; gnomAD_G_OTH: 1.3238%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.65978496A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.2265+10196T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.65990074A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.2160-1277T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66065240G>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.2159+4068C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66165489T>TA [0/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1885-62241_1885-62240insT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66329581A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1733-48960T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66367880AATTATTATTATTATT>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1732+11257_1732+11272delAATAATAATAATAATTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66534487T>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-13714A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66543907GTGTGTA>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1375-23140_1375-23134delTACACACins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66584982T>TGGCACAGCATCTTGCAATTGAGTACGACCCATTTTTAAGATGTTCGCAAACTCTTTTGCTTTATTATCAAAACCGTCGTGTAAATATTGAATTTTATCGATCAATTTTAAGATG [0/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1374+36709_1374+36710insCATCTTAAAATTGATCGATAAAATTCAATATTTACACGACGGTTTTGATAATAAAGCAAAAGAGTTTGCGAACATCTTAAAAATGGGTCGTACTCAATTGCAAGATGCTGTGCC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66642271CACACACAA>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1282-20495_1282-20487delTTGTGTGTGins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66917521T>TGTATCTTATGTCGATATTGTAGGAGAAGATAAAATGCTCAATCCTGTTGAAGATTATGAATTGACTTTAAAAATTGAAATTGTGAAAGAAAGAGGTGCTA [0/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1048-141998_1048-141997insTAGCACCTCTTTCTTTCACAATTTCAATTTTTAAAGTCAATTCATAATCTTCAACAGGATTGAGCATTTTATCTTCTCCTACAATATCGACATAAGATAC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.66978067TACAC>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+202246_1047+202250delGTGTAins:p.(=); CTNNA3:ENST00000361320.5:c.1536+49615_1536+49619delTACACins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67043135CT>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.1047+137181_1047+137182delAGins:p.(=); CTNNA3:ENST00000361320.5:c.1537-54452_1537-54451delCTins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.67237122GTATGTATATATATATATATATATATATATATATATATATA>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA3:ENST00000433211.7:c.580-17292_580-17252delTATATATATATATATATATATATATATATATATATACATACins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PIAS2

Exomiser Score: 0.196

Phenotype Score: 0.511

Variant Score: 0.715

Phenotype matches:

Proximity score 0.511 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.196

Phenotype Score: 0.511

Variant Score: 0.715

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.46825157C>T [0/1] rs1399246562 (variation viewer)

Variant score: 0.715 CONTRIBUTING VARIANT

Transcripts:: PIAS2:ENST00000324794.11:c.1508+2802G>A:p.(=); PIAS2:ENST00000545673.5:c.638+2802G>A:p.(=); PIAS2:ENST00000585916.6:c.1508+2802G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7147012; CADD: 0.715 (5.447)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.034

Phenotype Score: 0.511

Variant Score: 0.504

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.46825157C>T [0/1] rs1399246562 (variation viewer)

Variant score: 0.715 CONTRIBUTING VARIANT

Transcripts:: PIAS2:ENST00000324794.11:c.1508+2802G>A:p.(=); PIAS2:ENST00000545673.5:c.638+2802G>A:p.(=); PIAS2:ENST00000585916.6:c.1508+2802G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7147012; CADD: 0.715 (5.447)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.46911454G>A [0/1] rs947770605 (variation viewer)

Variant score: 0.293 CONTRIBUTING VARIANT

Transcripts:: PIAS2:ENST00000324794.11:c.24+5868C>T:p.(=); PIAS2:ENST00000585916.6:c.24+5868C>T:p.(=); PIAS2:ENST00000545673.5:c.-372+5868C>T:p.(=)

Pathogenicity Data:: Best Score: 0.29773664; CADD: 0.298 (1.535)

Frequency Data:: TOPMed: 0.0056%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0067%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr18:g.46807389T>A [1/1] rs1484485715 (variation viewer)

Variant score: 0.332

Transcripts:: PIAS2:ENST00000585916.6:c.*5044A>T:p.(=)

Pathogenicity Data:: Best Score: 0.35612732; CADD: 0.356 (1.912)

Frequency Data:: gnomAD_G_AFR: 0.4014%; gnomAD_G_NFE: 0.1819%

THREE_PRIME_UTR_EXON_VARIANT chr18:g.46807387T>A [1/1] rs866953303 (variation viewer)

Variant score: 0.310

Transcripts:: PIAS2:ENST00000585916.6:c.*5046A>T:p.(=)

Pathogenicity Data:: Best Score: 0.36583835; CADD: 0.366 (1.978)

Frequency Data:: gnomAD_G_AFR: 0.6320%; gnomAD_G_NFE: 0.2922%; gnomAD_G_OTH: 0.7576%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.46859427CAA>C [-/1] rs55776913 (variation viewer)

Variant score: 0.223

Transcripts:: PIAS2:ENST00000324794.11:c.585-3814_585-3813del:p.(=); PIAS2:ENST00000585916.6:c.585-3814_585-3813del:p.(=); PIAS2:ENST00000545673.5:c.-286-3814_-286-3813del:p.(=)

Pathogenicity Data:: Best Score: 0.2230376; CADD: 0.223 (1.096)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr18:g.46806353C>CTTTTTTT [0/1] rs869187746 (variation viewer)

Variant score: 0.116

Transcripts:: PIAS2:ENST00000585916.6:c.*6073_*6079dup:p.(=)

Pathogenicity Data:: Best Score: 0.11590284; CADD: 0.116 (0.535)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr18:g.46800639C>CATATAT [0/1] rs773664073 (variation viewer)

Variant score: 0.101

Transcripts:: PIAS2:ENST00000585916.6::; PIAS2:ENST00000315087.11::

Pathogenicity Data:: Best Score: 0.10050243; CADD: 0.101 (0.460)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr18:g.46807383ATT>A [1/1] rs869285083 (variation viewer)

Variant score: 0.059

Transcripts:: PIAS2:ENST00000585916.6:c.*5048_*5049del:p.(=)

Pathogenicity Data:: Best Score: 0.058977544; CADD: 0.059 (0.264)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.46898851G>A [0/1] rs866399478 (variation viewer)

Variant score: 0.035

Transcripts:: PIAS2:ENST00000324794.11:c.25-7797C>T:p.(=); PIAS2:ENST00000585916.6:c.25-7797C>T:p.(=); PIAS2:ENST00000545673.5:c.-372+18471C>T:p.(=)

Pathogenicity Data:: Best Score: 0.03528285; CADD: 0.035 (0.156)

Frequency Data:: gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1027%

PSMD4

Exomiser Score: 0.194

Phenotype Score: 0.504

Variant Score: 0.721

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.194

Phenotype Score: 0.504

Variant Score: 0.721

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.151254821T>C [0/1] rs777559430 (variation viewer)

Variant score: 0.721 CONTRIBUTING VARIANT

Transcripts:: PSMD4:ENST00000368881.8:c.26+13T>C:p.(=); PSMD4:ENST00000368884.7:c.26+13T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7272279; CADD: 0.727 (5.642)

Frequency Data:: TOPMed: 0.0032%; ExAC AFR: 0.0485%; gnomAD_E_AFR: 0.0619%; gnomAD_G_AFR: 0.0115%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.078

Phenotype Score: 0.504

Variant Score: 0.607

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.151254821T>C [0/1] rs777559430 (variation viewer)

Variant score: 0.721 CONTRIBUTING VARIANT

Transcripts:: PSMD4:ENST00000368881.8:c.26+13T>C:p.(=); PSMD4:ENST00000368884.7:c.26+13T>C:p.(=)

Pathogenicity Data:: Best Score: 0.7272279; CADD: 0.727 (5.642)

Frequency Data:: TOPMed: 0.0032%; ExAC AFR: 0.0485%; gnomAD_E_AFR: 0.0619%; gnomAD_G_AFR: 0.0115%

REGULATORY_REGION_VARIANT chr1:g.151195884A>ATTTTT [-/1] rs1157195462 (variation viewer)

Variant score: 0.493 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.49277574; CADD: 0.493 (2.948)

Frequency Data:: No frequency data

Other passed variants:

REGULATORY_REGION_VARIANT chr1:g.151195884ATT>A [-/1] rs1157195462 (variation viewer)

Variant score: 0.405

Transcripts:

Pathogenicity Data:: Best Score: 0.40502328; CADD: 0.405 (2.255)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr1:g.151269732G>A [0|1] rs1030726342 (variation viewer)

Variant score: 0.306

Transcripts:: PSMD4:ENST00000368884.7::; PSMD4:ENST00000324048.9::

Pathogenicity Data:: Best Score: 0.306095; CADD: 0.306 (1.587)

Frequency Data:: TOPMed: 0.0008%

DOWNSTREAM_GENE_VARIANT chr1:g.151269728C>A [0|1]

Variant score: 0.245

Transcripts:: PSMD4:ENST00000368884.7::; PSMD4:ENST00000324048.9::

Pathogenicity Data:: Best Score: 0.24473387; CADD: 0.245 (1.219)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr1:g.151253953CAAAAAAAAAAAAAA>C [1/1] rs1157709326 (variation viewer)

Variant score: 0.113

Transcripts:: PSMD4:ENST00000368884.7::; PSMD4:ENST00000368890.8::

Pathogenicity Data:: Best Score: 0.11345661; CADD: 0.113 (0.523)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr1:g.151269715G>C [0|1]

Variant score: 0.089

Transcripts:: PSMD4:ENST00000368884.7::; PSMD4:ENST00000324048.9::

Pathogenicity Data:: Best Score: 0.08903855; CADD: 0.089 (0.405)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.151256359ATAAT>* [-/1]

Variant score: 0.000

Transcripts:: PSMD4:ENST00000368881.8:c.26+1551_26+1555delATAATins*:p.(=); PSMD4:ENST00000368884.7:c.26+1551_26+1555delATAATins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SGPP2

Exomiser Score: 0.192

Phenotype Score: 0.505

Variant Score: 0.719

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.192

Phenotype Score: 0.505

Variant Score: 0.719

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.222483836C>G [0/1] rs528968696 (variation viewer)

Variant score: 0.851 CONTRIBUTING VARIANT

Transcripts:: SGPP2:ENST00000321276.8:c.378+9110C>G:p.(=)

Pathogenicity Data:: Best Score: 0.91330385; CADD: 0.913 (10.620)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.2501%; UK10K: 0.3703%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.3866%; gnomAD_G_OTH: 0.4073%

DOWNSTREAM_GENE_VARIANT chr2:g.222563192CAG>C [0/1] rs752304465 (variation viewer)

Variant score: 0.586 CONTRIBUTING VARIANT

Transcripts:: SGPP2:ENST00000321276.8::

Pathogenicity Data:: Best Score: 0.6794469; CADD: 0.679 (4.941)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.3655%; UK10K: 0.7009%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.4599%; gnomAD_G_OTH: 0.6110%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.222460690C>T [0/1] rs182690496 (variation viewer)

Variant score: 0.568

Transcripts:: SGPP2:ENST00000321276.8:c.220-13878C>T:p.(=)

Pathogenicity Data:: Best Score: 0.57762325; CADD: 0.578 (3.743)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0263%; UK10K: 0.0132%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.222500688G>A [0/1] rs545242349 (variation viewer)

Variant score: 0.343

Transcripts:: SGPP2:ENST00000321276.8:c.379-21079G>A:p.(=)

Pathogenicity Data:: Best Score: 0.35002; CADD: 0.350 (1.871)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1234%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.1399%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.222557256T>C [0/1] rs567514762 (variation viewer)

Variant score: 0.272

Transcripts:: SGPP2:ENST00000321276.8:c.649-1091T>C:p.(=)

Pathogenicity Data:: Best Score: 0.2802196; CADD: 0.280 (1.428)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1816%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.2000%; gnomAD_G_OTH: 0.2037%

RRM2

Exomiser Score: 0.186

Phenotype Score: 0.501

Variant Score: 0.719

Phenotype matches:

Proximity score 0.501 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.501

Variant Score: 0.064

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.10174399C>T [0/1] rs1472214151 (variation viewer)

Variant score: 0.064 CONTRIBUTING VARIANT

Transcripts:: RRM2:ENST00000619640.3:c.193+32024C>T:p.(=)

Pathogenicity Data:: Best Score: 0.06437892; CADD: 0.064 (0.289)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.186

Phenotype Score: 0.501

Variant Score: 0.719

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.10157016C>CTTT [1/1] rs71391198 (variation viewer)

Variant score: 0.719 CONTRIBUTING VARIANT

Transcripts:: RRM2:ENST00000619640.3:c.193+14641_193+14642insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.7188747; CADD: 0.719 (5.511)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.10199800A>ACAAAAAAAAAC [1|1] rs771864776 (variation viewer)

Variant score: 0.592

Transcripts:: RRM2:ENST00000619640.3:c.194-10511_194-10510insCAAAAAAAAAC:p.(=)

Pathogenicity Data:: Best Score: 0.5923382; CADD: 0.592 (3.897)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.10204937G>A [0/1] rs192518193 (variation viewer)

Variant score: 0.353

Transcripts:: RRM2:ENST00000619640.3:c.194-5374G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8281696; CADD: 0.828 (7.649)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.2660%; UK10K: 0.2116%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.3198%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.10210064G>A [0/1] rs573358876 (variation viewer)

Variant score: 0.227

Transcripts:: RRM2:ENST00000619640.3:c.194-247G>A:p.(=)

Pathogenicity Data:: Best Score: 0.23563641; CADD: 0.236 (1.167)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0518%; UK10K: 0.0397%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.2406%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.10176968G>A [0/1] rs186403629 (variation viewer)

Variant score: 0.049

Transcripts:: RRM2:ENST00000619640.3:c.194-33343G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11427277; CADD: 0.114 (0.527)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.2692%; UK10K: 0.1719%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.2799%; gnomAD_G_OTH: 0.3055%

INTERGENIC_VARIANT chr2:g.10223327A>G [0|1] rs923854617 (variation viewer)

Variant score: 0.024

Transcripts:: RRM2:ENST00000619640.3::

Pathogenicity Data:: Best Score: 0.023662448; CADD: 0.024 (0.104)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0199%

INTERGENIC_VARIANT chr2:g.10113385ATATATATATATATATATATAT>* [-/1]

Variant score: 0.000

Transcripts:: RRM2:ENST00000641198.1::; RRM2:ENST00000381813.4::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UCHL3

Exomiser Score: 0.185

Phenotype Score: 0.504

Variant Score: 0.715

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.185

Phenotype Score: 0.504

Variant Score: 0.715

Variants contributing to score:

REGULATORY_REGION_VARIANT chr13:g.76756464C>CA [-/1] rs57463502 (variation viewer)

Variant score: 0.715 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.7146355; CADD: 0.715 (5.446)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.029

Phenotype Score: 0.504

Variant Score: 0.492

Variants contributing to score:

REGULATORY_REGION_VARIANT chr13:g.76756464C>CA [-/1] rs57463502 (variation viewer)

Variant score: 0.715 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.7146355; CADD: 0.715 (5.446)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.75574282A>AT [0/1] rs200631129 (variation viewer)

Variant score: 0.270 CONTRIBUTING VARIANT

Transcripts:: UCHL3:ENST00000377595.7:c.474+4775_474+4776insT:p.(=); UCHL3:ENST00000618773.4:c.366+4775_366+4776insT:p.(=)

Pathogenicity Data:: Best Score: 0.27856034; CADD: 0.279 (1.418)

Frequency Data:: gnomAD_G_AFR: 0.0816%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 0.0678%; gnomAD_G_NFE: 0.1983%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.75595597C>CAAA [0/1] rs58733406 (variation viewer)

Variant score: 0.196

Transcripts:: UCHL3:ENST00000377595.7:c.550+607_550+608insAAA:p.(=); UCHL3:ENST00000618773.4:c.442+607_442+608insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.19591862; CADD: 0.196 (0.947)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.75592446A>ATACATATATATATATATGTATATATG [-/1] rs36133915 (variation viewer)

Variant score: 0.139

Transcripts:: UCHL3:ENST00000377595.7:c.475-2469_475-2468insTACATATATATATATATGTATATATG:p.(=); UCHL3:ENST00000618773.4:c.367-2469_367-2468insTACATATATATATATATGTATATATG:p.(=)

Pathogenicity Data:: Best Score: 0.13860965; CADD: 0.139 (0.648)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.75592446A>ATACATATATACATATATATATATATGTATATATG [-/1] rs36133915 (variation viewer)

Variant score: 0.119

Transcripts:: UCHL3:ENST00000377595.7:c.475-2469_475-2468insTACATATATACATATATATATATATGTATATATG:p.(=); UCHL3:ENST00000618773.4:c.367-2469_367-2468insTACATATATACATATATATATATATGTATATATG:p.(=)

Pathogenicity Data:: Best Score: 0.11874825; CADD: 0.119 (0.549)

Frequency Data:: No frequency data

COX15

Exomiser Score: 0.185

Phenotype Score: 0.252

Variant Score: 1.000

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with COX15.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615119 Mitochondrial complex IV deficiency, nuclear type 6 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.185

Phenotype Score: 0.252

Variant Score: 1.000

Variants contributing to score:

MISSENSE_VARIANT chr10:g.99727044T>C [0/1] rs201881501 (variation viewer)

Variant score: 1.000 CONTRIBUTING VARIANT

Transcripts:: COX15:ENST00000016171.5:c.506A>G:p.(Tyr169Cys); COX15:ENST00000370483.9:c.506A>G:p.(Tyr169Cys); COX15:ENST00000649102.1:c.423A>G:p.(=)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.992 (D); Mutation Taster: 1.000 (P); SIFT: 0.002 (D); CADD: 0.999 (28.700)

Frequency Data:: ExAC NFE: 0.0015%; gnomAD_E_NFE: 0.0018%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.093

Phenotype Score: 0.504

Variant Score: 0.628

Variants contributing to score:

MISSENSE_VARIANT chr10:g.99727044T>C [0/1] rs201881501 (variation viewer)

Variant score: 1.000 CONTRIBUTING VARIANT

Transcripts:: COX15:ENST00000016171.5:c.506A>G:p.(Tyr169Cys); COX15:ENST00000370483.9:c.506A>G:p.(Tyr169Cys); COX15:ENST00000649102.1:c.423A>G:p.(=)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.992 (D); Mutation Taster: 1.000 (P); SIFT: 0.002 (D); CADD: 0.999 (28.700)

Frequency Data:: ExAC NFE: 0.0015%; gnomAD_E_NFE: 0.0018%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.99717606C>A [0/1] rs375568985 (variation viewer)

Variant score: 0.256 CONTRIBUTING VARIANT

Transcripts:: COX15:ENST00000016171.5:c.987+740G>T:p.(=); COX15:ENST00000370483.9:c.987+740G>T:p.(=); COX15:ENST00000649102.1:c.*346+740G>T:p.(=)

Pathogenicity Data:: Best Score: 0.27037448; CADD: 0.270 (1.369)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.0796%; UK10K: 0.0132%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0800%; gnomAD_G_OTH: 0.1020%

Other passed variants:

MCM5

Exomiser Score: 0.184

Phenotype Score: 0.252

Variant Score: 1.000

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617564 ?Meier-Gorlin syndrome 8 (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.184

Phenotype Score: 0.252

Variant Score: 1.000

Variants contributing to score:

SPLICE_DONOR_VARIANT chr22:g.35423343T>TG [0|1]

Variant score: 1.000 CONTRIBUTING VARIANT

Transcripts:: MCM5:ENST00000216122.9:c.2103+2_2103+3insG:p.?; MCM5:ENST00000382011.9:c.1974+2_1974+3insG:p.?

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.030

Phenotype Score: 0.503

Variant Score: 0.500

Variants contributing to score:

SPLICE_DONOR_VARIANT chr22:g.35423343T>TG [0|1]

Variant score: 1.000 CONTRIBUTING VARIANT

Transcripts:: MCM5:ENST00000216122.9:c.2103+2_2103+3insG:p.?; MCM5:ENST00000382011.9:c.1974+2_1974+3insG:p.?

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423352C>CAGAAGA [0|1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: MCM5:ENST00000216122.9:c.2103+11_2103+12insAGAAGA:p.(=); MCM5:ENST00000382011.9:c.1974+11_1974+12insAGAAGA:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr22:g.35445325C>CTTT [1/1] rs759262388 (variation viewer)

Variant score: 0.158

Transcripts:: MCM5:ENST00000216122.9::; MCM5:ENST00000417397.2::

Pathogenicity Data:: Best Score: 0.15782952; CADD: 0.158 (0.746)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423367T>TCACA [0/1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+26_2103+27insCACA:p.(=); MCM5:ENST00000382011.9:c.1974+26_1974+27insCACA:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423369AG>A [0/1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+29del:p.(=); MCM5:ENST00000382011.9:c.1974+29del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423372C>CTTTT [0/1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+31_2103+32insTTTT:p.(=); MCM5:ENST00000382011.9:c.1974+31_1974+32insTTTT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423377CGGG>C [0/1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+37_2103+39del:p.(=); MCM5:ENST00000382011.9:c.1974+37_1974+39del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423382TG>T [0/1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+42del:p.(=); MCM5:ENST00000382011.9:c.1974+42del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423387G>GAAAT [0/1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+46_2103+47insAAAT:p.(=); MCM5:ENST00000382011.9:c.1974+46_1974+47insAAAT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.35423393TGC>T [0|1]

Variant score: 0.000

Transcripts:: MCM5:ENST00000216122.9:c.2103+53_2103+54del:p.(=); MCM5:ENST00000382011.9:c.1974+53_1974+54del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

EIF4E

Exomiser Score: 0.183

Phenotype Score: 0.502

Variant Score: 0.716

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.502

Variant Score: 0.227

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.98911661C>CAAA [0/1] rs767631331 (variation viewer)

Variant score: 0.227 CONTRIBUTING VARIANT

Transcripts:: EIF4E:ENST00000280892.10:c.79-9680_79-9679insTTT:p.(=); EIF4E:ENST00000450253.6:c.19-9680_19-9679insTTT:p.(=); EIF4E:ENST00000505992.1:c.19-9680_19-9679insTTT:p.(=); EIF4E:ENST00000504432.5:c.-180-1703_-180-1702insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.22696352; CADD: 0.227 (1.118)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.183

Phenotype Score: 0.502

Variant Score: 0.716

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.98927654CAAAAAAA>C [1/1] rs774720176 (variation viewer)

Variant score: 0.716 CONTRIBUTING VARIANT

Transcripts:: EIF4E:ENST00000280892.10:c.78+1234_78+1240del:p.(=); EIF4E:ENST00000450253.6:c.18+1434_18+1440del:p.(=); EIF4E:ENST00000505992.1:c.18+1434_18+1440del:p.(=); EIF4E:ENST00000504432.5:c.-181+1434_-181+1440del:p.(=)

Pathogenicity Data:: Best Score: 0.716012; CADD: 0.716 (5.467)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.98914393T>A [0/1] rs750564228 (variation viewer)

Variant score: 0.552

Transcripts:: EIF4E:ENST00000280892.10:c.79-12411A>T:p.(=); EIF4E:ENST00000450253.6:c.19-12411A>T:p.(=); EIF4E:ENST00000505992.1:c.19-12411A>T:p.(=); EIF4E:ENST00000504432.5:c.-180-4434A>T:p.(=)

Pathogenicity Data:: Best Score: 0.634994; CADD: 0.635 (4.377)

Frequency Data:: UK10K: 0.6083%; gnomAD_G_AFR: 0.1694%; gnomAD_G_FIN: 0.6770%; gnomAD_G_NFE: 0.3405%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.98883392A>AT [0/1] rs1479416116 (variation viewer)

Variant score: 0.311

Transcripts:: EIF4E:ENST00000280892.10:c.599+1529_599+1530insA:p.(=); EIF4E:ENST00000450253.6:c.539+1529_539+1530insA:p.(=); EIF4E:ENST00000504432.5:c.623+1529_623+1530insA:p.(=); EIF4E:ENST00000505992.1:c.632+1529_632+1530insA:p.(=)

Pathogenicity Data:: Best Score: 0.43336946; CADD: 0.433 (2.467)

Frequency Data:: gnomAD_G_AFR: 0.2614%; gnomAD_G_AMR: 0.1488%; gnomAD_G_ASJ: 1.1278%; gnomAD_G_FIN: 0.0861%; gnomAD_G_NFE: 1.0095%; gnomAD_G_OTH: 0.2525%

THREE_PRIME_UTR_EXON_VARIANT chr4:g.98874784C>CT [-/1] rs561809078 (variation viewer)

Variant score: 0.038

Transcripts:: EIF4E:ENST00000450253.6:c.*6243dup:p.(=)

Pathogenicity Data:: Best Score: 0.037944794; CADD: 0.038 (0.168)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr4:g.98874784C>CTT [-/1] rs561809078 (variation viewer)

Variant score: 0.037

Transcripts:: EIF4E:ENST00000450253.6:c.*6242_*6243dup:p.(=)

Pathogenicity Data:: Best Score: 0.037058294; CADD: 0.037 (0.164)

Frequency Data:: No frequency data

GMPS

Exomiser Score: 0.176

Phenotype Score: 0.515

Variant Score: 0.696

Phenotype matches:

Proximity score 0.515 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.515

Variant Score: 0.130

Variants contributing to score:

REGULATORY_REGION_VARIANT chr3:g.155746814CA>C [0/1] rs533773685 (variation viewer)

Variant score: 0.130 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.12963784; CADD: 0.130 (0.603)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.176

Phenotype Score: 0.515

Variant Score: 0.696

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.155873638C>CTTTTTTTTTTTTTT [1/1] rs58365650 (variation viewer)

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: GMPS:ENST00000295920.7:c.27+2741_27+2742insTTTTTTTTTTTTTT:p.(=); GMPS:ENST00000496455.7:c.27+2741_27+2742insTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.6959115; CADD: 0.696 (5.170)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr3:g.155954979C>CTTT [1/1] rs1176274562 (variation viewer)

Variant score: 0.528

Transcripts:: GMPS:ENST00000496455.7::; GMPS:ENST00000497538.1::

Pathogenicity Data:: Best Score: 0.52750194; CADD: 0.528 (3.256)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.155928019C>CT [1/1] rs35962523 (variation viewer)

Variant score: 0.518

Transcripts:: GMPS:ENST00000295920.7:c.1263+2653_1263+2654insT:p.(=); GMPS:ENST00000496455.7:c.1560+2653_1560+2654insT:p.(=)

Pathogenicity Data:: Best Score: 0.51771915; CADD: 0.518 (3.167)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.155953850A>ATTT [1/1] rs60173748 (variation viewer)

Variant score: 0.206

Transcripts:: GMPS:ENST00000496455.7::; GMPS:ENST00000497538.1::

Pathogenicity Data:: Best Score: 0.20622027; CADD: 0.206 (1.003)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.155881164GT>G [1/1] rs11334499 (variation viewer)

Variant score: 0.022

Transcripts:: GMPS:ENST00000295920.7:c.27+10268del:p.(=); GMPS:ENST00000496455.7:c.27+10268del:p.(=)

Pathogenicity Data:: Best Score: 0.022312641; CADD: 0.022 (0.098)

Frequency Data:: No frequency data

SMPD1

Exomiser Score: 0.174

Phenotype Score: 0.913

Variant Score: 0.244

Phenotype matches:

Phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:257200 Niemann-Pick disease, type A - autosomal recessive; OMIM:607616 Niemann-Pick disease, type B - autosomal recessive; ORPHA:77293 Niemann-Pick disease type B

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.174

Phenotype Score: 0.913

Variant Score: 0.244

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.6387249C>CAT [1/1] rs56152752 (variation viewer)

Variant score: 0.244 CONTRIBUTING VARIANT

Transcripts:: SMPD1:ENST00000342245.9::; SMPD1:ENST00000530979.1::

Pathogenicity Data:: Best Score: 0.24351555; CADD: 0.244 (1.212)

Frequency Data:: No frequency data

Other passed variants:

ASS1

Exomiser Score: 0.169

Phenotype Score: 0.518

Variant Score: 0.687

Phenotype matches:

Proximity score 0.518 in interactome to SLC25A13 and phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

Known diseases:: OMIM:215700 Citrullinemia - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.259

Variant Score: 0.515

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.130465056A>T [-/1] rs7847222 (variation viewer)

Variant score: 0.515 CONTRIBUTING VARIANT

Transcripts:: ASS1:ENST00000352480.10:c.420+889A>T:p.(=); ASS1:ENST00000372393.7:c.420+889A>T:p.(=); ASS1:ENST00000372394.5:c.420+889A>T:p.(=)

Pathogenicity Data:: Best Score: 0.51459974; CADD: 0.515 (3.139)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.169

Phenotype Score: 0.518

Variant Score: 0.687

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.130506503C>T [1|1] rs747888775 (variation viewer)

Variant score: 0.687 CONTRIBUTING VARIANT

Transcripts:: ASS1:ENST00000372394.5::

Pathogenicity Data:: Best Score: 0.687104; CADD: 0.687 (5.046)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr9:g.130507832GTATATATA>G [-/1] rs59588687 (variation viewer)

Variant score: 0.281

Transcripts:: ASS1:ENST00000372394.5::

Pathogenicity Data:: Best Score: 0.28121334; CADD: 0.281 (1.434)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.130507832GTATATATATATA>G [-/1] rs59588687 (variation viewer)

Variant score: 0.267

Transcripts:: ASS1:ENST00000372394.5::

Pathogenicity Data:: Best Score: 0.2666691; CADD: 0.267 (1.347)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.130474062ACC>A [1/1] rs5900900 (variation viewer)

Variant score: 0.228

Transcripts:: ASS1:ENST00000352480.10:c.597+2548_597+2549del:p.(=); ASS1:ENST00000372393.7:c.597+2548_597+2549del:p.(=); ASS1:ENST00000372394.5:c.597+2548_597+2549del:p.(=)

Pathogenicity Data:: Best Score: 0.22820848; CADD: 0.228 (1.125)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.130507369C>CAGGGAGAGGGACAGGGAG [1/1] rs71387356 (variation viewer)

Variant score: 0.181

Transcripts:: ASS1:ENST00000372394.5::

Pathogenicity Data:: Best Score: 0.18115819; CADD: 0.181 (0.868)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.130435676C>CTTTTTTT [1/1] rs56001433 (variation viewer)

Variant score: 0.075

Transcripts:: ASS1:ENST00000352480.10::

Pathogenicity Data:: Best Score: 0.07487589; CADD: 0.075 (0.338)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.130448422G>GCGCA [-/1] rs71387350 (variation viewer)

Variant score: 0.067

Transcripts:: ASS1:ENST00000352480.10:c.-6+3427_-6+3428insCGCA:p.(=); ASS1:ENST00000372393.7:c.-67-1850_-67-1849insCGCA:p.(=); ASS1:ENST00000372394.5:c.-447-3180_-447-3179insCGCA:p.(=)

Pathogenicity Data:: Best Score: 0.06696057; CADD: 0.067 (0.301)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.130448422GCA>G [-/1] rs3085579 (variation viewer)

Variant score: 0.050

Transcripts:: ASS1:ENST00000352480.10:c.-6+3428_-6+3429del:p.(=); ASS1:ENST00000372393.7:c.-67-1849_-67-1848del:p.(=); ASS1:ENST00000372394.5:c.-447-3179_-447-3178del:p.(=)

Pathogenicity Data:: Best Score: 0.05048901; CADD: 0.050 (0.225)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.130461385G>* [-/1]

Variant score: 0.000

Transcripts:: ASS1:ENST00000352480.10:c.364-2726G>*:p.(=); ASS1:ENST00000372393.7:c.364-2726G>*:p.(=); ASS1:ENST00000372394.5:c.364-2726G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.130465056A>* [-/1]

Variant score: 0.000

Transcripts:: ASS1:ENST00000352480.10:c.420+889A>*:p.(=); ASS1:ENST00000372393.7:c.420+889A>*:p.(=); ASS1:ENST00000372394.5:c.420+889A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.130507842A>* [-/1]

Variant score: 0.000

Transcripts:: ASS1:ENST00000372394.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.130507844A>* [-/1]

Variant score: 0.000

Transcripts:: ASS1:ENST00000372394.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

BCL6

Exomiser Score: 0.168

Phenotype Score: 0.251

Variant Score: 0.989

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: ORPHA:545 Follicular lymphoma

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.168

Phenotype Score: 0.251

Variant Score: 0.989

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.187744147G>A [0/1]

Variant score: 0.989 CONTRIBUTING VARIANT

Transcripts:: BCL6:ENST00000406870.7:c.-50+1263C>T:p.(=); BCL6:ENST00000621333.4:c.-50+1263C>T:p.(=); BCL6:ENST00000648485.1:c.-71+103G>A:p.(=)

Pathogenicity Data:: Best Score: 0.98877984; CADD: 0.989 (19.500)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.094

Phenotype Score: 0.251

Variant Score: 0.916

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.187744147G>A [0/1]

Variant score: 0.989 CONTRIBUTING VARIANT

Transcripts:: BCL6:ENST00000406870.7:c.-50+1263C>T:p.(=); BCL6:ENST00000621333.4:c.-50+1263C>T:p.(=); BCL6:ENST00000648485.1:c.-71+103G>A:p.(=)

Pathogenicity Data:: Best Score: 0.98877984; CADD: 0.989 (19.500)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr3:g.187721435G>A [0/1] rs564704619 (variation viewer)

Variant score: 0.843 CONTRIBUTING VARIANT

Transcripts:: BCL6:ENST00000406870.7:c.*1023C>T:p.(=); BCL6:ENST00000621333.4:c.*1023C>T:p.(=)

Pathogenicity Data:: Best Score: 0.94871384; CADD: 0.949 (12.900)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.2947%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.2862%; gnomAD_G_NFE: 0.4863%; gnomAD_G_OTH: 0.4073%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr3:g.187719015A>G [0/1] rs999870184 (variation viewer)

Variant score: 0.064

Transcripts:: BCL6:ENST00000621333.4::; BCL6:ENST00000358241.1::

Pathogenicity Data:: Best Score: 0.06416345; CADD: 0.064 (0.288)

Frequency Data:: TOPMed: 0.0008%

AK5

Exomiser Score: 0.167

Phenotype Score: 0.503

Variant Score: 0.702

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.167

Phenotype Score: 0.503

Variant Score: 0.702

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77358332T>G [0/1] rs935110202 (variation viewer)

Variant score: 0.702 CONTRIBUTING VARIANT

Transcripts:: AK5:ENST00000344720.9:c.813+17764T>G:p.(=); AK5:ENST00000354567.7:c.891+17764T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7037216; CADD: 0.704 (5.283)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.036

Phenotype Score: 0.503

Variant Score: 0.520

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77358332T>G [0/1] rs935110202 (variation viewer)

Variant score: 0.702 CONTRIBUTING VARIANT

Transcripts:: AK5:ENST00000344720.9:c.813+17764T>G:p.(=); AK5:ENST00000354567.7:c.891+17764T>G:p.(=)

Pathogenicity Data:: Best Score: 0.7037216; CADD: 0.704 (5.283)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_NFE: 0.0133%

REGULATORY_REGION_VARIANT chr1:g.77248013C>CAA [0/1] rs10671265 (variation viewer)

Variant score: 0.337 CONTRIBUTING VARIANT

Transcripts:: AK5:ENST00000354567.7::

Pathogenicity Data:: Best Score: 0.33717328; CADD: 0.337 (1.786)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77486684A>G [0/1] rs374643454 (variation viewer)

Variant score: 0.153

Transcripts:: AK5:ENST00000344720.9:c.1069+332A>G:p.(=); AK5:ENST00000354567.7:c.1147+332A>G:p.(=)

Pathogenicity Data:: Best Score: 0.15763563; CADD: 0.158 (0.745)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_EAS: 0.1856%; gnomAD_G_NFE: 0.0271%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77368245A>AT [-/1] rs1553140332 (variation viewer)

Variant score: 0.151

Transcripts:: AK5:ENST00000344720.9:c.813+27677_813+27678insT:p.(=); AK5:ENST00000354567.7:c.891+27677_891+27678insT:p.(=)

Pathogenicity Data:: Best Score: 0.15081954; CADD: 0.151 (0.710)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr1:g.77279234CTTTTTT>C [1/1] rs56173314 (variation viewer)

Variant score: 0.146

Transcripts:: AK5:ENST00000354567.7::; AK5:ENST00000445065.5::

Pathogenicity Data:: Best Score: 0.14552373; CADD: 0.146 (0.683)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77367569A>ATGT [0/1] rs1462793828 (variation viewer)

Variant score: 0.142

Transcripts:: AK5:ENST00000344720.9:c.813+27001_813+27002insTGT:p.(=); AK5:ENST00000354567.7:c.891+27001_891+27002insTGT:p.(=)

Pathogenicity Data:: Best Score: 0.14177728; CADD: 0.142 (0.664)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77367579A>ATGTT [0/1] rs71075732 (variation viewer)

Variant score: 0.137

Transcripts:: AK5:ENST00000344720.9:c.813+27011_813+27012insTGTT:p.(=); AK5:ENST00000354567.7:c.891+27011_891+27012insTGTT:p.(=)

Pathogenicity Data:: Best Score: 0.13702142; CADD: 0.137 (0.640)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77358018T>TGTGTGTGAGAGAGAGA [-/1] rs762714026 (variation viewer)

Variant score: 0.121

Transcripts:: AK5:ENST00000344720.9:c.813+17450_813+17451insGTGTGTGAGAGAGAGA:p.(=); AK5:ENST00000354567.7:c.891+17450_891+17451insGTGTGTGAGAGAGAGA:p.(=)

Pathogenicity Data:: Best Score: 0.12057257; CADD: 0.121 (0.558)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77391525A>ATATATATATATATG [0/1] rs146163792 (variation viewer)

Variant score: 0.119

Transcripts:: AK5:ENST00000344720.9:c.814-19456_814-19455insTATATATATATATG:p.(=); AK5:ENST00000354567.7:c.892-19456_892-19455insTATATATATATATG:p.(=)

Pathogenicity Data:: Best Score: 0.11915398; CADD: 0.119 (0.551)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77358018T>TGTGTGTGTGTGTGTGTGTGTGTGA [-/1] rs762714026 (variation viewer)

Variant score: 0.103

Transcripts:: AK5:ENST00000344720.9:c.813+17450_813+17451insGTGTGTGTGTGTGTGTGTGTGTGA:p.(=); AK5:ENST00000354567.7:c.891+17450_891+17451insGTGTGTGTGTGTGTGTGTGTGTGA:p.(=)

Pathogenicity Data:: Best Score: 0.10277784; CADD: 0.103 (0.471)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77374418C>CTT [-/1] rs34141642 (variation viewer)

Variant score: 0.096

Transcripts:: AK5:ENST00000344720.9:c.813+33850_813+33851insTT:p.(=); AK5:ENST00000354567.7:c.891+33850_891+33851insTT:p.(=)

Pathogenicity Data:: Best Score: 0.14611381; CADD: 0.146 (0.686)

Frequency Data:: gnomAD_G_AFR: 0.3010%; gnomAD_G_AMR: 0.4367%; gnomAD_G_EAS: 0.1359%; gnomAD_G_FIN: 1.2563%; gnomAD_G_NFE: 0.1435%; gnomAD_G_OTH: 0.8251%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77368245A>ATATATATATATATGTTATATATAT [-/1] rs376578923 (variation viewer)

Variant score: 0.096

Transcripts:: AK5:ENST00000344720.9:c.813+27677_813+27678insTATATATATATATGTTATATATAT:p.(=); AK5:ENST00000354567.7:c.891+27677_891+27678insTATATATATATATGTTATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.095517874; CADD: 0.096 (0.436)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77499869CA>C [0/1] rs370388964 (variation viewer)

Variant score: 0.092

Transcripts:: AK5:ENST00000344720.9:c.1069+13518del:p.(=); AK5:ENST00000354567.7:c.1147+13518del:p.(=)

Pathogenicity Data:: Best Score: 0.09238851; CADD: 0.092 (0.421)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77491304ATT>A [-/1]

Variant score: 0.088

Transcripts:: AK5:ENST00000344720.9:c.1069+4953_1069+4954del:p.(=); AK5:ENST00000354567.7:c.1147+4953_1147+4954del:p.(=)

Pathogenicity Data:: Best Score: 0.08819914; CADD: 0.088 (0.401)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77324980C>CTTTTTTTTTTT [0/1] rs374298984 (variation viewer)

Variant score: 0.073

Transcripts:: AK5:ENST00000344720.9:c.622-15397_622-15396insTTTTTTTTTTT:p.(=); AK5:ENST00000354567.7:c.700-15397_700-15396insTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.32376134; CADD: 0.324 (1.699)

Frequency Data:: UK10K: 1.9043%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77308458AT>* [-/1]

Variant score: 0.000

Transcripts:: AK5:ENST00000344720.9:c.621+10511_621+10512delATins*:p.(=); AK5:ENST00000354567.7:c.699+10511_699+10512delATins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77339644CTT>* [-/1]

Variant score: 0.000

Transcripts:: AK5:ENST00000344720.9:c.622-733_622-731delCTTins*:p.(=); AK5:ENST00000354567.7:c.700-733_700-731delCTTins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77339645T>* [-/1]

Variant score: 0.000

Transcripts:: AK5:ENST00000344720.9:c.622-732T>*:p.(=); AK5:ENST00000354567.7:c.700-732T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77376448AAAC>* [-/1]

Variant score: 0.000

Transcripts:: AK5:ENST00000344720.9:c.814-34533_814-34530delAAACins*:p.(=); AK5:ENST00000354567.7:c.892-34533_892-34530delAAACins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77475191ATATATGTG>* [-/1]

Variant score: 0.000

Transcripts:: AK5:ENST00000344720.9:c.982-8126_982-8118delATATATGTGins*:p.(=); AK5:ENST00000354567.7:c.1060-8126_1060-8118delATATATGTGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.77499870A>* [-/1]

Variant score: 0.000

Transcripts:: AK5:ENST00000344720.9:c.1069+13518A>*:p.(=); AK5:ENST00000354567.7:c.1147+13518A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

BIRC6

Exomiser Score: 0.167

Phenotype Score: 0.505

Variant Score: 0.700

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.019

Phenotype Score: 0.505

Variant Score: 0.448

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32521365C>CAA [-/1] rs35410265 (variation viewer)

Variant score: 0.448 CONTRIBUTING VARIANT

Transcripts:: BIRC6:ENST00000421745.6:c.11623+2419_11623+2420insAA:p.(=)

Pathogenicity Data:: Best Score: 0.44830382; CADD: 0.448 (2.583)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.167

Phenotype Score: 0.505

Variant Score: 0.700

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32480621CTTTTTTT>C [1/1] rs560251664 (variation viewer)

Variant score: 0.700 CONTRIBUTING VARIANT

Transcripts:: BIRC6:ENST00000421745.6:c.7409-698_7409-692del:p.(=)

Pathogenicity Data:: Best Score: 0.70042884; CADD: 0.700 (5.235)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr2:g.32627312C>T [0/1] rs551983165 (variation viewer)

Variant score: 0.590

Transcripts:: BIRC6:ENST00000421745.6::

Pathogenicity Data:: Best Score: 0.6260617; CADD: 0.626 (4.272)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0980%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3580%; gnomAD_G_NFE: 0.1535%; gnomAD_G_OTH: 0.1018%

UPSTREAM_GENE_VARIANT chr2:g.32356858C>A [0/1] rs567387151 (variation viewer)

Variant score: 0.585

Transcripts:: BIRC6:ENST00000421745.6::; BIRC6:ENST00000238831.9::

Pathogenicity Data:: Best Score: 0.7711768; CADD: 0.771 (6.405)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4500%; gnomAD_G_AFR: 0.1493%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.7450%; gnomAD_G_NFE: 0.7541%; gnomAD_G_OTH: 1.0246%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32442564T>C [0/1] rs574780306 (variation viewer)

Variant score: 0.465

Transcripts:: BIRC6:ENST00000421745.6:c.4238+109T>C:p.(=)

Pathogenicity Data:: Best Score: 0.49405885; CADD: 0.494 (2.959)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0996%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3589%; gnomAD_G_NFE: 0.1466%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32567894A>C [0/1] rs554666952 (variation viewer)

Variant score: 0.445

Transcripts:: BIRC6:ENST00000421745.6:c.13145-7262A>C:p.(=); BIRC6:ENST00000623382.1:n.236+6689T>G:

Pathogenicity Data:: Best Score: 0.47313422; CADD: 0.473 (2.783)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1043%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3589%; gnomAD_G_NFE: 0.1534%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32532134C>CGTGTGTGTGTGTGTGT [1/1] rs138437601 (variation viewer)

Variant score: 0.435

Transcripts:: BIRC6:ENST00000421745.6:c.12291+583_12291+584insGTGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.43454248; CADD: 0.435 (2.476)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32521365C>CAAAAA [-/1] rs35410265 (variation viewer)

Variant score: 0.431

Transcripts:: BIRC6:ENST00000421745.6:c.11623+2419_11623+2420insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.43127805; CADD: 0.431 (2.451)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32393433C>G [0|1] rs539673150 (variation viewer)

Variant score: 0.369

Transcripts:: BIRC6:ENST00000421745.6:c.951+1283C>G:p.(=)

Pathogenicity Data:: Best Score: 0.4026897; CADD: 0.403 (2.238)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1019%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0343%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.1465%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32532849G>A [0/1] rs543956310 (variation viewer)

Variant score: 0.336

Transcripts:: BIRC6:ENST00000421745.6:c.12291+1298G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3567201; CADD: 0.357 (1.916)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1003%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.3580%; gnomAD_G_NFE: 0.1468%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32450233C>G [0/1] rs34710857 (variation viewer)

Variant score: 0.335

Transcripts:: BIRC6:ENST00000421745.6:c.4618+1305C>G:p.(=)

Pathogenicity Data:: Best Score: 0.46617365; CADD: 0.466 (2.726)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.5224%; UK10K: 0.8596%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.7441%; gnomAD_G_NFE: 0.9132%; gnomAD_G_OTH: 1.1224%

INTERGENIC_VARIANT chr2:g.32351313C>T [0/1] rs867324974 (variation viewer)

Variant score: 0.323

Transcripts:: BIRC6:ENST00000421745.6::; BIRC6:ENST00000238831.9::

Pathogenicity Data:: Best Score: 0.3228264; CADD: 0.323 (1.693)

Frequency Data:: TOPMed: 0.0016%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32579862A>AT [0/1] rs796180938 (variation viewer)

Variant score: 0.321

Transcripts:: BIRC6:ENST00000421745.6:c.13355+4496_13355+4497insT:p.(=)

Pathogenicity Data:: Best Score: 0.6648803; CADD: 0.665 (4.748)

Frequency Data:: gnomAD_G_AFR: 1.5721%; gnomAD_G_AMR: 0.4587%; gnomAD_G_FIN: 0.0397%; gnomAD_G_NFE: 0.1868%; gnomAD_G_OTH: 0.2257%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32536253T>G [0/1] rs867212982 (variation viewer)

Variant score: 0.315

Transcripts:: BIRC6:ENST00000421745.6:c.12291+4702T>G:p.(=)

Pathogenicity Data:: Best Score: 0.31545818; CADD: 0.315 (1.646)

Frequency Data:: TOPMed: 0.0104%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32572573T>TA [0/1] rs558697546 (variation viewer)

Variant score: 0.218

Transcripts:: BIRC6:ENST00000421745.6:c.13145-2583_13145-2582insA:p.(=); BIRC6:ENST00000623382.1:n.236+2009_236+2010insT:

Pathogenicity Data:: Best Score: 0.2626053; CADD: 0.263 (1.323)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2907%; UK10K: 0.5951%; gnomAD_G_AFR: 0.0916%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.6297%; gnomAD_G_NFE: 0.5732%; gnomAD_G_OTH: 0.8147%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32535150C>CA [0/1] rs1158856665 (variation viewer)

Variant score: 0.186

Transcripts:: BIRC6:ENST00000421745.6:c.12291+3599_12291+3600insA:p.(=)

Pathogenicity Data:: Best Score: 0.18567085; CADD: 0.186 (0.892)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32607975C>CA [-/1] rs35242178 (variation viewer)

Variant score: 0.137

Transcripts:: BIRC6:ENST00000421745.6:c.14259+332_14259+333insA:p.(=)

Pathogenicity Data:: Best Score: 0.13722014; CADD: 0.137 (0.641)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32553197CAAAAAAA>C [0/1] rs763552918 (variation viewer)

Variant score: 0.119

Transcripts:: BIRC6:ENST00000421745.6:c.13144+3717_13144+3723del:p.(=)

Pathogenicity Data:: Best Score: 0.11915398; CADD: 0.119 (0.551)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32607975CAAA>C [-/1] rs35242178 (variation viewer)

Variant score: 0.105

Transcripts:: BIRC6:ENST00000421745.6:c.14259+333_14259+335del:p.(=)

Pathogenicity Data:: Best Score: 0.10484135; CADD: 0.105 (0.481)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr2:g.32353266G>T [0/1] rs189577651 (variation viewer)

Variant score: 0.080

Transcripts:: BIRC6:ENST00000421745.6::; BIRC6:ENST00000238831.9::

Pathogenicity Data:: Best Score: 0.08187884; CADD: 0.082 (0.371)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1051%; gnomAD_G_AFR: 0.1722%

INTERGENIC_VARIANT chr2:g.32342706CA>C [1/1] rs70938339 (variation viewer)

Variant score: 0.077

Transcripts:: BIRC6:ENST00000421745.6::; BIRC6:ENST00000238831.9::

Pathogenicity Data:: Best Score: 0.07657844; CADD: 0.077 (0.346)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32460272A>ATATT [1/1] rs1278940587 (variation viewer)

Variant score: 0.068

Transcripts:: BIRC6:ENST00000421745.6:c.4754-2922_4754-2921insTATT:p.(=)

Pathogenicity Data:: Best Score: 0.06803417; CADD: 0.068 (0.306)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32436333C>G [0/1] rs140265401 (variation viewer)

Variant score: 0.061

Transcripts:: BIRC6:ENST00000421745.6:c.3631+149C>G:p.(=)

Pathogenicity Data:: Best Score: 0.079974234; CADD: 0.080 (0.362)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.5248%; UK10K: 0.8596%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.7441%; gnomAD_G_NFE: 0.9000%; gnomAD_G_OTH: 1.0183%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32463560A>C [0/1] rs866474936 (variation viewer)

Variant score: 0.056

Transcripts:: BIRC6:ENST00000421745.6:c.4941+179A>C:p.(=)

Pathogenicity Data:: Best Score: 0.056156456; CADD: 0.056 (0.251)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32508809G>C [0/1] rs13005444 (variation viewer)

Variant score: 0.047

Transcripts:: BIRC6:ENST00000421745.6:c.9980+550G>C:p.(=)

Pathogenicity Data:: Best Score: 0.06157404; CADD: 0.062 (0.276)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4523%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1490%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.6304%; gnomAD_G_NFE: 0.8001%; gnomAD_G_OTH: 1.0225%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.32455173T>TC [0/1]

Variant score: 0.000

Transcripts:: BIRC6:ENST00000421745.6:c.4753+1231_4753+1232insC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

RRM2B

Exomiser Score: 0.165

Phenotype Score: 0.864

Variant Score: 0.292

Phenotype matches:

Phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.517 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612075 Mitochondrial DNA depletion syndrome 8A (encephalomyopathic type with renal tubulopathy) - autosomal recessive; OMIM:613077 Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 5 - autosomal dominant; ORPHA:254892 Autosomal dominant progressive external ophthalmoplegia; ORPHA:298 Mitochondrial neurogastrointestinal encephalomyopathy; ORPHA:329336 Adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy; ORPHA:480 Kearns-Sayre syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.165

Phenotype Score: 0.864

Variant Score: 0.292

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.102215944CAAAAA>C [0/1] rs60059243 (variation viewer)

Variant score: 0.292 CONTRIBUTING VARIANT

Transcripts:: RRM2B:ENST00000251810.8:c.685-1791_685-1787del:p.(=); RRM2B:ENST00000395912.6:c.529-1791_529-1787del:p.(=); RRM2B:ENST00000519317.5:c.49-1791_49-1787del:p.(=); RRM2B:ENST00000519962.5:c.49-7664_49-7660del:p.(=); RRM2B:ENST00000621845.1:c.523-1791_523-1787del:p.(=)

Pathogenicity Data:: Best Score: 0.29189116; CADD: 0.292 (1.499)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.070

Phenotype Score: 0.864

Variant Score: 0.188

Variants contributing to score:

REGULATORY_REGION_VARIANT chr8:g.102426087C>CA [1/1] rs1183622039 (variation viewer)

Variant score: 0.188 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.18773079; CADD: 0.188 (0.903)

Frequency Data:: No frequency data

Other passed variants:

PTPN11

Exomiser Score: 0.160

Phenotype Score: 0.504

Variant Score: 0.696

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:151100 LEOPARD syndrome 1 - autosomal dominant; OMIM:156250 Metachondromatosis - autosomal dominant; OMIM:163950 Noonan syndrome 1 - autosomal dominant; OMIM:607785 Leukemia, juvenile myelomonocytic, somatic - autosomal dominant; ORPHA:2499 Metachondromatosis; ORPHA:500 Noonan syndrome with multiple lentigines; ORPHA:648 Noonan syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.160

Phenotype Score: 0.504

Variant Score: 0.696

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112422326G>A [0/1] rs576723455 (variation viewer)

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: PTPN11:ENST00000351677.6:c.14+3201G>A:p.(=); PTPN11:ENST00000392597.5:c.14+3201G>A:p.(=); PTPN11:ENST00000635625.1:c.14+3201G>A:p.(=); PTPN11:ENST00000639857.1:c.14+3201G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6999456; CADD: 0.700 (5.228)

Frequency Data:: TOPMed: 0.0215%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.029

Phenotype Score: 0.252

Variant Score: 0.778

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr12:g.112506117G>A [0/1] rs192080780 (variation viewer)

ClinVar: CONFLICTING_PATHOGENICITY_INTERPRETATIONS (criteria_provided,_conflicting_interpretations)

Variant score: 0.861 CONTRIBUTING VARIANT

Transcripts:: PTPN11:ENST00000351677.6:c.*325G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9706911; CADD: 0.971 (15.330)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.3687%; UK10K: 0.6083%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.4785%; gnomAD_G_FIN: 0.1147%; gnomAD_G_NFE: 0.3796%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112422326G>A [0/1] rs576723455 (variation viewer)

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: PTPN11:ENST00000351677.6:c.14+3201G>A:p.(=); PTPN11:ENST00000392597.5:c.14+3201G>A:p.(=); PTPN11:ENST00000635625.1:c.14+3201G>A:p.(=); PTPN11:ENST00000639857.1:c.14+3201G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6999456; CADD: 0.700 (5.228)

Frequency Data:: TOPMed: 0.0215%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0200%

Other passed variants:

INTERGENIC_VARIANT chr12:g.112529355G>A [0/1] rs139724198 (variation viewer)

Variant score: 0.672

Transcripts:: PTPN11:ENST00000351677.6::

Pathogenicity Data:: Best Score: 0.7528276; CADD: 0.753 (6.070)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.3679%; UK10K: 0.5819%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3799%; gnomAD_G_OTH: 0.1018%

INTERGENIC_VARIANT chr12:g.112410554C>CTTT [1/1]

Variant score: 0.626

Transcripts:: PTPN11:ENST00000392597.5::

Pathogenicity Data:: Best Score: 0.6257171; CADD: 0.626 (4.268)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112443400C>T [0/1] rs138076567 (variation viewer)

Variant score: 0.278

Transcripts:: PTPN11:ENST00000351677.6:c.15-2876C>T:p.(=); PTPN11:ENST00000392597.5:c.15-2876C>T:p.(=); PTPN11:ENST00000635625.1:c.15-2876C>T:p.(=); PTPN11:ENST00000639857.1:c.15-2876C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2972514; CADD: 0.297 (1.532)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.3759%; gnomAD_G_AFR: 0.1401%; gnomAD_G_AMR: 0.3632%; gnomAD_G_FIN: 0.1208%; gnomAD_G_NFE: 0.3874%; gnomAD_G_OTH: 0.1064%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112457945G>A [0/1] rs912621241 (variation viewer)

Variant score: 0.174

Transcripts:: PTPN11:ENST00000351677.6:c.756+1882G>A:p.(=); PTPN11:ENST00000392597.5:c.756+1882G>A:p.(=); PTPN11:ENST00000635625.1:c.756+1882G>A:p.(=)

Pathogenicity Data:: Best Score: 0.1743424; CADD: 0.174 (0.832)

Frequency Data:: gnomAD_G_NFE: 0.0067%

UPSTREAM_GENE_VARIANT chr12:g.112415994C>T [0/1] rs568386090 (variation viewer)

Variant score: 0.173

Transcripts:: PTPN11:ENST00000392597.5::; PTPN11:ENST00000202773.13::

Pathogenicity Data:: Best Score: 0.19406503; CADD: 0.194 (0.937)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0998%; gnomAD_G_AFR: 0.1180%; gnomAD_G_NFE: 0.5906%; gnomAD_G_OTH: 0.2625%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112476537G>A [0/1] rs146871619 (variation viewer)

Variant score: 0.120

Transcripts:: PTPN11:ENST00000351677.6:c.854-1114G>A:p.(=); PTPN11:ENST00000392597.5:c.854-1114G>A:p.(=); PTPN11:ENST00000635625.1:c.854-1114G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13503206; CADD: 0.135 (0.630)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.3759%; UK10K: 0.5951%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.4785%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3796%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112448436C>CG [0/1] rs373492048 (variation viewer)

Variant score: 0.067

Transcripts:: PTPN11:ENST00000351677.6:c.138-1882_138-1881insG:p.(=); PTPN11:ENST00000392597.5:c.138-1882_138-1881insG:p.(=); PTPN11:ENST00000635625.1:c.138-1882_138-1881insG:p.(=); PTPN11:ENST00000639857.1:c.138-1882_138-1881insG:p.(=)

Pathogenicity Data:: Best Score: 0.08018601; CADD: 0.080 (0.363)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3369%; UK10K: 0.7802%; gnomAD_G_AFR: 0.1034%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.6620%; gnomAD_G_OTH: 0.3080%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.112442830T>TTATATA [0|1] rs71086107 (variation viewer)

Variant score: 0.049

Transcripts:: PTPN11:ENST00000351677.6:c.15-3446_15-3445insTATATA:p.(=); PTPN11:ENST00000392597.5:c.15-3446_15-3445insTATATA:p.(=); PTPN11:ENST00000635625.1:c.15-3446_15-3445insTATATA:p.(=); PTPN11:ENST00000639857.1:c.15-3446_15-3445insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.049176276; CADD: 0.049 (0.219)

Frequency Data:: No frequency data

MARCHF4

Exomiser Score: 0.159

Phenotype Score: 0.504

Variant Score: 0.696

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.159

Phenotype Score: 0.504

Variant Score: 0.696

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216302899A>T [0|1]

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: MARCHF4:ENST00000273067.5:c.517-19170T>A:p.(=)

Pathogenicity Data:: Best Score: 0.69584143; CADD: 0.696 (5.169)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.081

Phenotype Score: 0.504

Variant Score: 0.612

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216302899A>T [0|1]

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: MARCHF4:ENST00000273067.5:c.517-19170T>A:p.(=)

Pathogenicity Data:: Best Score: 0.69584143; CADD: 0.696 (5.169)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216302921A>G [0|1] rs1574469078 (variation viewer)

Variant score: 0.528 CONTRIBUTING VARIANT

Transcripts:: MARCHF4:ENST00000273067.5:c.517-19192T>C:p.(=)

Pathogenicity Data:: Best Score: 0.52804565; CADD: 0.528 (3.261)

Frequency Data:: No frequency data

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr2:g.216258507GGTGT>G [-/1] rs61382542 (variation viewer)

Variant score: 0.453

Transcripts:: MARCHF4:ENST00000273067.5:c.*801_*804del:p.(=)

Pathogenicity Data:: Best Score: 0.45260602; CADD: 0.453 (2.617)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216354060C>A [0/1] rs151153179 (variation viewer)

Variant score: 0.215

Transcripts:: MARCHF4:ENST00000273067.5:c.516+15685G>T:p.(=)

Pathogenicity Data:: Best Score: 0.34385473; CADD: 0.344 (1.830)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.6833%; UK10K: 1.0447%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.3148%; gnomAD_G_NFE: 0.7999%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216365133G>T [0/1]

Variant score: 0.206

Transcripts:: MARCHF4:ENST00000273067.5:c.516+4612C>A:p.(=)

Pathogenicity Data:: Best Score: 0.20567179; CADD: 0.206 (1.000)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216302895A>C [0|1] rs1326765504 (variation viewer)

Variant score: 0.202

Transcripts:: MARCHF4:ENST00000273067.5:c.517-19166T>G:p.(=)

Pathogenicity Data:: Best Score: 0.20329052; CADD: 0.203 (0.987)

Frequency Data:: gnomAD_G_FIN: 0.0514%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216293893T>A [0/1] rs532018317 (variation viewer)

Variant score: 0.130

Transcripts:: MARCHF4:ENST00000273067.5:c.517-10164A>T:p.(=)

Pathogenicity Data:: Best Score: 0.8573079; CADD: 0.857 (8.456)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0599%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0117%; gnomAD_G_AMR: 0.4098%; gnomAD_G_ASJ: 1.9841%; gnomAD_G_NFE: 0.1247%; gnomAD_G_OTH: 0.3817%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.216302892T>A [0|1] rs1229180667 (variation viewer)

Variant score: 0.126

Transcripts:: MARCHF4:ENST00000273067.5:c.517-19163A>T:p.(=)

Pathogenicity Data:: Best Score: 0.12642539; CADD: 0.126 (0.587)

Frequency Data:: No frequency data

BCL2

Exomiser Score: 0.159

Phenotype Score: 0.258

Variant Score: 0.974

Phenotype matches:

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases - observed variants incompatible with mode of inheritance:: ORPHA:545 Follicular lymphoma

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.159

Phenotype Score: 0.258

Variant Score: 0.974

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63312926C>T [0/1] rs934939356 (variation viewer)

Variant score: 0.974 CONTRIBUTING VARIANT

Transcripts:: BCL2:ENST00000333681.5:c.585+5156G>A:p.(=); BCL2:ENST00000398117.1:c.585+5156G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9741774; CADD: 0.974 (15.880)

Frequency Data:: TOPMed: 0.0032%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.092

Phenotype Score: 0.258

Variant Score: 0.906

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63312926C>T [0/1] rs934939356 (variation viewer)

Variant score: 0.974 CONTRIBUTING VARIANT

Transcripts:: BCL2:ENST00000333681.5:c.585+5156G>A:p.(=); BCL2:ENST00000398117.1:c.585+5156G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9741774; CADD: 0.974 (15.880)

Frequency Data:: TOPMed: 0.0032%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212558AGGATTCCAAGCTTTCTCAAATAAAAGTTGCTACCTTGGCCG>A [0|1] rs1326907782 (variation viewer)

Variant score: 0.838 CONTRIBUTING VARIANT

Transcripts:: BCL2:ENST00000333681.5:c.586-83840_586-83800del:p.(=); BCL2:ENST00000398117.1:c.586-83840_586-83800del:p.(=)

Pathogenicity Data:: Best Score: 0.8426017; CADD: 0.843 (8.030)

Frequency Data:: gnomAD_G_NFE: 0.0410%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63236204T>A [0/1]

Variant score: 0.748

Transcripts:: BCL2:ENST00000333681.5:c.585+81878A>T:p.(=); BCL2:ENST00000398117.1:c.585+81878A>T:p.(=)

Pathogenicity Data:: Best Score: 0.7482323; CADD: 0.748 (5.990)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212615A>G [0|1] rs527528144 (variation viewer)

Variant score: 0.707

Transcripts:: BCL2:ENST00000333681.5:c.586-83856T>C:p.(=); BCL2:ENST00000398117.1:c.586-83856T>C:p.(=)

Pathogenicity Data:: Best Score: 0.8080448; CADD: 0.808 (7.168)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.5192%; gnomAD_G_AFR: 0.1626%; gnomAD_G_AMR: 0.2481%; gnomAD_G_FIN: 0.2349%; gnomAD_G_NFE: 0.6541%; gnomAD_G_OTH: 0.4158%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63213547AAC>A [-/1] rs57058660 (variation viewer)

Variant score: 0.681

Transcripts:: BCL2:ENST00000333681.5:c.586-84790_586-84789del:p.(=); BCL2:ENST00000398117.1:c.586-84790_586-84789del:p.(=)

Pathogenicity Data:: Best Score: 0.6807727; CADD: 0.681 (4.959)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63213547A>AACAC [-/1] rs57058660 (variation viewer)

Variant score: 0.595

Transcripts:: BCL2:ENST00000333681.5:c.586-84789_586-84788insGTGT:p.(=); BCL2:ENST00000398117.1:c.586-84789_586-84788insGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.5950513; CADD: 0.595 (3.926)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212131T>G [0|1] rs373026540 (variation viewer)

Variant score: 0.591

Transcripts:: BCL2:ENST00000333681.5:c.586-83372A>C:p.(=); BCL2:ENST00000398117.1:c.586-83372A>C:p.(=)

Pathogenicity Data:: Best Score: 0.7286061; CADD: 0.729 (5.664)

Frequency Data:: 1000Genomes: 0.6989%; gnomAD_G_AFR: 0.2931%; gnomAD_G_AMR: 0.4988%; gnomAD_G_ASJ: 0.3425%; gnomAD_G_FIN: 0.6777%; gnomAD_G_NFE: 0.8751%; gnomAD_G_OTH: 0.4246%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212616A>C [0|1] rs547649840 (variation viewer)

Variant score: 0.542

Transcripts:: BCL2:ENST00000333681.5:c.586-83857T>G:p.(=); BCL2:ENST00000398117.1:c.586-83857T>G:p.(=)

Pathogenicity Data:: Best Score: 0.62957525; CADD: 0.630 (4.313)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.5192%; gnomAD_G_AFR: 0.1740%; gnomAD_G_AMR: 0.3722%; gnomAD_G_FIN: 0.2353%; gnomAD_G_NFE: 0.7096%; gnomAD_G_OTH: 0.5208%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212128C>G [0|1] rs1337448479 (variation viewer)

Variant score: 0.392

Transcripts:: BCL2:ENST00000333681.5:c.586-83369G>C:p.(=); BCL2:ENST00000398117.1:c.586-83369G>C:p.(=)

Pathogenicity Data:: Best Score: 0.5021483; CADD: 0.502 (3.029)

Frequency Data:: gnomAD_G_AFR: 0.2207%; gnomAD_G_AMR: 0.4963%; gnomAD_G_ASJ: 0.6803%; gnomAD_G_FIN: 0.7571%; gnomAD_G_NFE: 0.9639%; gnomAD_G_OTH: 0.6211%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63264187G>C [0/1] rs146004012 (variation viewer)

Variant score: 0.336

Transcripts:: BCL2:ENST00000333681.5:c.585+53895C>G:p.(=); BCL2:ENST00000398117.1:c.585+53895C>G:p.(=)

Pathogenicity Data:: Best Score: 0.48984754; CADD: 0.490 (2.923)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.7669%; UK10K: 1.1108%; gnomAD_G_AFR: 0.2060%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.2021%; gnomAD_G_NFE: 0.8668%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63274277C>CT [0/1] rs74169950 (variation viewer)

Variant score: 0.152

Transcripts:: BCL2:ENST00000333681.5:c.585+43804_585+43805insA:p.(=); BCL2:ENST00000398117.1:c.585+43804_585+43805insA:p.(=)

Pathogenicity Data:: Best Score: 0.15160131; CADD: 0.152 (0.714)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr18:g.63122144G>C [0/1] rs147366221 (variation viewer)

Variant score: 0.117

Transcripts:: BCL2:ENST00000333681.5::; BCL2:ENST00000262719.10::

Pathogenicity Data:: Best Score: 0.13642514; CADD: 0.136 (0.637)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2015%; UK10K: 0.3835%; gnomAD_G_AFR: 0.0345%; gnomAD_G_AMR: 0.7212%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.2351%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63180157C>G [0/1] rs147955892 (variation viewer)

Variant score: 0.098

Transcripts:: BCL2:ENST00000333681.5:c.586-51398G>C:p.(=); BCL2:ENST00000398117.1:c.586-51398G>C:p.(=)

Pathogenicity Data:: Best Score: 0.12239313; CADD: 0.122 (0.567)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.6833%; UK10K: 0.8463%; gnomAD_G_AFR: 0.1490%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.9164%; gnomAD_G_NFE: 0.7662%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63140329C>A [0/1] rs111470430 (variation viewer)

Variant score: 0.084

Transcripts:: BCL2:ENST00000333681.5:c.586-11570G>T:p.(=); BCL2:ENST00000398117.1:c.586-11570G>T:p.(=)

Pathogenicity Data:: Best Score: 0.20090204; CADD: 0.201 (0.974)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.9357%; UK10K: 1.6662%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.4310%; gnomAD_G_NFE: 1.2592%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212110A>G [0|1] rs550877605 (variation viewer)

Variant score: 0.081

Transcripts:: BCL2:ENST00000333681.5:c.586-83351T>C:p.(=); BCL2:ENST00000398117.1:c.586-83351T>C:p.(=)

Pathogenicity Data:: Best Score: 0.1543318; CADD: 0.154 (0.728)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.3994%; gnomAD_G_AFR: 0.3363%; gnomAD_G_AMR: 1.2195%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 1.1072%; gnomAD_G_NFE: 1.5037%; gnomAD_G_OTH: 0.8368%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63132373C>T [0/1] rs112897237 (variation viewer)

Variant score: 0.057

Transcripts:: BCL2:ENST00000333681.5:c.586-3614G>A:p.(=); BCL2:ENST00000398117.1:c.586-3614G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13343728; CADD: 0.133 (0.622)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.9326%; UK10K: 1.6530%; gnomAD_G_AFR: 0.1374%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.4310%; gnomAD_G_NFE: 1.2587%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212092CTG>C [0|1] rs568731078 (variation viewer)

Variant score: 0.047

Transcripts:: BCL2:ENST00000333681.5:c.586-83335_586-83334del:p.(=); BCL2:ENST00000398117.1:c.586-83335_586-83334del:p.(=)

Pathogenicity Data:: Best Score: 0.19702876; CADD: 0.197 (0.953)

Frequency Data:: gnomAD_G_AFR: 0.4162%; gnomAD_G_AMR: 1.5700%; gnomAD_G_ASJ: 1.0000%; gnomAD_G_FIN: 1.2385%; gnomAD_G_NFE: 1.8917%; gnomAD_G_OTH: 0.9259%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212099A>G [0|1] rs376701546 (variation viewer)

Variant score: 0.038

Transcripts:: BCL2:ENST00000333681.5:c.586-83340T>C:p.(=); BCL2:ENST00000398117.1:c.586-83340T>C:p.(=)

Pathogenicity Data:: Best Score: 0.1081332; CADD: 0.108 (0.497)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.3994%; gnomAD_G_AFR: 0.3807%; gnomAD_G_AMR: 1.4528%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 1.2167%; gnomAD_G_NFE: 1.7540%; gnomAD_G_OTH: 0.8282%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63253390T>C [0/1] rs1284274549 (variation viewer)

Variant score: 0.032

Transcripts:: BCL2:ENST00000333681.5:c.585+64692A>G:p.(=); BCL2:ENST00000398117.1:c.585+64692A>G:p.(=)

Pathogenicity Data:: Best Score: 0.03172213; CADD: 0.032 (0.140)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212604C>T [0|1] rs150718975 (variation viewer)

Variant score: 0.026

Transcripts:: BCL2:ENST00000333681.5:c.586-83845G>A:p.(=); BCL2:ENST00000398117.1:c.586-83845G>A:p.(=)

Pathogenicity Data:: Best Score: 0.03905177; CADD: 0.039 (0.173)

Frequency Data:: 1000Genomes: 1.0780%; TOPMed: 0.3560%; gnomAD_G_AFR: 1.2451%; gnomAD_G_AMR: 0.4938%; gnomAD_G_EAS: 0.1239%; gnomAD_G_FIN: 0.1173%; gnomAD_G_NFE: 0.2509%; gnomAD_G_OTH: 0.2092%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212091G>C [0|1] rs558283260 (variation viewer)

Variant score: 0.013

Transcripts:: BCL2:ENST00000333681.5:c.586-83332C>G:p.(=); BCL2:ENST00000398117.1:c.586-83332C>G:p.(=)

Pathogenicity Data:: Best Score: 0.0654555; CADD: 0.065 (0.294)

Frequency Data:: gnomAD_G_AFR: 0.4147%; gnomAD_G_AMR: 1.5700%; gnomAD_G_ASJ: 1.0000%; gnomAD_G_FIN: 1.2658%; gnomAD_G_NFE: 1.9273%; gnomAD_G_OTH: 0.9278%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63242443C>T [0/1] rs917820651 (variation viewer)

Variant score: 0.012

Transcripts:: BCL2:ENST00000333681.5:c.585+75639G>A:p.(=); BCL2:ENST00000398117.1:c.585+75639G>A:p.(=)

Pathogenicity Data:: Best Score: 0.012356997; CADD: 0.012 (0.054)

Frequency Data:: TOPMed: 0.0032%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63212090G>GAT [0|1] rs879486064 (variation viewer)

Variant score: 0.010

Transcripts:: BCL2:ENST00000333681.5:c.586-83332_586-83331insAT:p.(=); BCL2:ENST00000398117.1:c.586-83332_586-83331insAT:p.(=)

Pathogenicity Data:: Best Score: 0.06157404; CADD: 0.062 (0.276)

Frequency Data:: gnomAD_G_AFR: 0.4127%; gnomAD_G_AMR: 1.5625%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.2629%; gnomAD_G_NFE: 1.9663%; gnomAD_G_OTH: 0.9184%

NDUFA8

Exomiser Score: 0.159

Phenotype Score: 0.504

Variant Score: 0.695

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.159

Phenotype Score: 0.504

Variant Score: 0.695

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.122158972T>C [0/1] rs538733127 (variation viewer)

Variant score: 0.695 CONTRIBUTING VARIANT

Transcripts:: NDUFA8:ENST00000373768.4:c.51+655A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6948594; CADD: 0.695 (5.155)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.243

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.122150971C>CA [1/1] rs71508152 (variation viewer)

Variant score: 0.243 CONTRIBUTING VARIANT

Transcripts:: NDUFA8:ENST00000373768.4:c.215+1273_215+1274insT:p.(=)

Pathogenicity Data:: Best Score: 0.24264413; CADD: 0.243 (1.207)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.122147617A>AT [1/1] rs34576446 (variation viewer)

Variant score: 0.158

Transcripts:: NDUFA8:ENST00000373768.4:c.381+494_381+495insA:p.(=)

Pathogenicity Data:: Best Score: 0.15821731; CADD: 0.158 (0.748)

Frequency Data:: No frequency data

STIM2

Exomiser Score: 0.157

Phenotype Score: 0.506

Variant Score: 0.692

Phenotype matches:

Proximity score 0.506 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.506

Variant Score: 0.279

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26887183C>CT [-/1] rs34736602 (variation viewer)

Variant score: 0.279 CONTRIBUTING VARIANT

Transcripts:: STIM2:ENST00000465503.5:c.151+25814_151+25815insT:p.(=); STIM2:ENST00000467011.5:c.151+25814_151+25815insT:p.(=); STIM2:ENST00000467087.5:c.151+25814_151+25815insT:p.(=); STIM2:ENST00000639195.1:c.151+25814_151+25815insT:p.(=); STIM2:ENST00000639640.1:c.151+25814_151+25815insT:p.(=)

Pathogenicity Data:: Best Score: 0.27889252; CADD: 0.279 (1.420)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.157

Phenotype Score: 0.506

Variant Score: 0.692

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26999079A>G [0/1] rs553644891 (variation viewer)

Variant score: 0.783 CONTRIBUTING VARIANT

Transcripts:: STIM2:ENST00000465503.5:c.510-153A>G:p.(=); STIM2:ENST00000467011.5:c.510-153A>G:p.(=); STIM2:ENST00000467087.5:c.510-153A>G:p.(=); STIM2:ENST00000639195.1:c.510-153A>G:p.(=); STIM2:ENST00000639640.1:c.510-153A>G:p.(=)

Pathogenicity Data:: Best Score: 0.82023716; CADD: 0.820 (7.453)

Frequency Data:: 1000Genomes: 0.0000%; TOPMed: 0.1871%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.2392%; gnomAD_G_FIN: 0.0289%; gnomAD_G_NFE: 0.2467%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26898283G>A [0/1] rs185517579 (variation viewer)

Variant score: 0.600 CONTRIBUTING VARIANT

Transcripts:: STIM2:ENST00000465503.5:c.152-21221G>A:p.(=); STIM2:ENST00000467011.5:c.152-21221G>A:p.(=); STIM2:ENST00000467087.5:c.152-21221G>A:p.(=); STIM2:ENST00000639195.1:c.152-21221G>A:p.(=); STIM2:ENST00000639640.1:c.152-21221G>A:p.(=)

Pathogenicity Data:: Best Score: 0.89346313; CADD: 0.893 (9.725)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.5328%; UK10K: 0.9786%; gnomAD_G_AFR: 0.1490%; gnomAD_G_AMR: 0.2392%; gnomAD_G_FIN: 1.2307%; gnomAD_G_NFE: 0.9933%; gnomAD_G_OTH: 0.7128%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.27020047A>G [0/1] rs114217964 (variation viewer)

Variant score: 0.206

Transcripts:: STIM2:ENST00000465503.5:c.1787+2063A>G:p.(=); STIM2:ENST00000467011.5:c.1764-954A>G:p.(=); STIM2:ENST00000467087.5:c.1763+2063A>G:p.(=); STIM2:ENST00000639195.1:c.1787+2063A>G:p.(=); STIM2:ENST00000639640.1:c.1763+2063A>G:p.(=)

Pathogenicity Data:: Best Score: 0.95783037; CADD: 0.958 (13.750)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 1.3000%; UK10K: 1.9175%; gnomAD_G_AFR: 0.2633%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.8338%; gnomAD_G_NFE: 1.8133%; gnomAD_G_OTH: 1.3265%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26941036A>G [0/1] rs139319545 (variation viewer)

Variant score: 0.172

Transcripts:: STIM2:ENST00000465503.5:c.283-16576A>G:p.(=); STIM2:ENST00000467011.5:c.283-16576A>G:p.(=); STIM2:ENST00000467087.5:c.283-16576A>G:p.(=); STIM2:ENST00000639195.1:c.283-16576A>G:p.(=); STIM2:ENST00000639640.1:c.283-16576A>G:p.(=)

Pathogenicity Data:: Best Score: 0.1785143; CADD: 0.179 (0.854)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1147%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1801%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26885821TTA>T [-/1] rs56851120 (variation viewer)

Variant score: 0.137

Transcripts:: STIM2:ENST00000465503.5:c.151+24453_151+24454del:p.(=); STIM2:ENST00000467011.5:c.151+24453_151+24454del:p.(=); STIM2:ENST00000467087.5:c.151+24453_151+24454del:p.(=); STIM2:ENST00000639195.1:c.151+24453_151+24454del:p.(=); STIM2:ENST00000639640.1:c.151+24453_151+24454del:p.(=)

Pathogenicity Data:: Best Score: 0.13702142; CADD: 0.137 (0.640)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr4:g.26851304C>CCTCT [0|1] rs71643694 (variation viewer)

Variant score: 0.129

Transcripts:: STIM2:ENST00000467087.5::

Pathogenicity Data:: Best Score: 0.12943739; CADD: 0.129 (0.602)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26923433G>A [0/1] rs140274580 (variation viewer)

Variant score: 0.077

Transcripts:: STIM2:ENST00000465503.5:c.282+3799G>A:p.(=); STIM2:ENST00000467011.5:c.282+3799G>A:p.(=); STIM2:ENST00000467087.5:c.282+3799G>A:p.(=); STIM2:ENST00000639195.1:c.282+3799G>A:p.(=); STIM2:ENST00000639640.1:c.282+3799G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2697022; CADD: 0.270 (1.365)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.5990%; gnomAD_G_AFR: 0.2642%; gnomAD_G_AMR: 1.0896%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 1.7589%; gnomAD_G_NFE: 1.8359%; gnomAD_G_OTH: 1.4675%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26920414G>A [0/1] rs116258701 (variation viewer)

Variant score: 0.017

Transcripts:: STIM2:ENST00000465503.5:c.282+780G>A:p.(=); STIM2:ENST00000467011.5:c.282+780G>A:p.(=); STIM2:ENST00000467087.5:c.282+780G>A:p.(=); STIM2:ENST00000639195.1:c.282+780G>A:p.(=); STIM2:ENST00000639640.1:c.282+780G>A:p.(=)

Pathogenicity Data:: Best Score: 0.06696057; CADD: 0.067 (0.301)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 1.3280%; UK10K: 1.8778%; gnomAD_G_AFR: 0.2639%; gnomAD_G_AMR: 1.0791%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.8041%; gnomAD_G_NFE: 1.8074%; gnomAD_G_OTH: 1.4257%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26915416G>A [0/1] rs114016840 (variation viewer)

Variant score: 0.016

Transcripts:: STIM2:ENST00000465503.5:c.152-4088G>A:p.(=); STIM2:ENST00000467011.5:c.152-4088G>A:p.(=); STIM2:ENST00000467087.5:c.152-4088G>A:p.(=); STIM2:ENST00000639195.1:c.152-4088G>A:p.(=); STIM2:ENST00000639640.1:c.152-4088G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0667457; CADD: 0.067 (0.300)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 1.3090%; UK10K: 1.8910%; gnomAD_G_AFR: 0.2759%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.8093%; gnomAD_G_NFE: 1.7845%; gnomAD_G_OTH: 1.3238%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26970221ATG>* [-/1]

Variant score: 0.000

Transcripts:: STIM2:ENST00000465503.5:c.397+12495_397+12497delATGins*:p.(=); STIM2:ENST00000467011.5:c.397+12495_397+12497delATGins*:p.(=); STIM2:ENST00000467087.5:c.397+12495_397+12497delATGins*:p.(=); STIM2:ENST00000639195.1:c.397+12495_397+12497delATGins*:p.(=); STIM2:ENST00000639640.1:c.397+12495_397+12497delATGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.26970245ATG>* [-/1]

Variant score: 0.000

Transcripts:: STIM2:ENST00000465503.5:c.397+12519_397+12521delATGins*:p.(=); STIM2:ENST00000467011.5:c.397+12519_397+12521delATGins*:p.(=); STIM2:ENST00000467087.5:c.397+12519_397+12521delATGins*:p.(=); STIM2:ENST00000639195.1:c.397+12519_397+12521delATGins*:p.(=); STIM2:ENST00000639640.1:c.397+12519_397+12521delATGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NDUFAB1

Exomiser Score: 0.155

Phenotype Score: 0.504

Variant Score: 0.691

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.155

Phenotype Score: 0.504

Variant Score: 0.691

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.23594449T>C [0/1]

Variant score: 0.691 CONTRIBUTING VARIANT

Transcripts:: NDUFAB1:ENST00000007516.8:c.168+1674A>G:p.(=); NDUFAB1:ENST00000570319.5:c.168+1674A>G:p.(=)

Pathogenicity Data:: Best Score: 0.69111276; CADD: 0.691 (5.102)

Frequency Data:: No frequency data

Other passed variants:

H2BC12

Exomiser Score: 0.151

Phenotype Score: 0.502

Variant Score: 0.691

Phenotype matches:

Proximity score 0.502 in interactome to HIRA and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with HIRA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.151

Phenotype Score: 0.502

Variant Score: 0.691

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr6:g.27143846T>TAAAAAAA [-/1] rs34292040 (variation viewer)

Variant score: 0.691 CONTRIBUTING VARIANT

Transcripts:: H2BC12:ENST00000356950.1::; H2BC12:ENST00000615353.1::

Pathogenicity Data:: Best Score: 0.6908281; CADD: 0.691 (5.098)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.043

Phenotype Score: 0.502

Variant Score: 0.542

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr6:g.27143846T>TAAAAAAA [-/1] rs34292040 (variation viewer)

Variant score: 0.691 CONTRIBUTING VARIANT

Transcripts:: H2BC12:ENST00000356950.1::; H2BC12:ENST00000615353.1::

Pathogenicity Data:: Best Score: 0.6908281; CADD: 0.691 (5.098)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.27143846TA>T [-/1] rs34292040 (variation viewer)

Variant score: 0.394 CONTRIBUTING VARIANT

Transcripts:: H2BC12:ENST00000356950.1::; H2BC12:ENST00000615353.1::

Pathogenicity Data:: Best Score: 0.39382225; CADD: 0.394 (2.174)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr6:g.27144460T>TG [1/1] rs59570458 (variation viewer)

Variant score: 0.360

Transcripts:: H2BC12:ENST00000356950.1::; H2BC12:ENST00000615353.1::

Pathogenicity Data:: Best Score: 0.3598231; CADD: 0.360 (1.937)

Frequency Data:: No frequency data

MAOA

Exomiser Score: 0.149

Phenotype Score: 0.505

Variant Score: 0.685

Phenotype matches:

Phenotypic similarity 0.428 to Brunner syndrome associated with MAOA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100710, Impulsivity

Phenotypic similarity 0.445 to mouse mutant involving MAOA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003459, increased fear-related response

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:300615 Brunner syndrome - X-linked recessive; OMIM:300615 Antisocial behavior (susceptibility); ORPHA:3057 Monoamine oxidase A deficiency

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.149

Phenotype Score: 0.505

Variant Score: 0.685

Variants contributing to score:

FIVE_PRIME_UTR_EXON_VARIANT chr23:g.43655100C>CACCGGCACCGGCACCAGTACCCGCACCAGT [1/1] rs1346551029 (variation viewer)

Variant score: 0.685 CONTRIBUTING VARIANT

Transcripts:: MAOA:ENST00000542639.5:c.-1673_-1644dup:p.(=)

Pathogenicity Data:: Best Score: 0.7613838; CADD: 0.761 (6.223)

Frequency Data:: gnomAD_G_AFR: 0.2463%; gnomAD_G_AMR: 0.5540%; gnomAD_G_FIN: 0.2292%; gnomAD_G_NFE: 0.2968%; gnomAD_G_OTH: 0.2342%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43684241G>A [1/1] rs186302269 (variation viewer)

Variant score: 0.387

Transcripts:: MAOA:ENST00000338702.3:c.168+634G>A:p.(=); MAOA:ENST00000542639.5:c.-232+634G>A:p.(=)

Pathogenicity Data:: Best Score: 0.55639136; CADD: 0.556 (3.530)

Frequency Data:: 1000Genomes: 0.1060%; TOPMed: 0.0438%; UK10K: 0.1061%; gnomAD_G_AMR: 0.1618%; gnomAD_G_FIN: 1.1774%; gnomAD_G_NFE: 0.1716%; gnomAD_G_OTH: 0.4132%

ATAD2B

Exomiser Score: 0.142

Phenotype Score: 0.524

Variant Score: 0.658

Phenotype matches:

Proximity score 0.524 in interactome to HIRA and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with HIRA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.030

Phenotype Score: 0.524

Variant Score: 0.474

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23921205C>CG [0/1] rs560022881 (variation viewer)

Variant score: 0.474 CONTRIBUTING VARIANT

Transcripts:: ATAD2B:ENST00000238789.10:c.216+5349_216+5350insC:p.(=)

Pathogenicity Data:: Best Score: 0.47410387; CADD: 0.474 (2.791)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.142

Phenotype Score: 0.524

Variant Score: 0.658

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23805254A>G [0/1] rs114901441 (variation viewer)

Variant score: 0.665 CONTRIBUTING VARIANT

Transcripts:: ATAD2B:ENST00000238789.10:c.2454+5062T>C:p.(=)

Pathogenicity Data:: Best Score: 0.911692; CADD: 0.912 (10.540)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.8028%; UK10K: 1.0976%; gnomAD_G_AFR: 0.1718%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.8888%; gnomAD_G_NFE: 1.0936%; gnomAD_G_OTH: 0.5133%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23837877G>A [0/1] rs188783646 (variation viewer)

Variant score: 0.650 CONTRIBUTING VARIANT

Transcripts:: ATAD2B:ENST00000238789.10:c.1569-3799C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8442601; CADD: 0.844 (8.076)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1473%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_NFE: 0.1333%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23822917C>CA [1/1] rs33911389 (variation viewer)

Variant score: 0.534

Transcripts:: ATAD2B:ENST00000238789.10:c.2131+340_2131+341insT:p.(=)

Pathogenicity Data:: Best Score: 0.5335555; CADD: 0.534 (3.312)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23853347T>C [0/1] rs148157934 (variation viewer)

Variant score: 0.429

Transcripts:: ATAD2B:ENST00000238789.10:c.1568+4068A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5928073; CADD: 0.593 (3.902)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.7972%; UK10K: 1.1108%; gnomAD_G_AFR: 0.1719%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.8872%; gnomAD_G_NFE: 1.0874%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23838322C>G [0/1] rs80232540 (variation viewer)

Variant score: 0.378

Transcripts:: ATAD2B:ENST00000238789.10:c.1569-4244G>C:p.(=)

Pathogenicity Data:: Best Score: 0.5214801; CADD: 0.521 (3.201)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.7940%; UK10K: 1.1108%; gnomAD_G_AFR: 0.1718%; gnomAD_G_AMR: 0.8413%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.8611%; gnomAD_G_NFE: 1.0803%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23892192C>G [0/1] rs190800790 (variation viewer)

Variant score: 0.196

Transcripts:: ATAD2B:ENST00000238789.10:c.368+3627G>C:p.(=)

Pathogenicity Data:: Best Score: 0.4589966; CADD: 0.459 (2.668)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1840%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.1467%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23910173C>CTTTT [0/1] rs756806271 (variation viewer)

Variant score: 0.145

Transcripts:: ATAD2B:ENST00000238789.10:c.217-14204_217-14203insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.1572476; CADD: 0.157 (0.743)

Frequency Data:: gnomAD_G_AFR: 0.0919%; gnomAD_G_ASJ: 0.4673%; gnomAD_G_NFE: 0.3318%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23834152C>CT [1/1] rs11378615 (variation viewer)

Variant score: 0.108

Transcripts:: ATAD2B:ENST00000238789.10:c.1569-75_1569-74insA:p.(=)

Pathogenicity Data:: Best Score: 0.1079278; CADD: 0.108 (0.496)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23769711G>GA [0/1] rs199842019 (variation viewer)

Variant score: 0.074

Transcripts:: ATAD2B:ENST00000238789.10:c.3134-4084_3134-4083insT:p.(=)

Pathogenicity Data:: Best Score: 0.07423663; CADD: 0.074 (0.335)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.23808068A>AATATATAAGTAATTATATATATAATTAT [1/1] rs1413440335 (variation viewer)

Variant score: 0.067

Transcripts:: ATAD2B:ENST00000238789.10:c.2454+2247_2454+2248insATAATTATATATATAATTACTTATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.067390144; CADD: 0.067 (0.303)

Frequency Data:: No frequency data

SCAP

Exomiser Score: 0.141

Phenotype Score: 0.504

Variant Score: 0.679

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.141

Phenotype Score: 0.504

Variant Score: 0.679

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.47469401A>G [0/1] rs867751477 (variation viewer)

Variant score: 0.679 CONTRIBUTING VARIANT

Transcripts:: SCAP:ENST00000265565.10:c.-99+6398T>C:p.(=); SCAP:ENST00000428413.5:c.-1020+6398T>C:p.(=); SCAP:ENST00000648151.1:c.-170-2954T>C:p.(=)

Pathogenicity Data:: Best Score: 0.68136024; CADD: 0.681 (4.967)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.133

Phenotype Score: 0.504

Variant Score: 0.672

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.47469401A>G [0/1] rs867751477 (variation viewer)

Variant score: 0.679 CONTRIBUTING VARIANT

Transcripts:: SCAP:ENST00000265565.10:c.-99+6398T>C:p.(=); SCAP:ENST00000428413.5:c.-1020+6398T>C:p.(=); SCAP:ENST00000648151.1:c.-170-2954T>C:p.(=)

Pathogenicity Data:: Best Score: 0.68136024; CADD: 0.681 (4.967)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.47471189G>T [0/1] rs868727082 (variation viewer)

Variant score: 0.665 CONTRIBUTING VARIANT

Transcripts:: SCAP:ENST00000265565.10:c.-99+4610C>A:p.(=); SCAP:ENST00000428413.5:c.-1020+4610C>A:p.(=); SCAP:ENST00000648151.1:c.-171+1582C>A:p.(=)

Pathogenicity Data:: Best Score: 0.66680384; CADD: 0.667 (4.773)

Frequency Data:: TOPMed: 0.0135%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47440879T>G [0/1] rs544358058 (variation viewer)

Variant score: 0.305

Transcripts:: SCAP:ENST00000265565.10:c.122+1993A>C:p.(=); SCAP:ENST00000545718.2:c.95+2020A>C:p.(=); SCAP:ENST00000648151.1:c.122+1993A>C:p.(=); SCAP:ENST00000428413.5:c.-800+1993A>C:p.(=)

Pathogenicity Data:: Best Score: 0.306095; CADD: 0.306 (1.587)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0200%; gnomAD_G_NFE: 0.0068%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47425659G>A [0/1] rs373115861 (variation viewer)

Variant score: 0.186

Transcripts:: SCAP:ENST00000265565.10:c.911-48C>T:p.(=); SCAP:ENST00000545718.2:c.96-3187C>T:p.(=); SCAP:ENST00000648151.1:c.911-48C>T:p.(=); SCAP:ENST00000428413.5:c.-11-48C>T:p.(=)

Pathogenicity Data:: Best Score: 0.18754369; CADD: 0.188 (0.902)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0096%; ESP AA: 0.0227%; ESP EA: 0.0116%; ESP All: 0.0154%; ExAC AFR: 0.0412%; ExAC AMR: 0.0175%; ExAC NFE: 0.0110%; gnomAD_E_AFR: 0.0337%; gnomAD_E_AMR: 0.0155%; gnomAD_E_ASJ: 0.0110%; gnomAD_E_EAS: 0.0118%; gnomAD_E_NFE: 0.0095%; gnomAD_E_OTH: 0.0192%; gnomAD_E_SAS: 0.0034%; gnomAD_G_NFE: 0.0067%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.47471070T>C [0/1] rs541381250 (variation viewer)

Variant score: 0.150

Transcripts:: SCAP:ENST00000265565.10:c.-99+4729A>G:p.(=); SCAP:ENST00000428413.5:c.-1020+4729A>G:p.(=); SCAP:ENST00000648151.1:c.-171+1701A>G:p.(=)

Pathogenicity Data:: Best Score: 0.15081954; CADD: 0.151 (0.710)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0135%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47435469TACAC>T [-/1] rs57702290 (variation viewer)

Variant score: 0.137

Transcripts:: SCAP:ENST00000265565.10:c.123-336_123-333del:p.(=); SCAP:ENST00000545718.2:c.95+7426_95+7429del:p.(=); SCAP:ENST00000648151.1:c.123-336_123-333del:p.(=); SCAP:ENST00000428413.5:c.-799-336_-799-333del:p.(=)

Pathogenicity Data:: Best Score: 0.1368227; CADD: 0.137 (0.639)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47435469TACACACACACACAC>T [-/1] rs57702290 (variation viewer)

Variant score: 0.122

Transcripts:: SCAP:ENST00000265565.10:c.123-346_123-333del:p.(=); SCAP:ENST00000545718.2:c.95+7416_95+7429del:p.(=); SCAP:ENST00000648151.1:c.123-346_123-333del:p.(=); SCAP:ENST00000428413.5:c.-799-346_-799-333del:p.(=)

Pathogenicity Data:: Best Score: 0.12198889; CADD: 0.122 (0.565)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.47472453T>A [0/1] rs867828178 (variation viewer)

Variant score: 0.085

Transcripts:: SCAP:ENST00000265565.10:c.-99+3346A>T:p.(=); SCAP:ENST00000428413.5:c.-1020+3346A>T:p.(=); SCAP:ENST00000648151.1:c.-171+318A>T:p.(=)

Pathogenicity Data:: Best Score: 0.15763563; CADD: 0.158 (0.745)

Frequency Data:: gnomAD_G_AFR: 0.5191%; gnomAD_G_EAS: 1.1834%; gnomAD_G_NFE: 1.4788%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47441874C>CT [1/1] rs1160447716 (variation viewer)

Variant score: 0.077

Transcripts:: SCAP:ENST00000265565.10:c.122+997_122+998insA:p.(=); SCAP:ENST00000545718.2:c.95+1024_95+1025insA:p.(=); SCAP:ENST00000648151.1:c.122+997_122+998insA:p.(=); SCAP:ENST00000428413.5:c.-800+997_-800+998insA:p.(=)

Pathogenicity Data:: Best Score: 0.07742858; CADD: 0.077 (0.350)

Frequency Data:: No frequency data

UBE2G1

Exomiser Score: 0.138

Phenotype Score: 0.504

Variant Score: 0.677

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.138

Phenotype Score: 0.504

Variant Score: 0.677

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4318626A>G [0/1]

Variant score: 0.677 CONTRIBUTING VARIANT

Transcripts:: UBE2G1:ENST00000396981.6:c.47-11503T>C:p.(=); UBE2G1:ENST00000572484.5:c.-167-11503T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6771506; CADD: 0.677 (4.910)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.079

Phenotype Score: 0.504

Variant Score: 0.609

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4318626A>G [0/1]

Variant score: 0.677 CONTRIBUTING VARIANT

Transcripts:: UBE2G1:ENST00000396981.6:c.47-11503T>C:p.(=); UBE2G1:ENST00000572484.5:c.-167-11503T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6771506; CADD: 0.677 (4.910)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4357506T>G [0/1] rs60921716 (variation viewer)

Variant score: 0.540 CONTRIBUTING VARIANT

Transcripts:: UBE2G1:ENST00000396981.6:c.46+8765A>C:p.(=); UBE2G1:ENST00000572484.5:c.-283+8765A>C:p.(=)

Pathogenicity Data:: Best Score: 0.5399553; CADD: 0.540 (3.372)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4355656A>T [0/1] rs562491773 (variation viewer)

Variant score: 0.349

Transcripts:: UBE2G1:ENST00000396981.6:c.46+10615T>A:p.(=); UBE2G1:ENST00000572484.5:c.-283+10615T>A:p.(=)

Pathogenicity Data:: Best Score: 0.4966153; CADD: 0.497 (2.981)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.3456%; gnomAD_G_AFR: 0.0621%; gnomAD_G_AMR: 0.2786%; gnomAD_G_FIN: 1.1637%; gnomAD_G_NFE: 0.5389%; gnomAD_G_OTH: 0.8294%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4328088G>A [0/1] rs8082123 (variation viewer)

Variant score: 0.290

Transcripts:: UBE2G1:ENST00000396981.6:c.47-20965C>T:p.(=); UBE2G1:ENST00000572484.5:c.-168+3686C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5705625; CADD: 0.571 (3.671)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.8824%; UK10K: 1.5340%; gnomAD_G_AFR: 0.2293%; gnomAD_G_AMR: 1.4320%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.6594%; gnomAD_G_NFE: 1.3463%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4284829CTTTTCTTTCTT>C [0/1]

Variant score: 0.183

Transcripts:: UBE2G1:ENST00000396981.6:c.427-1919_427-1909del:p.(=); UBE2G1:ENST00000572484.5:c.214-1919_214-1909del:p.(=)

Pathogenicity Data:: Best Score: 0.18322957; CADD: 0.183 (0.879)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4330976C>CCACACACA [1/1] rs57051928 (variation viewer)

Variant score: 0.154

Transcripts:: UBE2G1:ENST00000396981.6:c.47-23854_47-23853insTGTGTGTG:p.(=); UBE2G1:ENST00000572484.5:c.-168+797_-168+798insTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.15355253; CADD: 0.154 (0.724)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4347469C>CTTTT [-/1] rs34014821 (variation viewer)

Variant score: 0.131

Transcripts:: UBE2G1:ENST00000396981.6:c.46+18801_46+18802insAAAA:p.(=); UBE2G1:ENST00000572484.5:c.-282-15582_-282-15581insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.13103956; CADD: 0.131 (0.610)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.4347469CTTTTTTT>C [-/1] rs34014821 (variation viewer)

Variant score: 0.101

Transcripts:: UBE2G1:ENST00000396981.6:c.46+18795_46+18801del:p.(=); UBE2G1:ENST00000572484.5:c.-282-15588_-282-15582del:p.(=)

Pathogenicity Data:: Best Score: 0.100916564; CADD: 0.101 (0.462)

Frequency Data:: No frequency data

THREE_PRIME_UTR_INTRON_VARIANT chr17:g.4274493G>T [0/1] rs184754309 (variation viewer)

Variant score: 0.015

Transcripts:: UBE2G1:ENST00000396981.6:c.*38-1977C>A:p.(=); UBE2G1:ENST00000572484.5:c.*38-1977C>A:p.(=)

Pathogenicity Data:: Best Score: 0.09780586; CADD: 0.098 (0.447)

Frequency Data:: 1000Genomes: 0.9185%; TOPMed: 0.7470%; UK10K: 1.1505%; gnomAD_G_AFR: 0.3209%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.9805%; gnomAD_G_NFE: 1.2882%; gnomAD_G_OTH: 1.6360%

HLA-A

Exomiser Score: 0.136

Phenotype Score: 0.504

Variant Score: 0.675

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:179 Birdshot chorioretinopathy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.136

Phenotype Score: 0.504

Variant Score: 0.675

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr6:g.29948201A>C [0|1] rs9260274 (variation viewer)

Variant score: 0.675 CONTRIBUTING VARIANT

Transcripts:: HLA-A:ENST00000376802.2::; HLA-A:ENST00000439514.1::

Pathogenicity Data:: Best Score: 0.6746131; CADD: 0.675 (4.876)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.106

Phenotype Score: 0.504

Variant Score: 0.644

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr6:g.29948201A>C [0|1] rs9260274 (variation viewer)

Variant score: 0.675 CONTRIBUTING VARIANT

Transcripts:: HLA-A:ENST00000376802.2::; HLA-A:ENST00000439514.1::

Pathogenicity Data:: Best Score: 0.6746131; CADD: 0.675 (4.876)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.29941529C>T [0/1] rs867644033 (variation viewer)

Variant score: 0.614 CONTRIBUTING VARIANT

Transcripts:: HLA-A:ENST00000396634.5:c.-282+210C>T:p.(=)

Pathogenicity Data:: Best Score: 0.63708913; CADD: 0.637 (4.402)

Frequency Data:: gnomAD_G_AMR: 0.2404%; gnomAD_G_OTH: 0.1020%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.29943079G>A [0/1] rs576190891 (variation viewer)

Variant score: 0.360

Transcripts:: HLA-A:ENST00000376802.2:c.343+53G>A:p.(=); HLA-A:ENST00000376806.9:c.343+53G>A:p.(=); HLA-A:ENST00000376809.10:c.343+53G>A:p.(=); HLA-A:ENST00000396634.5:c.343+53G>A:p.(=); HLA-A:ENST00000638375.1:c.343+53G>A:p.(=)

Pathogenicity Data:: Best Score: 0.36114836; CADD: 0.361 (1.946)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0200%

DOWNSTREAM_GENE_VARIANT chr6:g.29949602C>CATGCATGTATGTATGTATGTATGTATGTATGTATGT [0|1] rs28749164 (variation viewer)

Variant score: 0.054

Transcripts:: HLA-A:ENST00000376802.2::; HLA-A:ENST00000439514.1::

Pathogenicity Data:: Best Score: 0.06179011; CADD: 0.062 (0.277)

Frequency Data:: gnomAD_G_AFR: 0.5087%; gnomAD_G_AMR: 0.3175%; gnomAD_G_EAS: 0.2703%; gnomAD_G_FIN: 0.4701%; gnomAD_G_NFE: 0.5448%; gnomAD_G_OTH: 0.6527%

INTERGENIC_VARIANT chr6:g.29936099G>* [-/1]

Variant score: 0.000

Transcripts:: HLA-A:ENST00000396634.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

HEXB

Exomiser Score: 0.136

Phenotype Score: 0.502

Variant Score: 0.677

Phenotype matches:

Proximity score 0.502 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:268800 Sandhoff disease, infantile, juvenile, and adult forms - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.273

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.74716016CAA>C [0/1] rs71600435 (variation viewer)

Variant score: 0.273 CONTRIBUTING VARIANT

Transcripts:: HEXB:ENST00000261416.12:c.1082+327_1082+328del:p.(=); HEXB:ENST00000511181.5:c.407+327_407+328del:p.(=)

Pathogenicity Data:: Best Score: 0.27305758; CADD: 0.273 (1.385)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.136

Phenotype Score: 0.502

Variant Score: 0.677

Variants contributing to score:

REGULATORY_REGION_VARIANT chr5:g.75057742G>A [0/1] rs112270430 (variation viewer)

Variant score: 0.712 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.795591; CADD: 0.796 (6.895)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3631%; UK10K: 0.4628%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.5730%; gnomAD_G_OTH: 0.3055%

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.74641405G>C [0/1] rs538248083 (variation viewer)

Variant score: 0.642 CONTRIBUTING VARIANT

Transcripts:: HEXB:ENST00000511181.5:c.-377+847G>C:p.(=)

Pathogenicity Data:: Best Score: 0.83449924; CADD: 0.834 (7.812)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.4898%; UK10K: 0.5951%; gnomAD_G_AFR: 0.1720%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.4582%; gnomAD_G_NFE: 0.6202%; gnomAD_G_OTH: 0.3055%

Other passed variants:

MISSENSE_VARIANT chr5:g.74685474C>T [0/1] rs147155126 (variation viewer)

ClinVar: CONFLICTING_PATHOGENICITY_INTERPRETATIONS (criteria_provided,_conflicting_interpretations)

Variant score: 0.582

Transcripts:: HEXB:ENST00000261416.12:c.214C>T:p.(Leu72Phe); HEXB:ENST00000511181.5:c.-376-3854C>T:p.(=)

Pathogenicity Data:: Best Score: 0.995; SIFT: 0.005 (D); CADD: 0.992 (20.800)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.8012%; UK10K: 1.2298%; ESP AA: 0.3404%; ESP EA: 1.1165%; ESP All: 0.8536%; ExAC AFR: 0.2373%; ExAC AMR: 0.5657%; ExAC EAS: 0.0119%; ExAC FIN: 0.9855%; ExAC NFE: 0.9811%; ExAC OTH: 0.6977%; ExAC SAS: 0.7064%; gnomAD_E_AFR: 0.1981%; gnomAD_E_AMR: 0.4744%; gnomAD_E_ASJ: 1.4029%; gnomAD_E_EAS: 0.0059%; gnomAD_E_FIN: 0.8141%; gnomAD_E_NFE: 0.9855%; gnomAD_E_OTH: 0.9081%; gnomAD_E_SAS: 0.7663%; gnomAD_G_AFR: 0.1505%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.0040%; gnomAD_G_NFE: 1.0089%; gnomAD_G_OTH: 1.1411%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.74704443A>G [0/1] rs186711505 (variation viewer)

Variant score: 0.543

Transcripts:: HEXB:ENST00000261416.12:c.670-776A>G:p.(=); HEXB:ENST00000511181.5:c.-6-776A>G:p.(=)

Pathogenicity Data:: Best Score: 0.73715484; CADD: 0.737 (5.803)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.4938%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1261%; gnomAD_G_AMR: 1.0791%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.8746%; gnomAD_G_NFE: 0.6061%; gnomAD_G_OTH: 0.9202%

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.74681182T>A [0/1] rs148275294 (variation viewer)

Variant score: 0.253

Transcripts:: HEXB:ENST00000511181.5:c.-376-8146T>A:p.(=)

Pathogenicity Data:: Best Score: 0.40310216; CADD: 0.403 (2.241)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.8163%; UK10K: 1.2166%; gnomAD_G_AFR: 0.1604%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.0023%; gnomAD_G_NFE: 1.0260%; gnomAD_G_OTH: 1.1224%

REGULATORY_REGION_VARIANT chr5:g.74232153C>CT [0/1] rs770423775 (variation viewer)

Variant score: 0.243

Transcripts:

Pathogenicity Data:: Best Score: 0.24281847; CADD: 0.243 (1.208)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.74700001CTT>C [1/1] rs58177670 (variation viewer)

Variant score: 0.194

Transcripts:: HEXB:ENST00000261416.12:c.669+2896_669+2897del:p.(=); HEXB:ENST00000511181.5:c.-7+2896_-7+2897del:p.(=)

Pathogenicity Data:: Best Score: 0.19369382; CADD: 0.194 (0.935)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.74679798CAA>C [1/1] rs70976121 (variation viewer)

Variant score: 0.085

Transcripts:: HEXB:ENST00000511181.5:c.-376-9529_-376-9528del:p.(=)

Pathogenicity Data:: Best Score: 0.08525509; CADD: 0.085 (0.387)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.74644764C>CTT [1/1] rs3058406 (variation viewer)

Variant score: 0.081

Transcripts:: HEXB:ENST00000511181.5:c.-377+4206_-377+4207insTT:p.(=)

Pathogenicity Data:: Best Score: 0.081455946; CADD: 0.081 (0.369)

Frequency Data:: No frequency data

NCOR1

Exomiser Score: 0.135

Phenotype Score: 0.516

Variant Score: 0.660

Phenotype matches:

Proximity score 0.516 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.135

Phenotype Score: 0.516

Variant Score: 0.660

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16086503CCT>C [0/1] rs879587609 (variation viewer)

Variant score: 0.660 CONTRIBUTING VARIANT

Transcripts:: NCOR1:ENST00000268712.8:c.3017-63_3017-62del:p.(=); NCOR1:ENST00000395851.5:c.3065-63_3065-62del:p.(=); NCOR1:ENST00000395857.7:c.2738-63_2738-62del:p.(=)

Pathogenicity Data:: Best Score: 0.6635659; CADD: 0.664 (4.731)

Frequency Data:: TOPMed: 0.0358%; gnomAD_G_NFE: 0.0333%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.028

Phenotype Score: 0.516

Variant Score: 0.476

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16086503CCT>C [0/1] rs879587609 (variation viewer)

Variant score: 0.660 CONTRIBUTING VARIANT

Transcripts:: NCOR1:ENST00000268712.8:c.3017-63_3017-62del:p.(=); NCOR1:ENST00000395851.5:c.3065-63_3065-62del:p.(=); NCOR1:ENST00000395857.7:c.2738-63_2738-62del:p.(=)

Pathogenicity Data:: Best Score: 0.6635659; CADD: 0.664 (4.731)

Frequency Data:: TOPMed: 0.0358%; gnomAD_G_NFE: 0.0333%

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.16208206A>ATTT [0/1] rs757019446 (variation viewer)

Variant score: 0.293 CONTRIBUTING VARIANT

Transcripts:: NCOR1:ENST00000268712.8:c.-71+7155_-71+7156insAAA:p.(=); NCOR1:ENST00000395857.7:c.-71+7155_-71+7156insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.29254305; CADD: 0.293 (1.503)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.16208035C>CT [0/1] rs71150278 (variation viewer)

Variant score: 0.278

Transcripts:: NCOR1:ENST00000268712.8:c.-71+7326_-71+7327insA:p.(=); NCOR1:ENST00000395857.7:c.-71+7326_-71+7327insA:p.(=)

Pathogenicity Data:: Best Score: 0.27789563; CADD: 0.278 (1.414)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16185826G>C [0/1] rs79363657 (variation viewer)

Variant score: 0.228

Transcripts:: NCOR1:ENST00000268712.8:c.242+728C>G:p.(=); NCOR1:ENST00000395848.5:c.108+8636C>G:p.(=); NCOR1:ENST00000395851.5:c.242+728C>G:p.(=); NCOR1:ENST00000395857.7:c.108+8636C>G:p.(=)

Pathogenicity Data:: Best Score: 0.26124573; CADD: 0.261 (1.315)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.3472%; UK10K: 0.5951%; gnomAD_G_AFR: 0.1382%; gnomAD_G_AMR: 0.3632%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0580%; gnomAD_G_NFE: 0.5903%; gnomAD_G_OTH: 0.3093%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16086211C>T [0/1] rs573068760 (variation viewer)

Variant score: 0.198

Transcripts:: NCOR1:ENST00000268712.8:c.3177+71G>A:p.(=); NCOR1:ENST00000395851.5:c.3225+71G>A:p.(=); NCOR1:ENST00000395857.7:c.2898+71G>A:p.(=)

Pathogenicity Data:: Best Score: 0.20237273; CADD: 0.202 (0.982)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1378%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1600%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16178498C>CA [0/1] rs564320622 (variation viewer)

Variant score: 0.175

Transcripts:: NCOR1:ENST00000268712.8:c.243-6504_243-6503insT:p.(=); NCOR1:ENST00000395848.5:c.109-13338_109-13337insT:p.(=); NCOR1:ENST00000395851.5:c.243-6504_243-6503insT:p.(=); NCOR1:ENST00000395857.7:c.109-13338_109-13337insT:p.(=)

Pathogenicity Data:: Best Score: 0.18059236; CADD: 0.181 (0.865)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1997%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16041404C>CTTTTTTT [0/1] rs3031059 (variation viewer)

Variant score: 0.142

Transcripts:: NCOR1:ENST00000268712.8:c.6680-911_6680-910insAAAAAAA:p.(=); NCOR1:ENST00000395851.5:c.6371-911_6371-910insAAAAAAA:p.(=); NCOR1:ENST00000395857.7:c.6392-911_6392-910insAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.14157963; CADD: 0.142 (0.663)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16092693ATATTTTTT>A [0/1] rs1357238339 (variation viewer)

Variant score: 0.134

Transcripts:: NCOR1:ENST00000268712.8:c.2821-643_2821-636del:p.(=); NCOR1:ENST00000395848.5:c.2542-643_2542-636del:p.(=); NCOR1:ENST00000395851.5:c.2869-643_2869-636del:p.(=); NCOR1:ENST00000395857.7:c.2542-643_2542-636del:p.(=)

Pathogenicity Data:: Best Score: 0.13363677; CADD: 0.134 (0.623)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16154015C>CT [0/1] rs61436082 (variation viewer)

Variant score: 0.133

Transcripts:: NCOR1:ENST00000268712.8:c.733-621_733-620insA:p.(=); NCOR1:ENST00000395848.5:c.406-621_406-620insA:p.(=); NCOR1:ENST00000395851.5:c.733-621_733-620insA:p.(=); NCOR1:ENST00000395857.7:c.406-621_406-620insA:p.(=)

Pathogenicity Data:: Best Score: 0.13323772; CADD: 0.133 (0.621)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.16181211A>ATGTGTGTG [0|1] rs61215793 (variation viewer)

Variant score: 0.131

Transcripts:: NCOR1:ENST00000268712.8:c.242+5342_242+5343insCACACACA:p.(=); NCOR1:ENST00000395848.5:c.108+13250_108+13251insCACACACA:p.(=); NCOR1:ENST00000395851.5:c.242+5342_242+5343insCACACACA:p.(=); NCOR1:ENST00000395857.7:c.108+13250_108+13251insCACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.13063931; CADD: 0.131 (0.608)

Frequency Data:: No frequency data

F9

Exomiser Score: 0.134

Phenotype Score: 0.508

Variant Score: 0.669

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300807 Thrombophilia, X-linked, due to factor IX defect - X-linked recessive; OMIM:300807 Deep venous thrombosis, protection against (susceptibility); OMIM:306900 Hemophilia B - X-linked recessive

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.134

Phenotype Score: 0.508

Variant Score: 0.669

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr23:g.139530559C>T [1/1]

Variant score: 0.669 CONTRIBUTING VARIANT

Transcripts:: F9:ENST00000218099.7::; F9:ENST00000442297.1::

Pathogenicity Data:: Best Score: 0.6687163; CADD: 0.669 (4.798)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.011

Phenotype Score: 0.254

Variant Score: 0.669

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr23:g.139530559C>T [1/1]

Variant score: 0.669 CONTRIBUTING VARIANT

Transcripts:: F9:ENST00000218099.7::; F9:ENST00000442297.1::

Pathogenicity Data:: Best Score: 0.6687163; CADD: 0.669 (4.798)

Frequency Data:: No frequency data

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr23:g.139562364C>T [1/1] rs747670394 (variation viewer)

ClinVar: UNCERTAIN_SIGNIFICANCE (criteria_provided,_single_submitter)

Variant score: 0.535

Transcripts:: F9:ENST00000218099.7:c.*293C>T:p.(=)

Pathogenicity Data:: Best Score: 0.59168065; CADD: 0.592 (3.890)

Frequency Data:: 1000Genomes: 0.0265%; TOPMed: 0.0518%; UK10K: 0.0455%; gnomAD_G_ASJ: 0.5348%; gnomAD_G_FIN: 0.0382%; gnomAD_G_NFE: 0.0571%

UPSTREAM_GENE_VARIANT chr23:g.139527606T>A [1/1] rs1401183319 (variation viewer)

Variant score: 0.372

Transcripts:: F9:ENST00000218099.7::; F9:ENST00000442297.1::

Pathogenicity Data:: Best Score: 0.4134568; CADD: 0.413 (2.317)

Frequency Data:: TOPMed: 0.1752%; gnomAD_G_AFR: 0.0170%; gnomAD_G_AMR: 0.1631%; gnomAD_G_ASJ: 0.5525%; gnomAD_G_NFE: 0.1330%

INTERGENIC_VARIANT chr23:g.139513954G>GTT [1|1] rs199926945 (variation viewer)

Variant score: 0.305

Transcripts:: F9:ENST00000218099.7::; F9:ENST00000442297.1::

Pathogenicity Data:: Best Score: 0.30481565; CADD: 0.305 (1.579)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.139531394TAA>T [1/1] rs994885035 (variation viewer)

Variant score: 0.173

Transcripts:: F9:ENST00000218099.7:c.88+543_88+544del:p.(=); F9:ENST00000394090.2:c.88+543_88+544del:p.(=)

Pathogenicity Data:: Best Score: 0.19090408; CADD: 0.191 (0.920)

Frequency Data:: TOPMed: 0.0207%; gnomAD_G_ASJ: 0.5291%; gnomAD_G_NFE: 0.0188%

KIF5A

Exomiser Score: 0.133

Phenotype Score: 0.507

Variant Score: 0.669

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:604187 Spastic paraplegia 10, autosomal dominant - autosomal dominant; OMIM:617235 Myoclonus, intractable, neonatal - autosomal dominant; OMIM:617921 Amyotrophic lateral sclerosis, susceptibility to, 25 (susceptibility); ORPHA:100991 Autosomal dominant spastic paraplegia type 10

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.133

Phenotype Score: 0.507

Variant Score: 0.669

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr12:g.57588641C>G [0/1]

Variant score: 0.669 CONTRIBUTING VARIANT

Transcripts:: KIF5A:ENST00000455537.7::

Pathogenicity Data:: Best Score: 0.6688689; CADD: 0.669 (4.800)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.254

Variant Score: 0.497

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr12:g.57588641C>G [0/1]

Variant score: 0.669 CONTRIBUTING VARIANT

Transcripts:: KIF5A:ENST00000455537.7::

Pathogenicity Data:: Best Score: 0.6688689; CADD: 0.669 (4.800)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.57577174C>T [0/1] rs775243 (variation viewer)

Variant score: 0.325 CONTRIBUTING VARIANT

Transcripts:: KIF5A:ENST00000286452.5:c.2033+312C>T:p.(=); KIF5A:ENST00000455537.7:c.2300+312C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3328861; CADD: 0.333 (1.758)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1131%; UK10K: 0.0793%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.1665%

Other passed variants:

LNP1

Exomiser Score: 0.129

Phenotype Score: 0.502

Variant Score: 0.670

Phenotype matches:

Proximity score 0.502 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.129

Phenotype Score: 0.502

Variant Score: 0.670

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.100472655C>T [0/1]

Variant score: 0.670 CONTRIBUTING VARIANT

Transcripts:: LNP1:ENST00000383693.8::

Pathogenicity Data:: Best Score: 0.6702385; CADD: 0.670 (4.818)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.052

Phenotype Score: 0.502

Variant Score: 0.562

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.100472655C>T [0/1]

Variant score: 0.670 CONTRIBUTING VARIANT

Transcripts:: LNP1:ENST00000383693.8::

Pathogenicity Data:: Best Score: 0.6702385; CADD: 0.670 (4.818)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.100450922A>G [0/1] rs542646969 (variation viewer)

Variant score: 0.454 CONTRIBUTING VARIANT

Transcripts:: LNP1:ENST00000383693.8:c.157-797A>G:p.(=); LNP1:ENST00000489752.1:c.157-758A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6685637; CADD: 0.669 (4.796)

Frequency Data:: UK10K: 1.2166%; gnomAD_G_AFR: 0.1490%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.7163%; gnomAD_G_NFE: 0.9867%; gnomAD_G_OTH: 0.8147%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.100424515G>A [0/1] rs192317171 (variation viewer)

Variant score: 0.251

Transcripts:: LNP1:ENST00000383693.8:c.-33-5182G>A:p.(=); LNP1:ENST00000489752.1:c.-33-5182G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3662762; CADD: 0.366 (1.981)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.5264%; UK10K: 1.2034%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.3597%; gnomAD_G_FIN: 0.6869%; gnomAD_G_NFE: 1.0263%; gnomAD_G_OTH: 0.8147%

POLG2

Exomiser Score: 0.126

Phenotype Score: 0.864

Variant Score: 0.258

Phenotype matches:

Phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.522 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:610131 Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 - autosomal dominant; OMIM:618528 Mitochondrial DNA depletion syndrome 16 (hepatic type) - autosomal recessive; ORPHA:254892 Autosomal dominant progressive external ophthalmoplegia

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.126

Phenotype Score: 0.864

Variant Score: 0.258

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.64495177C>CA [1/1] rs782184151 (variation viewer)

Variant score: 0.258 CONTRIBUTING VARIANT

Transcripts:: POLG2:ENST00000539111.7:c.562+1229_562+1230insT:p.(=)

Pathogenicity Data:: Best Score: 0.2578358; CADD: 0.258 (1.295)

Frequency Data:: No frequency data

Other passed variants:

ARHGAP35

Exomiser Score: 0.126

Phenotype Score: 0.507

Variant Score: 0.662

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.126

Phenotype Score: 0.507

Variant Score: 0.662

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr19:g.46857107A>ATT [0/1] rs35730347 (variation viewer)

Variant score: 0.662 CONTRIBUTING VARIANT

Transcripts:: ARHGAP35:ENST00000672722.1::; ARHGAP35:ENST00000263270.10::

Pathogenicity Data:: Best Score: 0.6616236; CADD: 0.662 (4.706)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.038

Phenotype Score: 0.507

Variant Score: 0.521

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr19:g.46857107A>ATT [0/1] rs35730347 (variation viewer)

Variant score: 0.662 CONTRIBUTING VARIANT

Transcripts:: ARHGAP35:ENST00000672722.1::; ARHGAP35:ENST00000263270.10::

Pathogenicity Data:: Best Score: 0.6616236; CADD: 0.662 (4.706)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.46879587A>AAAATAAATAAATAAAT [0/1] rs376342193 (variation viewer)

Variant score: 0.381 CONTRIBUTING VARIANT

Transcripts:: ARHGAP35:ENST00000672722.1:c.-189+18378_-189+18379insAAATAAATAAATAAAT:p.(=)

Pathogenicity Data:: Best Score: 0.3805589; CADD: 0.381 (2.080)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.46888261AATAT>A [-/1] rs1175667788 (variation viewer)

Variant score: 0.238

Transcripts:: ARHGAP35:ENST00000672722.1:c.-189+27053_-189+27056del:p.(=)

Pathogenicity Data:: Best Score: 0.23756993; CADD: 0.238 (1.178)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr19:g.47014638C>CT [1/1] rs71179285 (variation viewer)

Variant score: 0.209

Transcripts:: ARHGAP35:ENST00000672722.1::

Pathogenicity Data:: Best Score: 0.20859283; CADD: 0.209 (1.016)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.46888261AATATATATATATATAT>A [-/1] rs1175667788 (variation viewer)

Variant score: 0.197

Transcripts:: ARHGAP35:ENST00000672722.1:c.-189+27053_-189+27068del:p.(=)

Pathogenicity Data:: Best Score: 0.19739842; CADD: 0.197 (0.955)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.46883740C>T [0/1] rs142410636 (variation viewer)

Variant score: 0.134

Transcripts:: ARHGAP35:ENST00000672722.1:c.-189+22531C>T:p.(=)

Pathogenicity Data:: Best Score: 0.15957296; CADD: 0.160 (0.755)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.2787%; gnomAD_G_AFR: 0.7795%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.46983054C>CAAA [0/1] rs71179281 (variation viewer)

Variant score: 0.132

Transcripts:: ARHGAP35:ENST00000404338.8:c.3827-4935_3827-4934insAAA:p.(=); ARHGAP35:ENST00000614079.1:c.3827-4935_3827-4934insAAA:p.(=); ARHGAP35:ENST00000672722.1:c.3827-4935_3827-4934insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.13223928; CADD: 0.132 (0.616)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.46933137C>CT [1/1] rs1174653724 (variation viewer)

Variant score: 0.108

Transcripts:: ARHGAP35:ENST00000404338.8:c.3682-4127_3682-4126insT:p.(=); ARHGAP35:ENST00000614079.1:c.3682-4127_3682-4126insT:p.(=); ARHGAP35:ENST00000672722.1:c.3682-4127_3682-4126insT:p.(=)

Pathogenicity Data:: Best Score: 0.108338535; CADD: 0.108 (0.498)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.46874501C>CT [0/1] rs758783354 (variation viewer)

Variant score: 0.061

Transcripts:: ARHGAP35:ENST00000672722.1:c.-189+13292_-189+13293insT:p.(=)

Pathogenicity Data:: Best Score: 0.060709357; CADD: 0.061 (0.272)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.46931747G>A [0/1] rs1001996257 (variation viewer)

Variant score: 0.014

Transcripts:: ARHGAP35:ENST00000404338.8:c.3682-5517G>A:p.(=); ARHGAP35:ENST00000614079.1:c.3682-5517G>A:p.(=); ARHGAP35:ENST00000672722.1:c.3682-5517G>A:p.(=)

Pathogenicity Data:: Best Score: 0.014401555; CADD: 0.014 (0.063)

Frequency Data:: TOPMed: 0.0088%; gnomAD_G_AFR: 0.0573%

THREE_PRIME_UTR_EXON_VARIANT chr19:g.47003916ACG>* [-/1]

Variant score: 0.000

Transcripts:: ARHGAP35:ENST00000404338.8:c.*3228_*3230delACGins*:p.(=); ARHGAP35:ENST00000614079.1:c.*2805_*2807delACGins*:p.(=); ARHGAP35:ENST00000672722.1:c.*3228_*3230delACGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MCM9

Exomiser Score: 0.126

Phenotype Score: 0.503

Variant Score: 0.667

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616185 Ovarian dysgenesis 4 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.251

Variant Score: 0.564

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118872642T>G [0/1] rs1349304746 (variation viewer)

Variant score: 0.564 CONTRIBUTING VARIANT

Transcripts:: MCM9:ENST00000316316.10:c.1151-16097A>C:p.(=); MCM9:ENST00000619706.4:c.1151-16097A>C:p.(=)

Pathogenicity Data:: Best Score: 0.5644881; CADD: 0.564 (3.610)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.126

Phenotype Score: 0.503

Variant Score: 0.667

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.118934212A>C [0/1] rs553446907 (variation viewer)

Variant score: 0.744 CONTRIBUTING VARIANT

Transcripts:: MCM9:ENST00000316068.7:c.-16+679T>G:p.(=); MCM9:ENST00000316316.10:c.-16+679T>G:p.(=)

Pathogenicity Data:: Best Score: 0.76660043; CADD: 0.767 (6.319)

Frequency Data:: TOPMed: 0.0526%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0688%; gnomAD_G_NFE: 0.0733%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118910276T>TTATGACTCTA [0/1] rs569424117 (variation viewer)

Variant score: 0.589 CONTRIBUTING VARIANT

Transcripts:: MCM9:ENST00000316316.10:c.1150+1373_1150+1374insTAGAGTCATA:p.(=); MCM9:ENST00000619706.4:c.1150+1373_1150+1374insTAGAGTCATA:p.(=)

Pathogenicity Data:: Best Score: 0.6061779; CADD: 0.606 (4.047)

Frequency Data:: UK10K: 0.1851%; gnomAD_G_AFR: 0.0688%; gnomAD_G_NFE: 0.0733%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118872641G>A [0/1] rs145742201 (variation viewer)

Variant score: 0.273

Transcripts:: MCM9:ENST00000316316.10:c.1151-16096C>T:p.(=); MCM9:ENST00000619706.4:c.1151-16096C>T:p.(=)

Pathogenicity Data:: Best Score: 0.40570784; CADD: 0.406 (2.260)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.4523%; gnomAD_G_AFR: 1.2302%; gnomAD_G_OTH: 0.2066%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118883460AC>A [0|1] rs1167135926 (variation viewer)

Variant score: 0.251

Transcripts:: MCM9:ENST00000316316.10:c.1151-26916del:p.(=); MCM9:ENST00000619706.4:c.1151-26916del:p.(=)

Pathogenicity Data:: Best Score: 0.2513135; CADD: 0.251 (1.257)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.118933964C>CAAAAAAAAA [0/1] rs58109173 (variation viewer)

Variant score: 0.194

Transcripts:: MCM9:ENST00000316068.7:c.-16+926_-16+927insTTTTTTTTT:p.(=); MCM9:ENST00000316316.10:c.-16+926_-16+927insTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.19406503; CADD: 0.194 (0.937)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118847422CA>C [1/1] rs368957444 (variation viewer)

Variant score: 0.122

Transcripts:: MCM9:ENST00000316316.10:c.1325+8948del:p.(=); MCM9:ENST00000619706.4:c.1325+8948del:p.(=)

Pathogenicity Data:: Best Score: 0.121584475; CADD: 0.122 (0.563)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118869014C>CA [0/1] rs560272148 (variation viewer)

Variant score: 0.117

Transcripts:: MCM9:ENST00000316316.10:c.1151-12470_1151-12469insT:p.(=); MCM9:ENST00000619706.4:c.1151-12470_1151-12469insT:p.(=)

Pathogenicity Data:: Best Score: 0.57907957; CADD: 0.579 (3.758)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 1.1320%; UK10K: 1.9307%; gnomAD_G_AFR: 0.3896%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.7446%; gnomAD_G_NFE: 1.6660%; gnomAD_G_OTH: 0.9184%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118867879C>CTTT [0|1] rs1554258631 (variation viewer)

Variant score: 0.093

Transcripts:: MCM9:ENST00000316316.10:c.1151-11335_1151-11334insAAA:p.(=); MCM9:ENST00000619706.4:c.1151-11335_1151-11334insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.093015194; CADD: 0.093 (0.424)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118840174T>A [0|1] rs554190089 (variation viewer)

Variant score: 0.075

Transcripts:: MCM9:ENST00000316316.10:c.1326-10924A>T:p.(=); MCM9:ENST00000619706.4:c.1326-10924A>T:p.(=)

Pathogenicity Data:: Best Score: 0.0820902; CADD: 0.082 (0.372)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.3217%; gnomAD_G_AFR: 0.5020%; gnomAD_G_AMR: 0.1214%; gnomAD_G_FIN: 0.0596%; gnomAD_G_NFE: 0.2284%; gnomAD_G_OTH: 0.1075%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118843644A>ATATATATATATATATATATATACACGTATATATATATATATATACGTG [0/1]

Variant score: 0.053

Transcripts:: MCM9:ENST00000316316.10:c.1325+12726_1325+12727insCACGTATATATATATATATATACGTGTATATATATATATATATATATA:p.(=); MCM9:ENST00000619706.4:c.1325+12726_1325+12727insCACGTATATATATATATATATACGTGTATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.052890897; CADD: 0.053 (0.236)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118843658G>GTATATATATATATGTGTA [0|1] rs74206505 (variation viewer)

Variant score: 0.039

Transcripts:: MCM9:ENST00000316316.10:c.1325+12712_1325+12713insTACACATATATATATATA:p.(=); MCM9:ENST00000619706.4:c.1325+12712_1325+12713insTACACATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.03905177; CADD: 0.039 (0.173)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.118843655T>TATATACACGTATATATATATATATATATATAC [0/1] rs1491542240 (variation viewer)

Variant score: 0.034

Transcripts:: MCM9:ENST00000316316.10:c.1325+12715_1325+12716insGTATATATATATATATATATATACGTGTATAT:p.(=); MCM9:ENST00000619706.4:c.1325+12715_1325+12716insGTATATATATATATATATATATACGTGTATAT:p.(=)

Pathogenicity Data:: Best Score: 0.033726633; CADD: 0.034 (0.149)

Frequency Data:: No frequency data

NSMAF

Exomiser Score: 0.124

Phenotype Score: 0.504

Variant Score: 0.663

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.124

Phenotype Score: 0.504

Variant Score: 0.663

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.58600904A>G [0/1] rs373340694 (variation viewer)

Variant score: 0.869 CONTRIBUTING VARIANT

Transcripts:: NSMAF:ENST00000038176.8:c.1280+381T>C:p.(=); NSMAF:ENST00000427130.6:c.1373+381T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9265486; CADD: 0.927 (11.340)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.1561%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.1532%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.58587751T>A [0/1] rs759349945 (variation viewer)

Variant score: 0.457 CONTRIBUTING VARIANT

Transcripts:: NSMAF:ENST00000038176.8:c.2212-50A>T:p.(=); NSMAF:ENST00000427130.6:c.2305-50A>T:p.(=)

Pathogenicity Data:: Best Score: 0.47603774; CADD: 0.476 (2.807)

Frequency Data:: TOPMed: 0.0255%; ExAC NFE: 0.0092%; ExAC OTH: 0.2558%; gnomAD_E_AMR: 0.0268%; gnomAD_E_NFE: 0.0102%; gnomAD_E_OTH: 0.0403%; gnomAD_G_NFE: 0.0200%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.58600621C>CAA [1/1] rs35209612 (variation viewer)

Variant score: 0.401

Transcripts:: NSMAF:ENST00000038176.8:c.1281-601_1281-600insTT:p.(=); NSMAF:ENST00000427130.6:c.1374-601_1374-600insTT:p.(=)

Pathogenicity Data:: Best Score: 0.40076107; CADD: 0.401 (2.224)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr8:g.59158357C>CAA [1/1] rs11317853 (variation viewer)

Variant score: 0.367

Transcripts:

Pathogenicity Data:: Best Score: 0.36671382; CADD: 0.367 (1.984)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.58595345G>A [0/1] rs368652874 (variation viewer)

Variant score: 0.352

Transcripts:: NSMAF:ENST00000038176.8:c.1892+215C>T:p.(=); NSMAF:ENST00000427130.6:c.1985+215C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3756904; CADD: 0.376 (2.046)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.1593%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0115%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1533%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.58645031G>A [0/1] rs191899187 (variation viewer)

Variant score: 0.246

Transcripts:: NSMAF:ENST00000038176.8:c.60-1958C>T:p.(=); NSMAF:ENST00000427130.6:c.153-1958C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2602244; CADD: 0.260 (1.309)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.1426%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.1471%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.58626091CT>C [1|1] rs1225264071 (variation viewer)

Variant score: 0.011

Transcripts:: NSMAF:ENST00000038176.8:c.385-2312del:p.(=); NSMAF:ENST00000427130.6:c.478-2312del:p.(=)

Pathogenicity Data:: Best Score: 0.010763824; CADD: 0.011 (0.047)

Frequency Data:: No frequency data

ATP2A3

Exomiser Score: 0.123

Phenotype Score: 0.501

Variant Score: 0.666

Phenotype matches:

Proximity score 0.501 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.123

Phenotype Score: 0.501

Variant Score: 0.666

Variants contributing to score:

MISSENSE_VARIANT chr17:g.3930371C>T [0/1] rs141235119 (variation viewer)

Variant score: 0.893 CONTRIBUTING VARIANT

Transcripts:: ATP2A3:ENST00000309890.11:c.2674G>A:p.(Glu892Lys); ATP2A3:ENST00000352011.7:c.2674G>A:p.(Glu892Lys); ATP2A3:ENST00000359983.7:c.2674G>A:p.(Glu892Lys); ATP2A3:ENST00000397035.7:c.2674G>A:p.(Glu892Lys); ATP2A3:ENST00000397041.8:c.2674G>A:p.(Glu892Lys); ATP2A3:ENST00000397043.7:c.2674G>A:p.(Glu892Lys)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.095 (B); Mutation Taster: 1.000 (P); SIFT: 0.182 (T); CADD: 0.983 (17.670)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.3098%; UK10K: 0.4099%; ESP AA: 0.0908%; ESP EA: 0.5814%; ESP All: 0.4152%; ExAC AFR: 0.1247%; ExAC AMR: 0.4757%; ExAC FIN: 0.2025%; ExAC NFE: 0.5149%; ExAC OTH: 0.2500%; ExAC SAS: 0.0476%; gnomAD_E_AFR: 0.0927%; gnomAD_E_AMR: 0.3822%; gnomAD_E_ASJ: 0.2242%; gnomAD_E_FIN: 0.1856%; gnomAD_E_NFE: 0.4978%; gnomAD_E_OTH: 0.5141%; gnomAD_E_SAS: 0.0391%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2003%; gnomAD_G_NFE: 0.4599%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.3954502T>TC [0/1] rs1199717330 (variation viewer)

Variant score: 0.439 CONTRIBUTING VARIANT

Transcripts:: ATP2A3:ENST00000309890.11:c.119-793_119-792insG:p.(=); ATP2A3:ENST00000352011.7:c.119-793_119-792insG:p.(=); ATP2A3:ENST00000359983.7:c.119-793_119-792insG:p.(=); ATP2A3:ENST00000397035.7:c.119-793_119-792insG:p.(=); ATP2A3:ENST00000397041.8:c.119-793_119-792insG:p.(=); ATP2A3:ENST00000397043.7:c.119-793_119-792insG:p.(=)

Pathogenicity Data:: Best Score: 0.4578743; CADD: 0.458 (2.659)

Frequency Data:: gnomAD_G_AFR: 0.0243%; gnomAD_G_AMR: 0.2415%; gnomAD_G_FIN: 0.2267%; gnomAD_G_NFE: 0.2665%; gnomAD_G_OTH: 0.2294%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.3939786T>TA [1/1] rs71381543 (variation viewer)

Variant score: 0.205

Transcripts:: ATP2A3:ENST00000309890.11:c.2100+1184_2100+1185insT:p.(=); ATP2A3:ENST00000352011.7:c.2100+1184_2100+1185insT:p.(=); ATP2A3:ENST00000359983.7:c.2100+1184_2100+1185insT:p.(=); ATP2A3:ENST00000397035.7:c.2100+1184_2100+1185insT:p.(=); ATP2A3:ENST00000397041.8:c.2100+1184_2100+1185insT:p.(=); ATP2A3:ENST00000397043.7:c.2100+1184_2100+1185insT:p.(=)

Pathogenicity Data:: Best Score: 0.20530587; CADD: 0.205 (0.998)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.3956850G>A [0/1] rs138089783 (variation viewer)

Variant score: 0.006

Transcripts:: ATP2A3:ENST00000309890.11:c.119-3140C>T:p.(=); ATP2A3:ENST00000352011.7:c.119-3140C>T:p.(=); ATP2A3:ENST00000359983.7:c.119-3140C>T:p.(=); ATP2A3:ENST00000397035.7:c.119-3140C>T:p.(=); ATP2A3:ENST00000397041.8:c.119-3140C>T:p.(=); ATP2A3:ENST00000397043.7:c.119-3140C>T:p.(=)

Pathogenicity Data:: Best Score: 0.006197691; CADD: 0.006 (0.027)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1577%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.2577%; gnomAD_G_NFE: 0.3003%; gnomAD_G_OTH: 0.2037%

RYR2

Exomiser Score: 0.123

Phenotype Score: 0.508

Variant Score: 0.658

Phenotype matches:

Proximity score 0.508 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:600996 Arrhythmogenic right ventricular dysplasia 2 - autosomal dominant; OMIM:604772 Ventricular tachycardia, catecholaminergic polymorphic, 1 - autosomal dominant; ORPHA:3286 Catecholaminergic polymorphic ventricular tachycardia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.123

Phenotype Score: 0.508

Variant Score: 0.658

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237295594G>T [0|1] rs184895570 (variation viewer)

Variant score: 0.658 CONTRIBUTING VARIANT

Transcripts:: RYR2:ENST00000360064.7:c.120+24978G>T:p.(=); RYR2:ENST00000366574.7:c.168+24978G>T:p.(=)

Pathogenicity Data:: Best Score: 0.6599052; CADD: 0.660 (4.684)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.021

Phenotype Score: 0.254

Variant Score: 0.739

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237812126T>C [0/1] rs147394907 (variation viewer)

Variant score: 0.817 CONTRIBUTING VARIANT

Transcripts:: RYR2:ENST00000360064.7:c.14382+3091T>C:p.(=); RYR2:ENST00000366574.7:c.14433+3091T>C:p.(=)

Pathogenicity Data:: Best Score: 0.86288023; CADD: 0.863 (8.629)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.0669%; UK10K: 0.0264%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0666%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237343772T>C [0/1] rs189181927 (variation viewer)

Variant score: 0.662 CONTRIBUTING VARIANT

Transcripts:: RYR2:ENST00000360064.7:c.226-12193T>C:p.(=); RYR2:ENST00000366574.7:c.274-12193T>C:p.(=)

Pathogenicity Data:: Best Score: 0.687536; CADD: 0.688 (5.052)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1481%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.2445%; gnomAD_G_FIN: 0.0294%; gnomAD_G_NFE: 0.1339%; gnomAD_G_OTH: 0.1029%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237606464C>T [0/1] rs185371804 (variation viewer)

Variant score: 0.573

Transcripts:: RYR2:ENST00000360064.7:c.4636-4298C>T:p.(=); RYR2:ENST00000366574.7:c.4684-4298C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7447299; CADD: 0.745 (5.930)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.4715%; gnomAD_G_AFR: 0.6412%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2577%; gnomAD_G_NFE: 0.4933%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237132240A>G [0/1] rs546416477 (variation viewer)

Variant score: 0.572

Transcripts:: RYR2:ENST00000366574.7:c.48+89671A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5835144; CADD: 0.584 (3.804)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0605%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0866%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237568043T>G [0/1] rs139672578 (variation viewer)

Variant score: 0.498

Transcripts:: RYR2:ENST00000360064.7:c.3376-1102T>G:p.(=); RYR2:ENST00000366574.7:c.3424-1102T>G:p.(=)

Pathogenicity Data:: Best Score: 0.68384504; CADD: 0.684 (5.001)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.6116%; UK10K: 0.3835%; gnomAD_G_AFR: 1.1004%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2580%; gnomAD_G_NFE: 0.4797%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237594900T>TG [0|1] rs867419978 (variation viewer)

Variant score: 0.469

Transcripts:: RYR2:ENST00000360064.7:c.4389-598_4389-597insG:p.(=); RYR2:ENST00000366574.7:c.4437-598_4437-597insG:p.(=)

Pathogenicity Data:: Best Score: 0.6001473; CADD: 0.600 (3.981)

Frequency Data:: gnomAD_G_AFR: 0.8516%; gnomAD_G_ASJ: 0.9615%; gnomAD_G_NFE: 0.3373%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237792398CGT>C [1/1] rs71162418 (variation viewer)

Variant score: 0.468

Transcripts:: RYR2:ENST00000360064.7:c.13731+76_13731+77del:p.(=); RYR2:ENST00000366574.7:c.13782+76_13782+77del:p.(=)

Pathogenicity Data:: Best Score: 0.46813673; CADD: 0.468 (2.742)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237450754T>C [0/1] rs114468854 (variation viewer)

Variant score: 0.450

Transcripts:: RYR2:ENST00000360064.7:c.1245-3637T>C:p.(=); RYR2:ENST00000366574.7:c.1293-3637T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5466851; CADD: 0.547 (3.436)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.4691%; UK10K: 0.3042%; gnomAD_G_AFR: 0.7447%; gnomAD_G_AMR: 0.8353%; gnomAD_G_FIN: 0.2862%; gnomAD_G_NFE: 0.4265%; gnomAD_G_OTH: 0.6148%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237603474T>C [0/1] rs115864302 (variation viewer)

Variant score: 0.436

Transcripts:: RYR2:ENST00000360064.7:c.4635+1363T>C:p.(=); RYR2:ENST00000366574.7:c.4683+1363T>C:p.(=)

Pathogenicity Data:: Best Score: 0.597839; CADD: 0.598 (3.956)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6291%; UK10K: 0.4099%; gnomAD_G_AFR: 1.0997%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2576%; gnomAD_G_NFE: 0.4996%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237747773A>G [0/1] rs376323613 (variation viewer)

Variant score: 0.417

Transcripts:: RYR2:ENST00000360064.7:c.11097+5424A>G:p.(=); RYR2:ENST00000366574.7:c.11145+5424A>G:p.(=)

Pathogenicity Data:: Best Score: 0.43778813; CADD: 0.438 (2.501)

Frequency Data:: TOPMed: 0.0796%; UK10K: 0.0397%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0866%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237488793T>G [0|1] rs914171532 (variation viewer)

Variant score: 0.382

Transcripts:: RYR2:ENST00000360064.7:c.1661-3013T>G:p.(=); RYR2:ENST00000366574.7:c.1709-3013T>G:p.(=)

Pathogenicity Data:: Best Score: 0.38354695; CADD: 0.384 (2.101)

Frequency Data:: TOPMed: 0.0247%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237631613ATTTTTTTTTTT>A [1/1] rs556269614 (variation viewer)

Variant score: 0.360

Transcripts:: RYR2:ENST00000360064.7:c.6507+73_6507+83del:p.(=); RYR2:ENST00000366574.7:c.6555+73_6555+83del:p.(=)

Pathogenicity Data:: Best Score: 0.35967565; CADD: 0.360 (1.936)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237620459C>A [0/1] rs187805849 (variation viewer)

Variant score: 0.351

Transcripts:: RYR2:ENST00000360064.7:c.5868+2973C>A:p.(=); RYR2:ENST00000366574.7:c.5916+2973C>A:p.(=)

Pathogenicity Data:: Best Score: 0.36846125; CADD: 0.368 (1.996)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0685%; UK10K: 0.0529%; gnomAD_G_NFE: 0.0534%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237162476A>C [0/1] rs570812718 (variation viewer)

Variant score: 0.350

Transcripts:: RYR2:ENST00000366574.7:c.49-108021A>C:p.(=)

Pathogenicity Data:: Best Score: 0.35434574; CADD: 0.354 (1.900)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0542%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0734%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237546993A>T [0/1] rs2779381 (variation viewer)

Variant score: 0.277

Transcripts:: RYR2:ENST00000360064.7:c.2859-1438A>T:p.(=); RYR2:ENST00000366574.7:c.2907-1438A>T:p.(=)

Pathogenicity Data:: Best Score: 0.27673078; CADD: 0.277 (1.407)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237664058G>A [0/1] rs545746001 (variation viewer)

Variant score: 0.275

Transcripts:: RYR2:ENST00000360064.7:c.8389-2454G>A:p.(=); RYR2:ENST00000366574.7:c.8437-2454G>A:p.(=)

Pathogenicity Data:: Best Score: 0.29058564; CADD: 0.291 (1.491)

Frequency Data:: TOPMed: 0.0319%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237607126T>G [0/1] rs141392860 (variation viewer)

Variant score: 0.266

Transcripts:: RYR2:ENST00000360064.7:c.4636-3636T>G:p.(=); RYR2:ENST00000366574.7:c.4684-3636T>G:p.(=)

Pathogenicity Data:: Best Score: 0.36481535; CADD: 0.365 (1.971)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6275%; UK10K: 0.4099%; gnomAD_G_AFR: 1.0999%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2576%; gnomAD_G_NFE: 0.4997%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237795836G>GTGTGTATATATA [-/1] rs371932356 (variation viewer)

Variant score: 0.259

Transcripts:: RYR2:ENST00000360064.7:c.13905+505_13905+506insTGTGTATATATA:p.(=); RYR2:ENST00000366574.7:c.13956+505_13956+506insTGTGTATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.25851905; CADD: 0.259 (1.299)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237318896T>G [0/1] rs150896346 (variation viewer)

Variant score: 0.257

Transcripts:: RYR2:ENST00000360064.7:c.121-11982T>G:p.(=); RYR2:ENST00000366574.7:c.169-11982T>G:p.(=)

Pathogenicity Data:: Best Score: 0.6024425; CADD: 0.602 (4.006)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.2923%; UK10K: 0.3703%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0288%; gnomAD_G_NFE: 0.2268%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237598615A>C [0/1] rs78693701 (variation viewer)

Variant score: 0.252

Transcripts:: RYR2:ENST00000360064.7:c.4548+2958A>C:p.(=); RYR2:ENST00000366574.7:c.4596+2958A>C:p.(=)

Pathogenicity Data:: Best Score: 0.3458159; CADD: 0.346 (1.843)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6299%; UK10K: 0.4099%; gnomAD_G_AFR: 1.0997%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2589%; gnomAD_G_NFE: 0.4998%; gnomAD_G_OTH: 0.7128%

INTERGENIC_VARIANT chr1:g.237035919CTCCTTCCTTCCTTCCTTCCCTCTT>C [1/1] rs1257787817 (variation viewer)

Variant score: 0.249

Transcripts:: RYR2:ENST00000366574.7::; RYR2:ENST00000464121.3::

Pathogenicity Data:: Best Score: 0.24924195; CADD: 0.249 (1.245)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237149264G>A [0/1] rs577781886 (variation viewer)

Variant score: 0.237

Transcripts:: RYR2:ENST00000366574.7:c.48+106695G>A:p.(=)

Pathogenicity Data:: Best Score: 0.25629622; CADD: 0.256 (1.286)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.1035%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1202%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237204690G>C [0|1] rs868474987 (variation viewer)

Variant score: 0.234

Transcripts:: RYR2:ENST00000366574.7:c.49-65807G>C:p.(=)

Pathogenicity Data:: Best Score: 0.23440337; CADD: 0.234 (1.160)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr1:g.237025494C>A [0/1] rs367979813 (variation viewer)

Variant score: 0.222

Transcripts:: RYR2:ENST00000366574.7::; RYR2:ENST00000464121.3::

Pathogenicity Data:: Best Score: 0.237921; CADD: 0.238 (1.180)

Frequency Data:: 1000Genomes: 0.3195%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.1431%; gnomAD_G_NFE: 0.1133%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237198652G>T [0/1] rs192573951 (variation viewer)

Variant score: 0.214

Transcripts:: RYR2:ENST00000366574.7:c.49-71845G>T:p.(=)

Pathogenicity Data:: Best Score: 0.22642934; CADD: 0.226 (1.115)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.1131%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1337%; gnomAD_G_OTH: 0.2066%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237303292C>CT [0/1] rs386370109 (variation viewer)

Variant score: 0.205

Transcripts:: RYR2:ENST00000360064.7:c.121-27586_121-27585insT:p.(=); RYR2:ENST00000366574.7:c.169-27586_169-27585insT:p.(=)

Pathogenicity Data:: Best Score: 0.20548886; CADD: 0.205 (0.999)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237594886GT>G [0|1] rs776702428 (variation viewer)

Variant score: 0.197

Transcripts:: RYR2:ENST00000360064.7:c.4389-611del:p.(=); RYR2:ENST00000366574.7:c.4437-611del:p.(=)

Pathogenicity Data:: Best Score: 0.19665885; CADD: 0.197 (0.951)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237527336A>C [0/1] rs76347764 (variation viewer)

Variant score: 0.188

Transcripts:: RYR2:ENST00000360064.7:c.2775-3091A>C:p.(=); RYR2:ENST00000366574.7:c.2823-3091A>C:p.(=)

Pathogenicity Data:: Best Score: 0.2996744; CADD: 0.300 (1.547)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.4985%; UK10K: 0.3703%; gnomAD_G_AFR: 0.7906%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 0.5662%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237380359AATATATATATATATATATAT>A [-/1] rs57204036 (variation viewer)

Variant score: 0.183

Transcripts:: RYR2:ENST00000360064.7:c.528+2925_528+2944del:p.(=); RYR2:ENST00000366574.7:c.576+2925_576+2944del:p.(=)

Pathogenicity Data:: Best Score: 0.18322957; CADD: 0.183 (0.879)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237380359AATATATATATATATATATATAT>A [-/1] rs57204036 (variation viewer)

Variant score: 0.177

Transcripts:: RYR2:ENST00000360064.7:c.528+2925_528+2946del:p.(=); RYR2:ENST00000366574.7:c.576+2925_576+2946del:p.(=)

Pathogenicity Data:: Best Score: 0.1773786; CADD: 0.177 (0.848)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237579248CTT>C [0/1] rs546960253 (variation viewer)

Variant score: 0.168

Transcripts:: RYR2:ENST00000360064.7:c.3550+9930_3550+9931del:p.(=); RYR2:ENST00000366574.7:c.3598+9930_3598+9931del:p.(=)

Pathogenicity Data:: Best Score: 0.16766149; CADD: 0.168 (0.797)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237524230G>C [0/1] rs184410053 (variation viewer)

Variant score: 0.149

Transcripts:: RYR2:ENST00000360064.7:c.2775-6197G>C:p.(=); RYR2:ENST00000366574.7:c.2823-6197G>C:p.(=)

Pathogenicity Data:: Best Score: 0.2398488; CADD: 0.240 (1.191)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.4914%; UK10K: 0.3570%; gnomAD_G_AFR: 0.7909%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 0.5464%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237246843G>A [0/1] rs184016432 (variation viewer)

Variant score: 0.140

Transcripts:: RYR2:ENST00000366574.7:c.49-23654G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15023273; CADD: 0.150 (0.707)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2771%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.4070%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237594903T>TG [0|1] rs796797370 (variation viewer)

Variant score: 0.133

Transcripts:: RYR2:ENST00000360064.7:c.4389-595_4389-594insG:p.(=); RYR2:ENST00000366574.7:c.4437-595_4437-594insG:p.(=)

Pathogenicity Data:: Best Score: 0.24368972; CADD: 0.244 (1.213)

Frequency Data:: gnomAD_G_AFR: 0.7551%; gnomAD_G_ASJ: 1.4706%; gnomAD_G_NFE: 0.3761%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237674634T>C [0/1] rs561170005 (variation viewer)

Variant score: 0.131

Transcripts:: RYR2:ENST00000360064.7:c.8667-97T>C:p.(=); RYR2:ENST00000366574.7:c.8715-97T>C:p.(=)

Pathogenicity Data:: Best Score: 0.30753154; CADD: 0.308 (1.596)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0613%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0576%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237213915CT>C [1/1] rs71180008 (variation viewer)

Variant score: 0.129

Transcripts:: RYR2:ENST00000366574.7:c.49-56581del:p.(=)

Pathogenicity Data:: Best Score: 0.12923694; CADD: 0.129 (0.601)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237567977G>A [0/1] rs115967772 (variation viewer)

Variant score: 0.122

Transcripts:: RYR2:ENST00000360064.7:c.3376-1168G>A:p.(=); RYR2:ENST00000366574.7:c.3424-1168G>A:p.(=)

Pathogenicity Data:: Best Score: 0.19628882; CADD: 0.196 (0.949)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.6666%; UK10K: 0.3835%; gnomAD_G_AFR: 1.3367%; gnomAD_G_AMR: 0.7212%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2661%; gnomAD_G_NFE: 0.4927%; gnomAD_G_OTH: 0.6303%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237193167C>CAAAAAAAAAAAAAA [1/1] rs58552588 (variation viewer)

Variant score: 0.118

Transcripts:: RYR2:ENST00000366574.7:c.49-77330_49-77329insAAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.11813927; CADD: 0.118 (0.546)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237594896T>G [0|1] rs79216423 (variation viewer)

Variant score: 0.110

Transcripts:: RYR2:ENST00000360064.7:c.4389-602T>G:p.(=); RYR2:ENST00000366574.7:c.4437-602T>G:p.(=)

Pathogenicity Data:: Best Score: 0.120775044; CADD: 0.121 (0.559)

Frequency Data:: gnomAD_G_AFR: 0.1250%; gnomAD_G_EAS: 0.1567%; gnomAD_G_NFE: 0.0438%; gnomAD_G_OTH: 0.5000%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237594911T>TG [0|1] rs796848858 (variation viewer)

Variant score: 0.109

Transcripts:: RYR2:ENST00000360064.7:c.4389-587_4389-586insG:p.(=); RYR2:ENST00000366574.7:c.4437-587_4437-586insG:p.(=)

Pathogenicity Data:: Best Score: 0.12923694; CADD: 0.129 (0.601)

Frequency Data:: gnomAD_G_AFR: 0.5115%; gnomAD_G_ASJ: 0.7576%; gnomAD_G_NFE: 0.2275%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237107519C>CAAAAAAAAAAAAAA [1/1] rs71561857 (variation viewer)

Variant score: 0.108

Transcripts:: RYR2:ENST00000366574.7:c.48+64950_48+64951insAAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.107516885; CADD: 0.108 (0.494)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237604499G>A [0/1] rs143389392 (variation viewer)

Variant score: 0.097

Transcripts:: RYR2:ENST00000360064.7:c.4635+2388G>A:p.(=); RYR2:ENST00000366574.7:c.4683+2388G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13223928; CADD: 0.132 (0.616)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6212%; UK10K: 0.4099%; gnomAD_G_AFR: 1.0790%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2864%; gnomAD_G_NFE: 0.5067%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237436454CTTTT>C [0/1] rs551140501 (variation viewer)

Variant score: 0.092

Transcripts:: RYR2:ENST00000360064.7:c.958-4864_958-4861del:p.(=); RYR2:ENST00000366574.7:c.1006-4864_1006-4861del:p.(=)

Pathogenicity Data:: Best Score: 0.09217948; CADD: 0.092 (0.420)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237775075CAAAAAAA>C [0/1] rs5781992 (variation viewer)

Variant score: 0.089

Transcripts:: RYR2:ENST00000360064.7:c.11727+1428_11727+1434del:p.(=); RYR2:ENST00000366574.7:c.11775+1428_11775+1434del:p.(=)

Pathogenicity Data:: Best Score: 0.09029621; CADD: 0.090 (0.411)

Frequency Data:: TOPMed: 0.0661%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237608796GT>G [1/1] rs33945891 (variation viewer)

Variant score: 0.089

Transcripts:: RYR2:ENST00000360064.7:c.4636-1965del:p.(=); RYR2:ENST00000366574.7:c.4684-1965del:p.(=)

Pathogenicity Data:: Best Score: 0.08903855; CADD: 0.089 (0.405)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237148553T>TATATATATATAC [0/1] rs71178397 (variation viewer)

Variant score: 0.084

Transcripts:: RYR2:ENST00000366574.7:c.48+105984_48+105985insATATATATATAC:p.(=)

Pathogenicity Data:: Best Score: 0.084201336; CADD: 0.084 (0.382)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237529760TACAC>T [-/1] rs71561882 (variation viewer)

Variant score: 0.082

Transcripts:: RYR2:ENST00000360064.7:c.2775-666_2775-663del:p.(=); RYR2:ENST00000366574.7:c.2823-666_2823-663del:p.(=)

Pathogenicity Data:: Best Score: 0.08166742; CADD: 0.082 (0.370)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237477366G>A [0/1] rs150758308 (variation viewer)

Variant score: 0.079

Transcripts:: RYR2:ENST00000360064.7:c.1660+8179G>A:p.(=); RYR2:ENST00000366574.7:c.1708+8179G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09176129; CADD: 0.092 (0.418)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.4444%; UK10K: 0.3042%; gnomAD_G_AFR: 0.6190%; gnomAD_G_AMR: 0.7160%; gnomAD_G_FIN: 0.2865%; gnomAD_G_NFE: 0.4267%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237061276C>CATCTATCATCTATCT [-/1] rs1553275502 (variation viewer)

Variant score: 0.069

Transcripts:: RYR2:ENST00000366574.7:c.48+18707_48+18708insATCTATCATCTATCT:p.(=)

Pathogenicity Data:: Best Score: 0.06910652; CADD: 0.069 (0.311)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237405908T>TTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC [1/1]

Variant score: 0.060

Transcripts:: RYR2:ENST00000360064.7:c.726-11141_726-11140insTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC:p.(=); RYR2:ENST00000366574.7:c.774-11141_774-11140insTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC:p.(=)

Pathogenicity Data:: Best Score: 0.060060263; CADD: 0.060 (0.269)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237148527A>T [0/1] rs112592121 (variation viewer)

Variant score: 0.055

Transcripts:: RYR2:ENST00000366574.7:c.48+105958A>T:p.(=)

Pathogenicity Data:: Best Score: 0.05506921; CADD: 0.055 (0.246)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237082556TAA>T [0/1] rs71178387 (variation viewer)

Variant score: 0.036

Transcripts:: RYR2:ENST00000366574.7:c.48+39988_48+39989del:p.(=)

Pathogenicity Data:: Best Score: 0.12622422; CADD: 0.126 (0.586)

Frequency Data:: gnomAD_G_AFR: 0.8847%; gnomAD_G_AMR: 0.3049%; gnomAD_G_ASJ: 0.4167%; gnomAD_G_EAS: 0.9246%; gnomAD_G_FIN: 1.0938%; gnomAD_G_NFE: 1.8169%; gnomAD_G_OTH: 1.8405%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237383276C>T [0/1] rs544122043 (variation viewer)

Variant score: 0.035

Transcripts:: RYR2:ENST00000360064.7:c.529-4005C>T:p.(=); RYR2:ENST00000366574.7:c.577-4005C>T:p.(=)

Pathogenicity Data:: Best Score: 0.036836565; CADD: 0.037 (0.163)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1521%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0460%; gnomAD_G_NFE: 0.1337%; gnomAD_G_OTH: 0.2049%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237157018G>A [0/1] rs1303073237 (variation viewer)

Variant score: 0.031

Transcripts:: RYR2:ENST00000366574.7:c.49-113479G>A:p.(=)

Pathogenicity Data:: Best Score: 0.031276107; CADD: 0.031 (0.138)

Frequency Data:: TOPMed: 0.0032%; gnomAD_G_EAS: 0.0618%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237422138C>T [0/1] rs143837721 (variation viewer)

Variant score: 0.026

Transcripts:: RYR2:ENST00000360064.7:c.801-954C>T:p.(=); RYR2:ENST00000366574.7:c.849-954C>T:p.(=)

Pathogenicity Data:: Best Score: 0.032613575; CADD: 0.033 (0.144)

Frequency Data:: 1000Genomes: 0.4393%; UK10K: 0.2909%; gnomAD_G_AFR: 0.8820%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.3265%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237055725G>T [0/1] rs183260257 (variation viewer)

Variant score: 0.020

Transcripts:: RYR2:ENST00000366574.7:c.48+13156G>T:p.(=)

Pathogenicity Data:: Best Score: 0.025683641; CADD: 0.026 (0.113)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.2955%; UK10K: 0.2380%; gnomAD_G_AFR: 0.2410%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 0.2335%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237257349G>A [0/1] rs72764090 (variation viewer)

Variant score: 0.020

Transcripts:: RYR2:ENST00000366574.7:c.49-13148G>A:p.(=)

Pathogenicity Data:: Best Score: 0.02837205; CADD: 0.028 (0.125)

Frequency Data:: 1000Genomes: 1.0580%; TOPMed: 0.5304%; UK10K: 0.9521%; gnomAD_G_AFR: 0.1488%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 0.3708%; gnomAD_G_FIN: 0.3148%; gnomAD_G_NFE: 0.7934%; gnomAD_G_OTH: 1.0204%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237098387A>* [-/1]

Variant score: 0.000

Transcripts:: RYR2:ENST00000366574.7:c.48+55818A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237208938A>* [-/1]

Variant score: 0.000

Transcripts:: RYR2:ENST00000366574.7:c.49-61559A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237322956AT>A [0/1]

Variant score: 0.000

Transcripts:: RYR2:ENST00000360064.7:c.121-7921del:p.(=); RYR2:ENST00000366574.7:c.169-7921del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237542062ATTTATTTATT>* [-/1]

Variant score: 0.000

Transcripts:: RYR2:ENST00000360064.7:c.2859-6369_2859-6359delATTTATTTATTins*:p.(=); RYR2:ENST00000366574.7:c.2907-6369_2907-6359delATTTATTTATTins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.237582420A>* [-/1]

Variant score: 0.000

Transcripts:: RYR2:ENST00000360064.7:c.3551-7373A>*:p.(=); RYR2:ENST00000366574.7:c.3599-7373A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SEC23A

Exomiser Score: 0.121

Phenotype Score: 0.253

Variant Score: 0.945

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:607812 Craniolenticulosutural dysplasia - autosomal recessive; ORPHA:50814 Craniolenticulosutural dysplasia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.121

Phenotype Score: 0.253

Variant Score: 0.945

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39077837G>A [0/1]

Variant score: 0.945 CONTRIBUTING VARIANT

Transcripts:: SEC23A:ENST00000307712.11:c.829-1744C>T:p.(=); SEC23A:ENST00000537403.5:c.223-1744C>T:p.(=); SEC23A:ENST00000545328.6:c.742-1744C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9447923; CADD: 0.945 (12.580)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.049

Phenotype Score: 0.505

Variant Score: 0.553

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39077837G>A [0/1]

Variant score: 0.945 CONTRIBUTING VARIANT

Transcripts:: SEC23A:ENST00000307712.11:c.829-1744C>T:p.(=); SEC23A:ENST00000537403.5:c.223-1744C>T:p.(=); SEC23A:ENST00000545328.6:c.742-1744C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9447923; CADD: 0.945 (12.580)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39083563C>CTTTTTTTTT [-/1] rs71130810 (variation viewer)

Variant score: 0.161 CONTRIBUTING VARIANT

Transcripts:: SEC23A:ENST00000307712.11:c.828+2198_828+2199insAAAAAAAAA:p.(=); SEC23A:ENST00000537403.5:c.222+2198_222+2199insAAAAAAAAA:p.(=); SEC23A:ENST00000545328.6:c.741+2198_741+2199insAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.16053998; CADD: 0.161 (0.760)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39083563C>CTTTTTTTTTT [-/1] rs71130810 (variation viewer)

Variant score: 0.158

Transcripts:: SEC23A:ENST00000307712.11:c.828+2198_828+2199insAAAAAAAAAA:p.(=); SEC23A:ENST00000537403.5:c.222+2198_222+2199insAAAAAAAAAA:p.(=); SEC23A:ENST00000545328.6:c.741+2198_741+2199insAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.15763563; CADD: 0.158 (0.745)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39059300A>AAAAAAAAC [1|1] rs750336207 (variation viewer)

Variant score: 0.143

Transcripts:: SEC23A:ENST00000307712.11:c.1505+2464_1505+2465insGTTTTTTT:p.(=); SEC23A:ENST00000537403.5:c.899+2464_899+2465insGTTTTTTT:p.(=); SEC23A:ENST00000545328.6:c.1418+2464_1418+2465insGTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14296216; CADD: 0.143 (0.670)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39041409CA>C [0/1] rs56911438 (variation viewer)

Variant score: 0.134

Transcripts:: SEC23A:ENST00000307712.11:c.1987-523del:p.(=); SEC23A:ENST00000537403.5:c.1381-523del:p.(=); SEC23A:ENST00000545328.6:c.1900-523del:p.(=)

Pathogenicity Data:: Best Score: 0.13383627; CADD: 0.134 (0.624)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39036320C>CA [1/1] rs59018206 (variation viewer)

Variant score: 0.113

Transcripts:: SEC23A:ENST00000307712.11:c.2208+2710_2208+2711insT:p.(=); SEC23A:ENST00000537403.5:c.1602+2710_1602+2711insT:p.(=); SEC23A:ENST00000545328.6:c.2121+2710_2121+2711insT:p.(=)

Pathogenicity Data:: Best Score: 0.113048255; CADD: 0.113 (0.521)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.39065997CAAAAAAAAAAAAAAAAA>C [0/1] rs59260008 (variation viewer)

Variant score: 0.112

Transcripts:: SEC23A:ENST00000307712.11:c.1228-1021_1228-1005del:p.(=); SEC23A:ENST00000537403.5:c.622-1021_622-1005del:p.(=); SEC23A:ENST00000545328.6:c.1141-1021_1141-1005del:p.(=)

Pathogenicity Data:: Best Score: 0.11202651; CADD: 0.112 (0.516)

Frequency Data:: No frequency data

CERS6

Exomiser Score: 0.117

Phenotype Score: 0.505

Variant Score: 0.655

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.289

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168761032T>C [0/1] rs929152905 (variation viewer)

Variant score: 0.289 CONTRIBUTING VARIANT

Transcripts:: CERS6:ENST00000305747.10:c.846-4560T>C:p.(=); CERS6:ENST00000392687.4:c.846-4560T>C:p.(=)

Pathogenicity Data:: Best Score: 0.2897684; CADD: 0.290 (1.486)

Frequency Data:: TOPMed: 0.0303%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.117

Phenotype Score: 0.505

Variant Score: 0.655

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.168445651G>GTT [1/1] rs869186562 (variation viewer)

Variant score: 0.655 CONTRIBUTING VARIANT

Transcripts:: CERS6:ENST00000305747.10::; CERS6:ENST00000355999.5::

Pathogenicity Data:: Best Score: 0.6553328; CADD: 0.655 (4.626)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168458321A>G [0/1] rs557336147 (variation viewer)

Variant score: 0.727

Transcripts:: CERS6:ENST00000305747.10:c.170+1703A>G:p.(=); CERS6:ENST00000392687.4:c.170+1703A>G:p.(=)

Pathogenicity Data:: Best Score: 0.79212606; CADD: 0.792 (6.822)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1824%; UK10K: 0.3174%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.2531%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168559734C>T [1/1] rs56055132 (variation viewer)

Variant score: 0.303

Transcripts:: CERS6:ENST00000305747.10:c.277-1458C>T:p.(=); CERS6:ENST00000392687.4:c.277-1458C>T:p.(=)

Pathogenicity Data:: Best Score: 0.30321306; CADD: 0.303 (1.569)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168569790C>T [0/1] rs1030709462 (variation viewer)

Variant score: 0.242

Transcripts:: CERS6:ENST00000305747.10:c.407+8468C>T:p.(=); CERS6:ENST00000392687.4:c.407+8468C>T:p.(=)

Pathogenicity Data:: Best Score: 0.24924195; CADD: 0.249 (1.245)

Frequency Data:: TOPMed: 0.0143%; gnomAD_G_AFR: 0.0115%; gnomAD_G_FIN: 0.1717%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168531856C>T [0/1] rs192907270 (variation viewer)

Variant score: 0.229

Transcripts:: CERS6:ENST00000305747.10:c.171-15740C>T:p.(=); CERS6:ENST00000392687.4:c.171-15740C>T:p.(=)

Pathogenicity Data:: Best Score: 0.24993312; CADD: 0.250 (1.249)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1887%; gnomAD_G_AFR: 0.1156%; gnomAD_G_AMR: 0.4902%; gnomAD_G_NFE: 0.2293%; gnomAD_G_OTH: 0.1059%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168534365G>T [0/1] rs546130004 (variation viewer)

Variant score: 0.184

Transcripts:: CERS6:ENST00000305747.10:c.171-13231G>T:p.(=); CERS6:ENST00000392687.4:c.171-13231G>T:p.(=)

Pathogenicity Data:: Best Score: 0.1852957; CADD: 0.185 (0.890)

Frequency Data:: 1000Genomes: 0.0399%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168499945C>T [0/1]

Variant score: 0.139

Transcripts:: CERS6:ENST00000305747.10:c.170+43327C>T:p.(=); CERS6:ENST00000392687.4:c.170+43327C>T:p.(=)

Pathogenicity Data:: Best Score: 0.13880795; CADD: 0.139 (0.649)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168559733T>TTATATATATATATATATATATATATATATA [-/1] rs61031993 (variation viewer)

Variant score: 0.122

Transcripts:: CERS6:ENST00000305747.10:c.277-1459_277-1458insTATATATATATATATATATATATATATATA:p.(=); CERS6:ENST00000392687.4:c.277-1459_277-1458insTATATATATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.121584475; CADD: 0.122 (0.563)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168588162C>T [1/1] rs75234788 (variation viewer)

Variant score: 0.113

Transcripts:: CERS6:ENST00000305747.10:c.407+26840C>T:p.(=); CERS6:ENST00000392687.4:c.407+26840C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4341517; CADD: 0.434 (2.473)

Frequency Data:: 1000Genomes: 0.9185%; TOPMed: 1.0810%; UK10K: 1.1769%; gnomAD_G_AFR: 1.8677%; gnomAD_G_AMR: 0.8373%; gnomAD_G_FIN: 0.1445%; gnomAD_G_NFE: 1.0102%; gnomAD_G_OTH: 0.5112%

INTERGENIC_VARIANT chr2:g.168436520C>CAAAAAAAAA [1/1] rs572608527 (variation viewer)

Variant score: 0.108

Transcripts:: CERS6:ENST00000305747.10::; CERS6:ENST00000355999.5::

Pathogenicity Data:: Best Score: 0.1079278; CADD: 0.108 (0.496)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168559733T>TTATATATATATATATATATATATATATATATATATATATATATA [-/1]

Variant score: 0.092

Transcripts:: CERS6:ENST00000305747.10:c.277-1459_277-1458insTATATATATATATATATATATATATATATATATATATATATATA:p.(=); CERS6:ENST00000392687.4:c.277-1459_277-1458insTATATATATATATATATATATATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.09176129; CADD: 0.092 (0.418)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168739052ATTT>A [1/1] rs59967315 (variation viewer)

Variant score: 0.091

Transcripts:: CERS6:ENST00000305747.10:c.845+21075_845+21077del:p.(=); CERS6:ENST00000392687.4:c.845+21075_845+21077del:p.(=)

Pathogenicity Data:: Best Score: 0.09092438; CADD: 0.091 (0.414)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168631550T>TTTTAATATTTATATATTAAATATAATATATA [1/1]

Variant score: 0.067

Transcripts:: CERS6:ENST00000305747.10:c.465+508_465+509insTTTAATATTTATATATTAAATATAATATATA:p.(=); CERS6:ENST00000392687.4:c.465+508_465+509insTTTAATATTTATATATTAAATATAATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.06717539; CADD: 0.067 (0.302)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168555245C>T [0/1] rs529741286 (variation viewer)

Variant score: 0.008

Transcripts:: CERS6:ENST00000305747.10:c.277-5947C>T:p.(=); CERS6:ENST00000392687.4:c.277-5947C>T:p.(=)

Pathogenicity Data:: Best Score: 0.00848335; CADD: 0.008 (0.037)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1848%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.3597%; gnomAD_G_NFE: 0.2270%; gnomAD_G_OTH: 0.1029%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.168620062CAT>* [-/1]

Variant score: 0.000

Transcripts:: CERS6:ENST00000305747.10:c.408-10923_408-10921delCATins*:p.(=); CERS6:ENST00000392687.4:c.408-10923_408-10921delCATins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ALDH1A2

Exomiser Score: 0.116

Phenotype Score: 0.516

Variant Score: 0.641

Phenotype matches:

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.116

Phenotype Score: 0.516

Variant Score: 0.641

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58227865G>A [0/1] rs190259381 (variation viewer)

Variant score: 0.641 CONTRIBUTING VARIANT

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+51309C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6487632; CADD: 0.649 (4.544)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0446%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.112

Phenotype Score: 0.516

Variant Score: 0.637

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58227865G>A [0/1] rs190259381 (variation viewer)

Variant score: 0.641 CONTRIBUTING VARIANT

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+51309C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6487632; CADD: 0.649 (4.544)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0446%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58032677T>C [0/1] rs557370811 (variation viewer)

Variant score: 0.632 CONTRIBUTING VARIANT

Transcripts:: ALDH1A2:ENST00000249750.9:c.118-18396A>G:p.(=); ALDH1A2:ENST00000347587.7:c.118-18396A>G:p.(=); ALDH1A2:ENST00000537372.5:c.55-18396A>G:p.(=); ALDH1A2:ENST00000558231.5:c.31-18396A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6864549; CADD: 0.686 (5.037)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1489%; gnomAD_G_AFR: 0.4595%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58058083T>A [0/1] rs114997951 (variation viewer)

Variant score: 0.629

Transcripts:: ALDH1A2:ENST00000249750.9:c.117+7451A>T:p.(=); ALDH1A2:ENST00000347587.7:c.117+7451A>T:p.(=); ALDH1A2:ENST00000558231.5:c.31-43802A>T:p.(=); ALDH1A2:ENST00000537372.5:c.-18A>T:p.(=)

Pathogenicity Data:: Best Score: 0.85701185; CADD: 0.857 (8.447)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1426%; ExAC AFR: 0.5319%; ExAC AMR: 1.0870%; ExAC NFE: 0.0367%; ExAC OTH: 0.8475%; ExAC SAS: 0.0133%; gnomAD_E_AFR: 0.4647%; gnomAD_E_AMR: 0.0509%; gnomAD_E_ASJ: 0.0255%; gnomAD_E_NFE: 0.0178%; gnomAD_E_OTH: 0.0574%; gnomAD_E_SAS: 0.0223%; gnomAD_G_AFR: 0.4241%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.57958600G>A [0/1] rs912439685 (variation viewer)

Variant score: 0.491

Transcripts:: ALDH1A2:ENST00000249750.9:c.1484+2170C>T:p.(=); ALDH1A2:ENST00000347587.7:c.1370+2170C>T:p.(=); ALDH1A2:ENST00000537372.5:c.1421+2170C>T:p.(=); ALDH1A2:ENST00000558231.5:c.1397+2170C>T:p.(=); ALDH1A2:ENST00000559517.5:c.1196+2170C>T:p.(=)

Pathogenicity Data:: Best Score: 0.49137235; CADD: 0.491 (2.936)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58190076G>T [0/1] rs578155764 (variation viewer)

Variant score: 0.488

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+89098C>A:p.(=)

Pathogenicity Data:: Best Score: 0.48949498; CADD: 0.489 (2.920)

Frequency Data:: TOPMed: 0.0255%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58000783G>A [0/1] rs944735237 (variation viewer)

Variant score: 0.457

Transcripts:: ALDH1A2:ENST00000249750.9:c.494-5644C>T:p.(=); ALDH1A2:ENST00000347587.7:c.494-5644C>T:p.(=); ALDH1A2:ENST00000537372.5:c.431-5644C>T:p.(=); ALDH1A2:ENST00000558231.5:c.407-5644C>T:p.(=); ALDH1A2:ENST00000559517.5:c.206-5644C>T:p.(=)

Pathogenicity Data:: Best Score: 0.45924568; CADD: 0.459 (2.670)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_NFE: 0.0335%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58200789T>A [0/1] rs186495199 (variation viewer)

Variant score: 0.436

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+78385A>T:p.(=); ALDH1A2:ENST00000486795.2:n.184T>A:

Pathogenicity Data:: Best Score: 0.4789253; CADD: 0.479 (2.831)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.3178%; UK10K: 0.1058%; gnomAD_G_AFR: 0.5064%; gnomAD_G_AMR: 0.4796%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1075%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58088961A>G [0/1] rs1166079735 (variation viewer)

Variant score: 0.383

Transcripts:: ALDH1A2:ENST00000558231.5:c.31-74680T>C:p.(=)

Pathogenicity Data:: Best Score: 0.383263; CADD: 0.383 (2.099)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58187045T>C [0/1] rs150278175 (variation viewer)

Variant score: 0.370

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+92129A>G:p.(=)

Pathogenicity Data:: Best Score: 0.40062308; CADD: 0.401 (2.223)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.3114%; UK10K: 0.1190%; gnomAD_G_AFR: 0.4469%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.1133%

REGULATORY_REGION_VARIANT chr15:g.57890851CAAAAAAA>C [0/1] rs763553696 (variation viewer)

Variant score: 0.370

Transcripts:: ALDH1A2:ENST00000537372.5::; ALDH1A2:ENST00000299638.8::

Pathogenicity Data:: Best Score: 0.36962354; CADD: 0.370 (2.004)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58080274G>A [0/1] rs539488449 (variation viewer)

Variant score: 0.230

Transcripts:: ALDH1A2:ENST00000558231.5:c.31-65993C>T:p.(=)

Pathogenicity Data:: Best Score: 0.23122364; CADD: 0.231 (1.142)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0159%; gnomAD_G_AFR: 0.0229%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58028172T>G [0/1] rs573436398 (variation viewer)

Variant score: 0.212

Transcripts:: ALDH1A2:ENST00000249750.9:c.118-13891A>C:p.(=); ALDH1A2:ENST00000347587.7:c.118-13891A>C:p.(=); ALDH1A2:ENST00000537372.5:c.55-13891A>C:p.(=); ALDH1A2:ENST00000558231.5:c.31-13891A>C:p.(=)

Pathogenicity Data:: Best Score: 0.22909653; CADD: 0.229 (1.130)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1386%; gnomAD_G_AFR: 0.4356%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58060463C>CT [1/1] rs35187901 (variation viewer)

Variant score: 0.200

Transcripts:: ALDH1A2:ENST00000249750.9:c.117+5070_117+5071insA:p.(=); ALDH1A2:ENST00000347587.7:c.117+5070_117+5071insA:p.(=); ALDH1A2:ENST00000558231.5:c.31-46183_31-46182insA:p.(=); ALDH1A2:ENST00000537372.5:c.-43-2356_-43-2355insA:p.(=)

Pathogenicity Data:: Best Score: 0.20016575; CADD: 0.200 (0.970)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.57977339T>C [0/1] rs764150027 (variation viewer)

Variant score: 0.192

Transcripts:: ALDH1A2:ENST00000249750.9:c.799-11512A>G:p.(=); ALDH1A2:ENST00000347587.7:c.685-11512A>G:p.(=); ALDH1A2:ENST00000537372.5:c.736-11512A>G:p.(=); ALDH1A2:ENST00000558231.5:c.712-11512A>G:p.(=); ALDH1A2:ENST00000559517.5:c.511-11512A>G:p.(=)

Pathogenicity Data:: Best Score: 0.19350815; CADD: 0.194 (0.934)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0459%; gnomAD_G_EAS: 0.0617%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58217053C>CAAAAAAA [-/1] rs749683493 (variation viewer)

Variant score: 0.162

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+62120_30+62121insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.1624707; CADD: 0.162 (0.770)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58106435G>T [0/1]

Variant score: 0.159

Transcripts:: ALDH1A2:ENST00000558231.5:c.31-92154C>A:p.(=)

Pathogenicity Data:: Best Score: 0.15899223; CADD: 0.159 (0.752)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58195199C>T [0/1] rs184067444 (variation viewer)

Variant score: 0.150

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+83975G>A:p.(=)

Pathogenicity Data:: Best Score: 0.20768112; CADD: 0.208 (1.011)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.5256%; gnomAD_G_AFR: 1.1116%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1066%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58217053CAAAAAA>C [-/1] rs749683493 (variation viewer)

Variant score: 0.146

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+62115_30+62120del:p.(=)

Pathogenicity Data:: Best Score: 0.14552373; CADD: 0.146 (0.683)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58209934G>C [0/1] rs148032389 (variation viewer)

Variant score: 0.141

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+69240C>G:p.(=)

Pathogenicity Data:: Best Score: 0.15821731; CADD: 0.158 (0.748)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.3018%; UK10K: 0.0661%; gnomAD_G_AFR: 0.5841%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0733%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58179509A>ATGTGTGTGTGTGTG [-/1] rs3052103 (variation viewer)

Variant score: 0.107

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+99664_30+99665insCACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.106900156; CADD: 0.107 (0.491)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58109504G>A [0/1] rs117055157 (variation viewer)

Variant score: 0.082

Transcripts:: ALDH1A2:ENST00000558231.5:c.31-95223C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14532697; CADD: 0.145 (0.682)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.9103%; UK10K: 1.4414%; gnomAD_G_AFR: 0.2407%; gnomAD_G_AMR: 0.5967%; gnomAD_G_EAS: 0.6180%; gnomAD_G_FIN: 0.5441%; gnomAD_G_NFE: 1.3063%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58211081CTATATATA>C [0|1] rs59234349 (variation viewer)

Variant score: 0.075

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+68085_30+68092del:p.(=)

Pathogenicity Data:: Best Score: 0.07487589; CADD: 0.075 (0.338)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.57986711C>T [0/1] rs115288522 (variation viewer)

Variant score: 0.037

Transcripts:: ALDH1A2:ENST00000249750.9:c.798+5994G>A:p.(=); ALDH1A2:ENST00000347587.7:c.684+6234G>A:p.(=); ALDH1A2:ENST00000537372.5:c.735+5994G>A:p.(=); ALDH1A2:ENST00000558231.5:c.711+5994G>A:p.(=); ALDH1A2:ENST00000559517.5:c.510+5994G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09822124; CADD: 0.098 (0.449)

Frequency Data:: 1000Genomes: 0.7788%; TOPMed: 1.2340%; UK10K: 1.5472%; gnomAD_G_AFR: 0.7574%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.6105%; gnomAD_G_NFE: 1.7280%; gnomAD_G_OTH: 0.9259%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58212888G>A [0/1] rs115175134 (variation viewer)

Variant score: 0.003

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+66286C>T:p.(=)

Pathogenicity Data:: Best Score: 0.003906727; CADD: 0.004 (0.017)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.3018%; UK10K: 0.0926%; gnomAD_G_AFR: 0.5843%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0799%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58013175G>A [0/1] rs368931116 (variation viewer)

Variant score: 0.001

Transcripts:: ALDH1A2:ENST00000249750.9:c.363+683C>T:p.(=); ALDH1A2:ENST00000347587.7:c.363+683C>T:p.(=); ALDH1A2:ENST00000537372.5:c.300+683C>T:p.(=); ALDH1A2:ENST00000558231.5:c.276+683C>T:p.(=); ALDH1A2:ENST00000559517.5:c.75+683C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0013806224; CADD: 0.001 (0.006)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1410%; gnomAD_G_AFR: 0.4357%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.58187432G>* [-/1]

Variant score: 0.000

Transcripts:: ALDH1A2:ENST00000558231.5:c.30+91742C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TUFT1

Exomiser Score: 0.115

Phenotype Score: 0.510

Variant Score: 0.648

Phenotype matches:

Proximity score 0.510 in interactome to CLCN4 and phenotypic similarity 0.864 to Raynaud-Claes syndrome associated with CLCN4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.115

Phenotype Score: 0.510

Variant Score: 0.648

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.151599285C>T [1|1] rs201853814 (variation viewer)

Variant score: 0.648 CONTRIBUTING VARIANT

Transcripts:: TUFT1:ENST00000368849.8::; TUFT1:ENST00000642376.1::

Pathogenicity Data:: Best Score: 0.6479535; CADD: 0.648 (4.534)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.151552707C>CAA [1/1] rs869244649 (variation viewer)

Variant score: 0.244

Transcripts:: TUFT1:ENST00000353024.4:c.61-9878_61-9877insAA:p.(=); TUFT1:ENST00000368848.6:c.61-9878_61-9877insAA:p.(=); TUFT1:ENST00000368849.8:c.61-9384_61-9383insAA:p.(=); TUFT1:ENST00000392712.7:c.61-9878_61-9877insAA:p.(=)

Pathogenicity Data:: Best Score: 0.24386382; CADD: 0.244 (1.214)

Frequency Data:: No frequency data

GABPA

Exomiser Score: 0.114

Phenotype Score: 0.519

Variant Score: 0.636

Phenotype matches:

Proximity score 0.519 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.114

Phenotype Score: 0.519

Variant Score: 0.636

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.25762092G>A [0/1] rs751952276 (variation viewer)

Variant score: 0.636 CONTRIBUTING VARIANT

Transcripts:: GABPA:ENST00000354828.7:c.749-220G>A:p.(=); GABPA:ENST00000400075.3:c.749-220G>A:p.(=)

Pathogenicity Data:: Best Score: 0.641986; CADD: 0.642 (4.461)

Frequency Data:: TOPMed: 0.0454%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0334%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.026

Phenotype Score: 0.519

Variant Score: 0.466

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.25762092G>A [0/1] rs751952276 (variation viewer)

Variant score: 0.636 CONTRIBUTING VARIANT

Transcripts:: GABPA:ENST00000354828.7:c.749-220G>A:p.(=); GABPA:ENST00000400075.3:c.749-220G>A:p.(=)

Pathogenicity Data:: Best Score: 0.641986; CADD: 0.642 (4.461)

Frequency Data:: TOPMed: 0.0454%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0334%

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.25763272AT>A [0/1] rs1394518784 (variation viewer)

Variant score: 0.297 CONTRIBUTING VARIANT

Transcripts:: GABPA:ENST00000354828.7:c.802+908del:p.(=); GABPA:ENST00000400075.3:c.802+908del:p.(=); GABPA:ENST00000436405.1:n.61del:

Pathogenicity Data:: Best Score: 0.2967658; CADD: 0.297 (1.529)

Frequency Data:: TOPMed: 0.0032%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr21:g.25771835C>T [0/1] rs183804750 (variation viewer)

Variant score: 0.274

Transcripts:: GABPA:ENST00000354828.7:c.*2603C>T:p.(=); GABPA:ENST00000400075.3:c.*2603C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5489756; CADD: 0.549 (3.458)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.5360%; UK10K: 1.1637%; gnomAD_G_AFR: 0.1606%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 1.5482%; gnomAD_G_NFE: 1.1976%; gnomAD_G_OTH: 0.4090%

INTERGENIC_VARIANT chr21:g.25778019C>T [0/1] rs551944991 (variation viewer)

Variant score: 0.229

Transcripts:: GABPA:ENST00000400075.3::

Pathogenicity Data:: Best Score: 0.23193145; CADD: 0.232 (1.146)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0701%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.25766149G>A [0/1] rs940202920 (variation viewer)

Variant score: 0.151

Transcripts:: GABPA:ENST00000354828.7:c.1136+1362G>A:p.(=); GABPA:ENST00000400075.3:c.1136+1362G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15101504; CADD: 0.151 (0.711)

Frequency Data:: No frequency data

MMP20

Exomiser Score: 0.111

Phenotype Score: 0.510

Variant Score: 0.644

Phenotype matches:

Proximity score 0.510 in interactome to CLCN4 and phenotypic similarity 0.864 to Raynaud-Claes syndrome associated with CLCN4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612529 Amelogenesis imperfecta, type IIA2 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.255

Variant Score: 0.555

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.102624401CATATATATATATATATATATAT>C [-/1] rs58212685 (variation viewer)

Variant score: 0.555 CONTRIBUTING VARIANT

Transcripts:: MMP20:ENST00000260228.3:c.126+771_126+792del:p.(=)

Pathogenicity Data:: Best Score: 0.5546515; CADD: 0.555 (3.513)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.111

Phenotype Score: 0.510

Variant Score: 0.644

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.102589166T>TG [0/1] rs752482726 (variation viewer)

Variant score: 0.733 CONTRIBUTING VARIANT

Transcripts:: MMP20:ENST00000260228.3:c.1247+4272_1247+4273insC:p.(=)

Pathogenicity Data:: Best Score: 0.7456686; CADD: 0.746 (5.946)

Frequency Data:: TOPMed: 0.0581%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0115%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.0999%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.102624401CATATATATATATATATATATAT>C [-/1] rs58212685 (variation viewer)

Variant score: 0.555 CONTRIBUTING VARIANT

Transcripts:: MMP20:ENST00000260228.3:c.126+771_126+792del:p.(=)

Pathogenicity Data:: Best Score: 0.5546515; CADD: 0.555 (3.513)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.102623494G>C [0/1] rs191077604 (variation viewer)

Variant score: 0.391

Transcripts:: MMP20:ENST00000260228.3:c.126+1700C>G:p.(=)

Pathogenicity Data:: Best Score: 0.44499105; CADD: 0.445 (2.557)

Frequency Data:: 1000Genomes: 0.6390%; TOPMed: 0.1410%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_EAS: 0.0618%; gnomAD_G_NFE: 0.1666%; gnomAD_G_OTH: 0.1018%

CRADD

Exomiser Score: 0.108

Phenotype Score: 0.504

Variant Score: 0.646

Phenotype matches:

Phenotypic similarity 0.470 to Autosomal recessive non-syndromic intellectual disability associated with CRADD.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:614499 Mental retardation, autosomal recessive 34, with variant lissencephaly - autosomal recessive; ORPHA:88616 Autosomal recessive non-syndromic intellectual disability

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.323

Variants contributing to score:

INTERGENIC_VARIANT chr12:g.93658336C>CT [0/1] rs35940106 (variation viewer)

Variant score: 0.323 CONTRIBUTING VARIANT

Transcripts:: CRADD:ENST00000552983.5::; CRADD:ENST00000548270.1::

Pathogenicity Data:: Best Score: 0.32267052; CADD: 0.323 (1.692)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.108

Phenotype Score: 0.504

Variant Score: 0.646

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93872097A>G [0/1] rs186823021 (variation viewer)

Variant score: 0.895 CONTRIBUTING VARIANT

Transcripts:: CRADD:ENST00000548483.5:c.299-21953A>G:p.(=)

Pathogenicity Data:: Best Score: 0.9108749; CADD: 0.911 (10.500)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0518%; gnomAD_G_AMR: 0.1199%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0600%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93694952G>GA [0/1] rs564507333 (variation viewer)

Variant score: 0.398 CONTRIBUTING VARIANT

Transcripts:: CRADD:ENST00000332896.8:c.298+15880_298+15881insA:p.(=); CRADD:ENST00000542893.2:c.298+15880_298+15881insA:p.(=); CRADD:ENST00000548483.5:c.298+15880_298+15881insA:p.(=); CRADD:ENST00000552033.5:c.298+15880_298+15881insA:p.(=); CRADD:ENST00000552983.5:c.298+15880_298+15881insA:p.(=)

Pathogenicity Data:: Best Score: 0.78703904; CADD: 0.787 (6.717)

Frequency Data:: 1000Genomes: 1.5380%; TOPMed: 0.8187%; UK10K: 1.1108%; gnomAD_G_AFR: 0.2178%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0618%; gnomAD_G_FIN: 0.7480%; gnomAD_G_NFE: 1.2104%; gnomAD_G_OTH: 0.7128%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93703978C>CT [0/1] rs71071759 (variation viewer)

Variant score: 0.159

Transcripts:: CRADD:ENST00000332896.8:c.298+24906_298+24907insT:p.(=); CRADD:ENST00000542893.2:c.298+24906_298+24907insT:p.(=); CRADD:ENST00000548483.5:c.298+24906_298+24907insT:p.(=); CRADD:ENST00000552033.5:c.298+24906_298+24907insT:p.(=); CRADD:ENST00000552983.5:c.298+24906_298+24907insT:p.(=)

Pathogenicity Data:: Best Score: 0.15860486; CADD: 0.159 (0.750)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93711055C>CT [0/1] rs397850463 (variation viewer)

Variant score: 0.150

Transcripts:: CRADD:ENST00000332896.8:c.298+31983_298+31984insT:p.(=); CRADD:ENST00000542893.2:c.298+31983_298+31984insT:p.(=); CRADD:ENST00000548483.5:c.298+31983_298+31984insT:p.(=); CRADD:ENST00000552033.5:c.299-27349_299-27348insT:p.(=); CRADD:ENST00000552983.5:c.299-27145_299-27144insT:p.(=)

Pathogenicity Data:: Best Score: 0.15023273; CADD: 0.150 (0.707)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr12:g.93900124T>TACACACAC [-/1] rs56902144 (variation viewer)

Variant score: 0.140

Transcripts:: CRADD:ENST00000548483.5::; CRADD:ENST00000548294.1::

Pathogenicity Data:: Best Score: 0.13979888; CADD: 0.140 (0.654)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr12:g.93900124T>TACCCACACACACACAC [-/1] rs772433675 (variation viewer)

Variant score: 0.120

Transcripts:: CRADD:ENST00000548483.5::; CRADD:ENST00000548294.1::

Pathogenicity Data:: Best Score: 0.11976224; CADD: 0.120 (0.554)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93867405T>TATATATATATATATATATATATA [-/1]

Variant score: 0.084

Transcripts:: CRADD:ENST00000548483.5:c.299-26645_299-26644insATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.08441222; CADD: 0.084 (0.383)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93846581A>AACACACACACAC [0/1] rs761401611 (variation viewer)

Variant score: 0.039

Transcripts:: CRADD:ENST00000332896.8:c.299-3389_299-3388insACACACACACAC:p.(=); CRADD:ENST00000542893.2:c.299-3389_299-3388insACACACACACAC:p.(=); CRADD:ENST00000548483.5:c.299-47469_299-47468insACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.1427648; CADD: 0.143 (0.669)

Frequency Data:: gnomAD_G_AFR: 0.4076%; gnomAD_G_AMR: 0.6006%; gnomAD_G_ASJ: 1.5748%; gnomAD_G_EAS: 0.7772%; gnomAD_G_FIN: 0.7486%; gnomAD_G_NFE: 1.8519%; gnomAD_G_OTH: 1.0230%

ERBIN

Exomiser Score: 0.103

Phenotype Score: 0.509

Variant Score: 0.636

Phenotype matches:

Proximity score 0.509 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.099

Phenotype Score: 0.509

Variant Score: 0.631

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66065591CTGTGTG>C [-/1] rs56164922 (variation viewer)

Variant score: 0.631 CONTRIBUTING VARIANT

Transcripts:: ERBIN:ENST00000284037.9:c.3634-6577_3634-6572del:p.(=); ERBIN:ENST00000380935.5:c.3633+10641_3633+10646del:p.(=); ERBIN:ENST00000380938.6:c.3634-9432_3634-9427del:p.(=); ERBIN:ENST00000380943.6:c.3634-9432_3634-9427del:p.(=); ERBIN:ENST00000416865.6:c.1207-3285_1207-3280del:p.(=); ERBIN:ENST00000506030.5:c.3634-3285_3634-3280del:p.(=); ERBIN:ENST00000508515.1:c.3633+10641_3633+10646del:p.(=); ERBIN:ENST00000511297.5:c.3622-9432_3622-9427del:p.(=)

Pathogenicity Data:: Best Score: 0.63093746; CADD: 0.631 (4.329)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.103

Phenotype Score: 0.509

Variant Score: 0.636

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66033596T>C [0/1] rs183067606 (variation viewer)

Variant score: 0.640 CONTRIBUTING VARIANT

Transcripts:: ERBIN:ENST00000284037.9:c.1207-4787T>C:p.(=); ERBIN:ENST00000380935.5:c.1207-4787T>C:p.(=); ERBIN:ENST00000380938.6:c.1207-4787T>C:p.(=); ERBIN:ENST00000380943.6:c.1207-4787T>C:p.(=); ERBIN:ENST00000416865.6:c.1206+5253T>C:p.(=); ERBIN:ENST00000506030.5:c.1207-4787T>C:p.(=); ERBIN:ENST00000508515.1:c.1207-4787T>C:p.(=); ERBIN:ENST00000511297.5:c.1207-4787T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6955612; CADD: 0.696 (5.165)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2317%; UK10K: 0.4628%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.3865%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66065591CTGTGTG>C [-/1] rs56164922 (variation viewer)

Variant score: 0.631 CONTRIBUTING VARIANT

Transcripts:: ERBIN:ENST00000284037.9:c.3634-6577_3634-6572del:p.(=); ERBIN:ENST00000380935.5:c.3633+10641_3633+10646del:p.(=); ERBIN:ENST00000380938.6:c.3634-9432_3634-9427del:p.(=); ERBIN:ENST00000380943.6:c.3634-9432_3634-9427del:p.(=); ERBIN:ENST00000416865.6:c.1207-3285_1207-3280del:p.(=); ERBIN:ENST00000506030.5:c.3634-3285_3634-3280del:p.(=); ERBIN:ENST00000508515.1:c.3633+10641_3633+10646del:p.(=); ERBIN:ENST00000511297.5:c.3622-9432_3622-9427del:p.(=)

Pathogenicity Data:: Best Score: 0.63093746; CADD: 0.631 (4.329)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66031421T>TATTAAAGTACTTAA [0|1]

Variant score: 0.615

Transcripts:: ERBIN:ENST00000284037.9:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000380935.5:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000380938.6:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000380943.6:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000416865.6:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000506030.5:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000508515.1:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=); ERBIN:ENST00000511297.5:c.1206+3078_1206+3079insATTAAAGTACTTAA:p.(=)

Pathogenicity Data:: Best Score: 0.61540824; CADD: 0.615 (4.150)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66065591CTGTGTGTGTG>C [-/1] rs56164922 (variation viewer)

Variant score: 0.614

Transcripts:: ERBIN:ENST00000284037.9:c.3634-6577_3634-6568del:p.(=); ERBIN:ENST00000380935.5:c.3633+10641_3633+10650del:p.(=); ERBIN:ENST00000380938.6:c.3634-9432_3634-9423del:p.(=); ERBIN:ENST00000380943.6:c.3634-9432_3634-9423del:p.(=); ERBIN:ENST00000416865.6:c.1207-3285_1207-3276del:p.(=); ERBIN:ENST00000506030.5:c.3634-3285_3634-3276del:p.(=); ERBIN:ENST00000508515.1:c.3633+10641_3633+10650del:p.(=); ERBIN:ENST00000511297.5:c.3622-9432_3622-9423del:p.(=)

Pathogenicity Data:: Best Score: 0.6138998; CADD: 0.614 (4.133)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66031419T>A [0|1] rs1369525686 (variation viewer)

Variant score: 0.597

Transcripts:: ERBIN:ENST00000284037.9:c.1206+3076T>A:p.(=); ERBIN:ENST00000380935.5:c.1206+3076T>A:p.(=); ERBIN:ENST00000380938.6:c.1206+3076T>A:p.(=); ERBIN:ENST00000380943.6:c.1206+3076T>A:p.(=); ERBIN:ENST00000416865.6:c.1206+3076T>A:p.(=); ERBIN:ENST00000506030.5:c.1206+3076T>A:p.(=); ERBIN:ENST00000508515.1:c.1206+3076T>A:p.(=); ERBIN:ENST00000511297.5:c.1206+3076T>A:p.(=)

Pathogenicity Data:: Best Score: 0.59700465; CADD: 0.597 (3.947)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.65965382GTTTTTTTTTTTTTTTTTTTTTTTT>G [1/1] rs200847060 (variation viewer)

Variant score: 0.390

Transcripts:: ERBIN:ENST00000284037.9:c.-57-23252_-57-23229del:p.(=); ERBIN:ENST00000380935.5:c.-57-23252_-57-23229del:p.(=); ERBIN:ENST00000380938.6:c.-57-23252_-57-23229del:p.(=); ERBIN:ENST00000380943.6:c.-57-23252_-57-23229del:p.(=); ERBIN:ENST00000416865.6:c.-57-23252_-57-23229del:p.(=); ERBIN:ENST00000506030.5:c.-57-23252_-57-23229del:p.(=); ERBIN:ENST00000511297.5:c.-57-23252_-57-23229del:p.(=)

Pathogenicity Data:: Best Score: 0.38962042; CADD: 0.390 (2.144)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.66031416C>CTT [0|1]

Variant score: 0.248

Transcripts:: ERBIN:ENST00000284037.9:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000380935.5:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000380938.6:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000380943.6:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000416865.6:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000506030.5:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000508515.1:c.1206+3073_1206+3074insTT:p.(=); ERBIN:ENST00000511297.5:c.1206+3073_1206+3074insTT:p.(=)

Pathogenicity Data:: Best Score: 0.24785775; CADD: 0.248 (1.237)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.65948762G>GTTT [1/1] rs59712256 (variation viewer)

Variant score: 0.228

Transcripts:: ERBIN:ENST00000284037.9:c.-58+21956_-58+21957insTTT:p.(=); ERBIN:ENST00000380935.5:c.-58+21956_-58+21957insTTT:p.(=); ERBIN:ENST00000380938.6:c.-58+21956_-58+21957insTTT:p.(=); ERBIN:ENST00000380943.6:c.-58+21956_-58+21957insTTT:p.(=); ERBIN:ENST00000416865.6:c.-58+21956_-58+21957insTTT:p.(=); ERBIN:ENST00000506030.5:c.-58+21956_-58+21957insTTT:p.(=); ERBIN:ENST00000511297.5:c.-58+21956_-58+21957insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.22767514; CADD: 0.228 (1.122)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr5:g.66083048A>AT [0/1] rs35004347 (variation viewer)

Variant score: 0.182

Transcripts:: ERBIN:ENST00000284037.9::; ERBIN:ENST00000612404.4::

Pathogenicity Data:: Best Score: 0.18191206; CADD: 0.182 (0.872)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.65945370G>A [0/1] rs148588885 (variation viewer)

Variant score: 0.166

Transcripts:: ERBIN:ENST00000284037.9:c.-58+18564G>A:p.(=); ERBIN:ENST00000380935.5:c.-58+18564G>A:p.(=); ERBIN:ENST00000380938.6:c.-58+18564G>A:p.(=); ERBIN:ENST00000380943.6:c.-58+18564G>A:p.(=); ERBIN:ENST00000416865.6:c.-58+18564G>A:p.(=); ERBIN:ENST00000506030.5:c.-58+18564G>A:p.(=); ERBIN:ENST00000511297.5:c.-58+18564G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5214801; CADD: 0.521 (3.201)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.9397%; UK10K: 1.7985%; gnomAD_G_AFR: 0.2063%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.7732%; gnomAD_G_NFE: 1.5798%; gnomAD_G_OTH: 1.1202%

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.65954922G>C [0/1] rs1043588397 (variation viewer)

Variant score: 0.163

Transcripts:: ERBIN:ENST00000284037.9:c.-58+28116G>C:p.(=); ERBIN:ENST00000380935.5:c.-58+28116G>C:p.(=); ERBIN:ENST00000380938.6:c.-58+28116G>C:p.(=); ERBIN:ENST00000380943.6:c.-58+28116G>C:p.(=); ERBIN:ENST00000416865.6:c.-58+28116G>C:p.(=); ERBIN:ENST00000506030.5:c.-58+28116G>C:p.(=); ERBIN:ENST00000511297.5:c.-58+28116G>C:p.(=)

Pathogenicity Data:: Best Score: 0.16343439; CADD: 0.163 (0.775)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

INTERGENIC_VARIANT chr5:g.66089922CA>C [0/1] rs57571422 (variation viewer)

Variant score: 0.108

Transcripts:: ERBIN:ENST00000284037.9::; ERBIN:ENST00000612404.4::

Pathogenicity Data:: Best Score: 0.1077224; CADD: 0.108 (0.495)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr5:g.65906894G>GT [-/1] rs375934297 (variation viewer)

Variant score: 0.090

Transcripts:: ERBIN:ENST00000284037.9::; ERBIN:ENST00000502464.5::

Pathogenicity Data:: Best Score: 0.09008676; CADD: 0.090 (0.410)

Frequency Data:: No frequency data

CANX

Exomiser Score: 0.102

Phenotype Score: 0.514

Variant Score: 0.629

Phenotype matches:

Phenotypic similarity 0.514 to mouse mutant involving CANX.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.102

Phenotype Score: 0.514

Variant Score: 0.629

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.179701736C>CTTTT [1/1] rs558907168 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: CANX:ENST00000247461.9:c.-4+2634_-4+2635insTTTT:p.(=); CANX:ENST00000452673.6:c.-4+2687_-4+2688insTTTT:p.(=); CANX:ENST00000504734.5:c.-4+3133_-4+3134insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.6293193; CADD: 0.629 (4.310)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.179724828C>T [0/1] rs189605881 (variation viewer)

Variant score: 0.312

Transcripts:: CANX:ENST00000247461.9:c.1645+45C>T:p.(=); CANX:ENST00000452673.6:c.1645+45C>T:p.(=); CANX:ENST00000504734.5:c.1645+45C>T:p.(=)

Pathogenicity Data:: Best Score: 0.33303964; CADD: 0.333 (1.759)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.0382%; ESP AA: 0.0228%; ESP EA: 0.0934%; ESP All: 0.0695%; ExAC AFR: 0.0216%; ExAC AMR: 0.3382%; ExAC NFE: 0.0838%; ExAC OTH: 0.2381%; ExAC SAS: 0.3829%; gnomAD_E_AFR: 0.0103%; gnomAD_E_AMR: 0.0399%; gnomAD_E_NFE: 0.0740%; gnomAD_E_OTH: 0.1886%; gnomAD_E_SAS: 0.3853%; gnomAD_G_AFR: 0.0343%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.179714348T>C [0/1] rs538393141 (variation viewer)

Variant score: 0.307

Transcripts:: CANX:ENST00000247461.9:c.722-1757T>C:p.(=); CANX:ENST00000452673.6:c.722-1757T>C:p.(=); CANX:ENST00000504734.5:c.722-1757T>C:p.(=)

Pathogenicity Data:: Best Score: 0.3157733; CADD: 0.316 (1.648)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.0350%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.1020%

UPSTREAM_GENE_VARIANT chr5:g.179696267CT>C [1/1] rs34048949 (variation viewer)

Variant score: 0.130

Transcripts:: CANX:ENST00000504734.5::; CANX:ENST00000451823.2::

Pathogenicity Data:: Best Score: 0.1304391; CADD: 0.130 (0.607)

Frequency Data:: No frequency data

JMJD1C

Exomiser Score: 0.102

Phenotype Score: 0.864

Variant Score: 0.232

Phenotype matches:

Phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with JMJD1C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:567 22q11.2 deletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.102

Phenotype Score: 0.864

Variant Score: 0.232

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63427669G>A [0/1] rs957111196 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: JMJD1C:ENST00000399262.7:c.168+37826C>T:p.(=); JMJD1C:ENST00000450055.1:n.373G>A:

Pathogenicity Data:: Best Score: 0.23263848; CADD: 0.233 (1.150)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.432

Variant Score: 0.370

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63245478C>CTTT [1/1] rs71025134 (variation viewer)

Variant score: 0.370 CONTRIBUTING VARIANT

Transcripts:: JMJD1C:ENST00000399262.7:c.447+19172_447+19173insAAA:p.(=); JMJD1C:ENST00000542921.5:c.-100+19172_-100+19173insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.36962354; CADD: 0.370 (2.004)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63170954A>G [0/1] rs138996758 (variation viewer)

Variant score: 0.388

Transcripts:: JMJD1C:ENST00000399262.7:c.7402-2388T>C:p.(=); JMJD1C:ENST00000542921.5:c.6856-2388T>C:p.(=); JMJD1C:ENST00000639129.1:c.6856-2388T>C:p.(=)

Pathogenicity Data:: Best Score: 0.9085887; CADD: 0.909 (10.390)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.5384%; UK10K: 0.6480%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.6196%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63353787T>C [0|1] rs141061153 (variation viewer)

Variant score: 0.263

Transcripts:: JMJD1C:ENST00000399262.7:c.333+26531A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6155853; CADD: 0.616 (4.152)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5742%; UK10K: 0.7141%; gnomAD_G_AFR: 0.1261%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.6668%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63247719C>CAA [1/1] rs71025135 (variation viewer)

Variant score: 0.261

Transcripts:: JMJD1C:ENST00000399262.7:c.447+16931_447+16932insTT:p.(=); JMJD1C:ENST00000542921.5:c.-100+16931_-100+16932insTT:p.(=)

Pathogenicity Data:: Best Score: 0.26124573; CADD: 0.261 (1.315)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63424497C>CTT [1/1] rs59823871 (variation viewer)

Variant score: 0.201

Transcripts:: JMJD1C:ENST00000399262.7:c.168+40997_168+40998insAA:p.(=)

Pathogenicity Data:: Best Score: 0.20090204; CADD: 0.201 (0.974)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63387629A>AATT [-/1] rs1554915199 (variation viewer)

Variant score: 0.182

Transcripts:: JMJD1C:ENST00000399262.7:c.169-7148_169-7147insAAT:p.(=)

Pathogenicity Data:: Best Score: 0.18172365; CADD: 0.182 (0.871)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63387629A>AATTT [-/1] rs1554915199 (variation viewer)

Variant score: 0.179

Transcripts:: JMJD1C:ENST00000399262.7:c.169-7148_169-7147insAAAT:p.(=)

Pathogenicity Data:: Best Score: 0.1785143; CADD: 0.179 (0.854)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63234493T>TA [0/1] rs71025129 (variation viewer)

Variant score: 0.160

Transcripts:: JMJD1C:ENST00000399262.7:c.448-14511_448-14510insT:p.(=); JMJD1C:ENST00000542921.5:c.-99-14511_-99-14510insT:p.(=)

Pathogenicity Data:: Best Score: 0.16015333; CADD: 0.160 (0.758)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63305629C>CGTGTGT [-/1] rs36038855 (variation viewer)

Variant score: 0.157

Transcripts:: JMJD1C:ENST00000399262.7:c.334-40866_334-40865insACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.15744162; CADD: 0.157 (0.744)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63305629C>CGTGTGTGTGTGT [-/1] rs36038855 (variation viewer)

Variant score: 0.141

Transcripts:: JMJD1C:ENST00000399262.7:c.334-40866_334-40865insACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.14059079; CADD: 0.141 (0.658)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63375183C>CTTTT [-/1] rs67008681 (variation viewer)

Variant score: 0.120

Transcripts:: JMJD1C:ENST00000399262.7:c.333+5134_333+5135insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.11976224; CADD: 0.120 (0.554)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63375183C>CTTTTT [-/1] rs67008681 (variation viewer)

Variant score: 0.117

Transcripts:: JMJD1C:ENST00000399262.7:c.333+5134_333+5135insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63288889C>CAATAAT [-/1] rs61651313 (variation viewer)

Variant score: 0.098

Transcripts:: JMJD1C:ENST00000399262.7:c.334-24126_334-24125insATTATT:p.(=)

Pathogenicity Data:: Best Score: 0.09801358; CADD: 0.098 (0.448)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63248529G>GATAGATAGATAGATAAATAA [-/1] rs566828473 (variation viewer)

Variant score: 0.089

Transcripts:: JMJD1C:ENST00000399262.7:c.447+16121_447+16122insTTATTTATCTATCTATCTAT:p.(=); JMJD1C:ENST00000542921.5:c.-100+16121_-100+16122insTTATTTATCTATCTATCTAT:p.(=)

Pathogenicity Data:: Best Score: 0.0892483; CADD: 0.089 (0.406)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63276884C>CTTTTTTTT [1|1] rs760452367 (variation viewer)

Variant score: 0.086

Transcripts:: JMJD1C:ENST00000399262.7:c.334-12121_334-12120insAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.086307645; CADD: 0.086 (0.392)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63277731CTT>C [1/1] rs35442695 (variation viewer)

Variant score: 0.081

Transcripts:: JMJD1C:ENST00000399262.7:c.334-12969_334-12968del:p.(=)

Pathogenicity Data:: Best Score: 0.08124441; CADD: 0.081 (0.368)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63185045G>A [0/1] rs949883005 (variation viewer)

Variant score: 0.070

Transcripts:: JMJD1C:ENST00000399262.7:c.6831-307C>T:p.(=); JMJD1C:ENST00000542921.5:c.6285-307C>T:p.(=); JMJD1C:ENST00000639129.1:c.6285-307C>T:p.(=)

Pathogenicity Data:: Best Score: 0.070177615; CADD: 0.070 (0.316)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_AFR: 0.0116%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63338640AT>A [0/1] rs34238197 (variation viewer)

Variant score: 0.047

Transcripts:: JMJD1C:ENST00000399262.7:c.333+41677del:p.(=)

Pathogenicity Data:: Best Score: 0.04676497; CADD: 0.047 (0.208)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.63312094CT>C [0/1] rs35328965 (variation viewer)

Variant score: 0.045

Transcripts:: JMJD1C:ENST00000399262.7:c.334-47331del:p.(=)

Pathogenicity Data:: Best Score: 0.04522729; CADD: 0.045 (0.201)

Frequency Data:: No frequency data

GRIA1

Exomiser Score: 0.102

Phenotype Score: 0.503

Variant Score: 0.641

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving GRIA1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.503 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.025

Phenotype Score: 0.503

Variant Score: 0.479

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153656383T>TTATA [0|1] rs60245651 (variation viewer)

Variant score: 0.479 CONTRIBUTING VARIANT

Transcripts:: GRIA1:ENST00000285900.10:c.699+511_699+512insTATA:p.(=); GRIA1:ENST00000340592.9:c.699+511_699+512insTATA:p.(=); GRIA1:ENST00000448073.8:c.729+511_729+512insTATA:p.(=); GRIA1:ENST00000518142.5:c.459+511_459+512insTATA:p.(=); GRIA1:ENST00000518783.1:c.729+511_729+512insTATA:p.(=); GRIA1:ENST00000521843.6:c.492+511_492+512insTATA:p.(=)

Pathogenicity Data:: Best Score: 0.47928512; CADD: 0.479 (2.834)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.102

Phenotype Score: 0.503

Variant Score: 0.641

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153590506ATGTGTG>A [1/1] rs5872325 (variation viewer)

Variant score: 0.641 CONTRIBUTING VARIANT

Transcripts:: GRIA1:ENST00000285900.10:c.221-56421_221-56416del:p.(=); GRIA1:ENST00000340592.9:c.221-56421_221-56416del:p.(=); GRIA1:ENST00000448073.8:c.251-56421_251-56416del:p.(=); GRIA1:ENST00000518142.5:c.221-59823_221-59818del:p.(=); GRIA1:ENST00000518783.1:c.251-56421_251-56416del:p.(=); GRIA1:ENST00000521843.6:c.14-56421_14-56416del:p.(=)

Pathogenicity Data:: Best Score: 0.64058185; CADD: 0.641 (4.444)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr5:g.153827183T>C [0/1]

Variant score: 0.382

Transcripts:: GRIA1:ENST00000285900.10::

Pathogenicity Data:: Best Score: 0.3821259; CADD: 0.382 (2.091)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153582200A>T [0/1] rs189540667 (variation viewer)

Variant score: 0.292

Transcripts:: GRIA1:ENST00000285900.10:c.221-64728A>T:p.(=); GRIA1:ENST00000340592.9:c.221-64728A>T:p.(=); GRIA1:ENST00000448073.8:c.251-64728A>T:p.(=); GRIA1:ENST00000518142.5:c.221-68130A>T:p.(=); GRIA1:ENST00000518783.1:c.251-64728A>T:p.(=); GRIA1:ENST00000521843.6:c.14-64728A>T:p.(=)

Pathogenicity Data:: Best Score: 0.33411384; CADD: 0.334 (1.766)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.3608%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.2003%; gnomAD_G_NFE: 0.2864%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153568692CCTCA>C [0/1] rs556691743 (variation viewer)

Variant score: 0.275

Transcripts:: GRIA1:ENST00000285900.10:c.220+74628_220+74631del:p.(=); GRIA1:ENST00000340592.9:c.220+74628_220+74631del:p.(=); GRIA1:ENST00000448073.8:c.250+74628_250+74631del:p.(=); GRIA1:ENST00000518142.5:c.220+74628_220+74631del:p.(=); GRIA1:ENST00000518783.1:c.250+74628_250+74631del:p.(=); GRIA1:ENST00000521843.6:c.13+74628_13+74631del:p.(=)

Pathogenicity Data:: Best Score: 0.31545818; CADD: 0.315 (1.646)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.3639%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.2006%; gnomAD_G_NFE: 0.2800%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153600391C>CA [0/1] rs57395601 (variation viewer)

Variant score: 0.226

Transcripts:: GRIA1:ENST00000285900.10:c.221-46537_221-46536insA:p.(=); GRIA1:ENST00000340592.9:c.221-46537_221-46536insA:p.(=); GRIA1:ENST00000448073.8:c.251-46537_251-46536insA:p.(=); GRIA1:ENST00000518142.5:c.221-49939_221-49938insA:p.(=); GRIA1:ENST00000518783.1:c.251-46537_251-46536insA:p.(=); GRIA1:ENST00000521843.6:c.14-46537_14-46536insA:p.(=)

Pathogenicity Data:: Best Score: 0.22589475; CADD: 0.226 (1.112)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr5:g.152858566C>CT [1/1] rs71274338 (variation viewer)

Variant score: 0.210

Transcripts:: GRIA1:ENST00000518142.5::; GRIA1:ENST00000467232.1::

Pathogenicity Data:: Best Score: 0.21023113; CADD: 0.210 (1.025)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153600260C>T [0/1] rs551279617 (variation viewer)

Variant score: 0.065

Transcripts:: GRIA1:ENST00000285900.10:c.221-46668C>T:p.(=); GRIA1:ENST00000340592.9:c.221-46668C>T:p.(=); GRIA1:ENST00000448073.8:c.251-46668C>T:p.(=); GRIA1:ENST00000518142.5:c.221-50070C>T:p.(=); GRIA1:ENST00000518783.1:c.251-46668C>T:p.(=); GRIA1:ENST00000521843.6:c.14-46668C>T:p.(=)

Pathogenicity Data:: Best Score: 0.06567061; CADD: 0.066 (0.295)

Frequency Data:: gnomAD_G_NFE: 0.0202%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.153612702G>A [0/1] rs144526411 (variation viewer)

Variant score: 0.001

Transcripts:: GRIA1:ENST00000285900.10:c.221-34226G>A:p.(=); GRIA1:ENST00000340592.9:c.221-34226G>A:p.(=); GRIA1:ENST00000448073.8:c.251-34226G>A:p.(=); GRIA1:ENST00000518142.5:c.221-37628G>A:p.(=); GRIA1:ENST00000518783.1:c.251-34226G>A:p.(=); GRIA1:ENST00000521843.6:c.14-34226G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0013806224; CADD: 0.001 (0.006)

Frequency Data:: 1000Genomes: 0.7588%; TOPMed: 0.6363%; UK10K: 0.8992%; gnomAD_G_AFR: 0.1834%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.4871%; gnomAD_G_NFE: 0.8470%; gnomAD_G_OTH: 0.5102%

HIRA

Exomiser Score: 0.102

Phenotype Score: 0.864

Variant Score: 0.232

Phenotype matches:

Phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with HIRA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:567 22q11.2 deletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.102

Phenotype Score: 0.864

Variant Score: 0.232

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19429133C>CT [0/1] rs57853722 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: HIRA:ENST00000263208.5:c.37+2306_37+2307insA:p.(=); HIRA:ENST00000340170.8:c.37+2306_37+2307insA:p.(=)

Pathogenicity Data:: Best Score: 0.23193145; CADD: 0.232 (1.146)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.432

Variant Score: 0.391

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19362072G>A [0|1] rs41277615 (variation viewer)

Variant score: 0.550 CONTRIBUTING VARIANT

Transcripts:: HIRA:ENST00000263208.5:c.1776-141C>T:p.(=); HIRA:ENST00000340170.8:c.1776-5784C>T:p.(=)

Pathogenicity Data:: Best Score: 0.9396051; CADD: 0.940 (12.190)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.6913%; UK10K: 1.4017%; gnomAD_G_AFR: 0.2864%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.3150%; gnomAD_G_NFE: 0.8664%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19429133C>CT [0/1] rs57853722 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: HIRA:ENST00000263208.5:c.37+2306_37+2307insA:p.(=); HIRA:ENST00000340170.8:c.37+2306_37+2307insA:p.(=)

Pathogenicity Data:: Best Score: 0.23193145; CADD: 0.232 (1.146)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.19422171T>TACACACACACACAC [0/1] rs763716204 (variation viewer)

Variant score: 0.175

Transcripts:: HIRA:ENST00000263208.5:c.37+9268_37+9269insGTGTGTGTGTGTGT:p.(=); HIRA:ENST00000340170.8:c.37+9268_37+9269insGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.17548227; CADD: 0.175 (0.838)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr22:g.19327185ATT>A [0/1] rs58476128 (variation viewer)

Variant score: 0.162

Transcripts:: HIRA:ENST00000340170.8::; HIRA:ENST00000427926.6::

Pathogenicity Data:: Best Score: 0.16150594; CADD: 0.162 (0.765)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr22:g.19328611GTCT>G [0/1] rs374112597 (variation viewer)

Variant score: 0.094

Transcripts:: HIRA:ENST00000340170.8::; HIRA:ENST00000427926.6::

Pathogenicity Data:: Best Score: 0.15627676; CADD: 0.156 (0.738)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.6984%; UK10K: 1.3753%; gnomAD_G_AFR: 0.2753%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.3154%; gnomAD_G_NFE: 0.8601%; gnomAD_G_OTH: 0.6110%

TH

Exomiser Score: 0.100

Phenotype Score: 0.504

Variant Score: 0.637

Phenotype matches:

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:605407 Segawa syndrome, recessive - autosomal recessive; ORPHA:101150 Autosomal recessive dopa-responsive dystonia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.009

Phenotype Score: 0.252

Variant Score: 0.646

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.2182532C>T [0/1]

Variant score: 0.646 CONTRIBUTING VARIANT

Transcripts:: TH:ENST00000352909.7::; TH:ENST00000331289.4::

Pathogenicity Data:: Best Score: 0.6456765; CADD: 0.646 (4.506)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.100

Phenotype Score: 0.504

Variant Score: 0.637

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.2182532C>T [0/1]

Variant score: 0.646 CONTRIBUTING VARIANT

Transcripts:: TH:ENST00000352909.7::; TH:ENST00000331289.4::

Pathogenicity Data:: Best Score: 0.6456765; CADD: 0.646 (4.506)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.2164851C>T [0/1] rs564996751 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: TH:ENST00000333684.9:c.1052+381G>A:p.(=); TH:ENST00000352909.7:c.1334+381G>A:p.(=); TH:ENST00000381175.5:c.1415+381G>A:p.(=); TH:ENST00000381178.5:c.1427+381G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7031753; CADD: 0.703 (5.275)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.2819%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0574%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2864%; gnomAD_G_NFE: 0.5758%; gnomAD_G_OTH: 0.5133%

Other passed variants:

MYO1E

Exomiser Score: 0.099

Phenotype Score: 0.513

Variant Score: 0.626

Phenotype matches:

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:614131 Glomerulosclerosis, focal segmental, 6 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.081

Phenotype Score: 0.256

Variant Score: 0.892

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59218422G>C [0/1]

Variant score: 0.892 CONTRIBUTING VARIANT

Transcripts:: MYO1E:ENST00000288235.9:c.911-335C>G:p.(=)

Pathogenicity Data:: Best Score: 0.8918317; CADD: 0.892 (9.659)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.099

Phenotype Score: 0.513

Variant Score: 0.626

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59218422G>C [0/1]

Variant score: 0.892 CONTRIBUTING VARIANT

Transcripts:: MYO1E:ENST00000288235.9:c.911-335C>G:p.(=)

Pathogenicity Data:: Best Score: 0.8918317; CADD: 0.892 (9.659)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59260562G>A [0/1] rs560856201 (variation viewer)

Variant score: 0.360 CONTRIBUTING VARIANT

Transcripts:: MYO1E:ENST00000288235.9:c.237+858C>T:p.(=)

Pathogenicity Data:: Best Score: 0.3661303; CADD: 0.366 (1.980)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0462%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0666%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59297033T>C [1|1] rs56231025 (variation viewer)

Variant score: 0.521

Transcripts:: MYO1E:ENST00000288235.9:c.4-24584A>G:p.(=)

Pathogenicity Data:: Best Score: 0.52081853; CADD: 0.521 (3.195)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59297025G>T [1|1] rs76235980 (variation viewer)

Variant score: 0.242

Transcripts:: MYO1E:ENST00000288235.9:c.4-24576C>A:p.(=)

Pathogenicity Data:: Best Score: 0.24229527; CADD: 0.242 (1.205)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59268720A>ATTTTTTTTT [1/1] rs398027512 (variation viewer)

Variant score: 0.231

Transcripts:: MYO1E:ENST00000288235.9:c.147+3585_147+3586insAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.2305153; CADD: 0.231 (1.138)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59323168CAAA>C [0/1] rs10569332 (variation viewer)

Variant score: 0.217

Transcripts:: MYO1E:ENST00000288235.9:c.3+49327_3+49329del:p.(=)

Pathogenicity Data:: Best Score: 0.21711135; CADD: 0.217 (1.063)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59353543G>A [0/1] rs11853436 (variation viewer)

Variant score: 0.160

Transcripts:: MYO1E:ENST00000288235.9:c.3+18955C>T:p.(=)

Pathogenicity Data:: Best Score: 0.25766492; CADD: 0.258 (1.294)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.6921%; UK10K: 1.0050%; gnomAD_G_AFR: 0.2085%; gnomAD_G_AMR: 0.1199%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.0618%; gnomAD_G_FIN: 0.1804%; gnomAD_G_NFE: 1.0611%; gnomAD_G_OTH: 0.7415%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59273593G>A [0/1] rs76727706 (variation viewer)

Variant score: 0.152

Transcripts:: MYO1E:ENST00000288235.9:c.4-1144C>T:p.(=)

Pathogenicity Data:: Best Score: 0.17224842; CADD: 0.172 (0.821)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.3225%; UK10K: 0.6348%; gnomAD_G_AFR: 0.1604%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.4334%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59142920CA>C [0/1] rs10717979 (variation viewer)

Variant score: 0.125

Transcripts:: MYO1E:ENST00000288235.9:c.3081-4554del:p.(=)

Pathogenicity Data:: Best Score: 0.12541908; CADD: 0.125 (0.582)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59209815CTTTTTTTTTTTTT>C [0/1] rs71119441 (variation viewer)

Variant score: 0.106

Transcripts:: MYO1E:ENST00000288235.9:c.1362+686_1362+698del:p.(=)

Pathogenicity Data:: Best Score: 0.106488824; CADD: 0.106 (0.489)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59297437A>ATTTTTTTTTTTTTT [1/1] rs755470049 (variation viewer)

Variant score: 0.095

Transcripts:: MYO1E:ENST00000288235.9:c.4-24989_4-24988insAAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.09489286; CADD: 0.095 (0.433)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59149052GT>G [1|1] rs570700878 (variation viewer)

Variant score: 0.090

Transcripts:: MYO1E:ENST00000288235.9:c.3080+4537del:p.(=)

Pathogenicity Data:: Best Score: 0.08966762; CADD: 0.090 (0.408)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59283962G>A [0/1] rs192283097 (variation viewer)

Variant score: 0.078

Transcripts:: MYO1E:ENST00000288235.9:c.4-11513C>T:p.(=)

Pathogenicity Data:: Best Score: 0.09176129; CADD: 0.092 (0.418)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.4237%; UK10K: 0.7273%; gnomAD_G_AFR: 0.1505%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.6068%; gnomAD_G_OTH: 0.5198%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59297062C>G [1|1] rs4293319 (variation viewer)

Variant score: 0.070

Transcripts:: MYO1E:ENST00000288235.9:c.4-24613G>C:p.(=)

Pathogenicity Data:: Best Score: 0.069963515; CADD: 0.070 (0.315)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59217519C>CTTTTT [1/1] rs1164320277 (variation viewer)

Variant score: 0.045

Transcripts:: MYO1E:ENST00000288235.9:c.1107+371_1107+372insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.044787467; CADD: 0.045 (0.199)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59216666G>GTA [-/1] rs368761394 (variation viewer)

Variant score: 0.023

Transcripts:: MYO1E:ENST00000288235.9:c.1107+1224_1107+1225insTA:p.(=)

Pathogenicity Data:: Best Score: 0.02321273; CADD: 0.023 (0.102)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59216666G>GTATA [-/1] rs368761394 (variation viewer)

Variant score: 0.022

Transcripts:: MYO1E:ENST00000288235.9:c.1107+1224_1107+1225insTATA:p.(=)

Pathogenicity Data:: Best Score: 0.022312641; CADD: 0.022 (0.098)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59234246G>* [-/1]

Variant score: 0.000

Transcripts:: MYO1E:ENST00000288235.9:c.420+2339C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59234249C>* [-/1]

Variant score: 0.000

Transcripts:: MYO1E:ENST00000288235.9:c.420+2336G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59243819G>* [-/1]

Variant score: 0.000

Transcripts:: MYO1E:ENST00000288235.9:c.333-7147C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.59366997CAA>* [-/1]

Variant score: 0.000

Transcripts:: MYO1E:ENST00000288235.9:c.3+5499_3+5501delTTGins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ITPR2

Exomiser Score: 0.095

Phenotype Score: 0.506

Variant Score: 0.628

Phenotype matches:

Proximity score 0.506 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:106190 ?Anhidrosis, isolated, with normal sweat glands (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.008

Phenotype Score: 0.253

Variant Score: 0.629

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26733263A>G [0|1]

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: ITPR2:ENST00000242737.5:c.164-7498T>C:p.(=); ITPR2:ENST00000381340.8:c.164-7498T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6294899; CADD: 0.629 (4.312)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.095

Phenotype Score: 0.506

Variant Score: 0.628

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26733263A>G [0|1]

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: ITPR2:ENST00000242737.5:c.164-7498T>C:p.(=); ITPR2:ENST00000381340.8:c.164-7498T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6294899; CADD: 0.629 (4.312)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26733257T>C [0|1]

Variant score: 0.627 CONTRIBUTING VARIANT

Transcripts:: ITPR2:ENST00000242737.5:c.164-7492A>G:p.(=); ITPR2:ENST00000381340.8:c.164-7492A>G:p.(=)

Pathogenicity Data:: Best Score: 0.62692165; CADD: 0.627 (4.282)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26474494C>T [0/1] rs904624365 (variation viewer)

Variant score: 0.488

Transcripts:: ITPR2:ENST00000381340.8:c.6342+802G>A:p.(=)

Pathogenicity Data:: Best Score: 0.48890692; CADD: 0.489 (2.915)

Frequency Data:: TOPMed: 0.0127%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26676285T>C [0/1]

Variant score: 0.459

Transcripts:: ITPR2:ENST00000381340.8:c.1409+5589A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4587474; CADD: 0.459 (2.666)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26633884CCA>C [0/1] rs144966445 (variation viewer)

Variant score: 0.450

Transcripts:: ITPR2:ENST00000381340.8:c.2741-1827_2741-1826del:p.(=)

Pathogenicity Data:: Best Score: 0.9760117; CADD: 0.976 (16.200)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 0.8322%; UK10K: 1.3488%; gnomAD_G_AFR: 0.2175%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5158%; gnomAD_G_NFE: 1.6054%; gnomAD_G_OTH: 1.4257%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26545297G>A [0/1] rs149155470 (variation viewer)

Variant score: 0.422

Transcripts:: ITPR2:ENST00000381340.8:c.5073+4950C>T:p.(=)

Pathogenicity Data:: Best Score: 0.54804; CADD: 0.548 (3.449)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1800%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0344%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.1431%; gnomAD_G_NFE: 0.2598%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26768994A>AACACACACACAC [0/1] rs143843238 (variation viewer)

Variant score: 0.391

Transcripts:: ITPR2:ENST00000242737.5:c.163+21162_163+21163insGTGTGTGTGTGT:p.(=); ITPR2:ENST00000381340.8:c.163+21162_163+21163insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.39088404; CADD: 0.391 (2.153)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26790586T>TACACACACACACAC [-/1] rs10527860 (variation viewer)

Variant score: 0.320

Transcripts:: ITPR2:ENST00000242737.5:c.93-360_93-359insGTGTGTGTGTGTGT:p.(=); ITPR2:ENST00000381340.8:c.93-360_93-359insGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.31985736; CADD: 0.320 (1.674)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26790586TAC>T [-/1] rs10527860 (variation viewer)

Variant score: 0.314

Transcripts:: ITPR2:ENST00000242737.5:c.93-361_93-360del:p.(=); ITPR2:ENST00000381340.8:c.93-361_93-360del:p.(=)

Pathogenicity Data:: Best Score: 0.31356406; CADD: 0.314 (1.634)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26342497T>G [1/1] rs111376924 (variation viewer)

Variant score: 0.232

Transcripts:: ITPR2:ENST00000381340.8:c.7858-2169A>C:p.(=)

Pathogenicity Data:: Best Score: 0.23157763; CADD: 0.232 (1.144)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26614973A>T [0/1]

Variant score: 0.193

Transcripts:: ITPR2:ENST00000381340.8:c.3462+6150T>A:p.(=)

Pathogenicity Data:: Best Score: 0.19332242; CADD: 0.193 (0.933)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26816092C>CA [-/1] rs11409442 (variation viewer)

Variant score: 0.167

Transcripts:: ITPR2:ENST00000242737.5:c.92+16597_92+16598insT:p.(=); ITPR2:ENST00000381340.8:c.92+16597_92+16598insT:p.(=)

Pathogenicity Data:: Best Score: 0.1674698; CADD: 0.167 (0.796)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26461627AATATATATAT>A [-/1] rs754482854 (variation viewer)

Variant score: 0.164

Transcripts:: ITPR2:ENST00000381340.8:c.6342+13659_6342+13668del:p.(=)

Pathogenicity Data:: Best Score: 0.16381955; CADD: 0.164 (0.777)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26816092CA>C [-/1] rs11409442 (variation viewer)

Variant score: 0.131

Transcripts:: ITPR2:ENST00000242737.5:c.92+16597del:p.(=); ITPR2:ENST00000381340.8:c.92+16597del:p.(=)

Pathogenicity Data:: Best Score: 0.13123965; CADD: 0.131 (0.611)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26733258G>A [0|1] rs1279044953 (variation viewer)

Variant score: 0.128

Transcripts:: ITPR2:ENST00000242737.5:c.164-7493C>T:p.(=); ITPR2:ENST00000381340.8:c.164-7493C>T:p.(=)

Pathogenicity Data:: Best Score: 0.1304391; CADD: 0.130 (0.607)

Frequency Data:: gnomAD_G_AMR: 0.1241%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26634884CAA>C [0/1] rs55985706 (variation viewer)

Variant score: 0.123

Transcripts:: ITPR2:ENST00000381340.8:c.2741-2827_2741-2826del:p.(=)

Pathogenicity Data:: Best Score: 0.12259519; CADD: 0.123 (0.568)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26430752G>A [0/1] rs151155117 (variation viewer)

Variant score: 0.112

Transcripts:: ITPR2:ENST00000381340.8:c.6770-2664C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14532697; CADD: 0.145 (0.682)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.6076%; UK10K: 0.7538%; gnomAD_G_AFR: 0.2176%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.9180%; gnomAD_G_NFE: 0.8598%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26666135G>GAGATAGATAGATAGAT [0/1] rs71437306 (variation viewer)

Variant score: 0.108

Transcripts:: ITPR2:ENST00000381340.8:c.1410-85_1410-84insATCTATCTATCTATCT:p.(=)

Pathogenicity Data:: Best Score: 0.107516885; CADD: 0.108 (0.494)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26614614T>C [0/1] rs138809918 (variation viewer)

Variant score: 0.097

Transcripts:: ITPR2:ENST00000381340.8:c.3462+6509A>G:p.(=)

Pathogenicity Data:: Best Score: 0.25526804; CADD: 0.255 (1.280)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.8959%; UK10K: 1.4811%; gnomAD_G_AFR: 0.2634%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 1.7195%; gnomAD_G_OTH: 1.3238%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26462154C>CTTTTGTTTTGTTTTG [0/1] rs71069237 (variation viewer)

Variant score: 0.087

Transcripts:: ITPR2:ENST00000381340.8:c.6342+13141_6342+13142insCAAAACAAAACAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.08651799; CADD: 0.087 (0.393)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26414050T>TACACAC [-/1] rs777855580 (variation viewer)

Variant score: 0.066

Transcripts:: ITPR2:ENST00000381340.8:c.7306+1252_7306+1253insGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.06588572; CADD: 0.066 (0.296)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26414050T>TACACACACAC [-/1] rs777855580 (variation viewer)

Variant score: 0.061

Transcripts:: ITPR2:ENST00000381340.8:c.7306+1252_7306+1253insGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.060925603; CADD: 0.061 (0.273)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26503190A>AACACACACACAC [1/1] rs57271500 (variation viewer)

Variant score: 0.059

Transcripts:: ITPR2:ENST00000381340.8:c.5074-7931_5074-7930insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.05941075; CADD: 0.059 (0.266)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26494771G>GAAAAA [0/1] rs71069245 (variation viewer)

Variant score: 0.048

Transcripts:: ITPR2:ENST00000381340.8:c.5182+380_5182+381insTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.048300147; CADD: 0.048 (0.215)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26602056G>A [0/1] rs77599265 (variation viewer)

Variant score: 0.018

Transcripts:: ITPR2:ENST00000381340.8:c.3678+314C>T:p.(=)

Pathogenicity Data:: Best Score: 0.04764253; CADD: 0.048 (0.212)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.9158%; UK10K: 1.4679%; gnomAD_G_AFR: 0.2749%; gnomAD_G_AMR: 1.0791%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 1.7260%; gnomAD_G_OTH: 1.4257%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26461627AATATATATAT>* [-/1]

Variant score: 0.000

Transcripts:: ITPR2:ENST00000381340.8:c.6342+13659_6342+13669delATATATATATTins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26497488T>TCAATGCCTGAAATGATCTTCCTCCGTCTTACCTATGAACTGGTCCTATCTTCCCTCTTCATTCTACAAATATTCATTAGGTGC [0/1] rs71069246 (variation viewer)

Variant score: 0.000

Transcripts:: ITPR2:ENST00000381340.8:c.5074-2229_5074-2228insGCACCTAATGAATATTTGTAGAATGAAGAGGGAAGATAGGACCAGTTCATAGGTAAGACGGAGGAAGATCATTTCAGGCATTG:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26630447A>* [-/1]

Variant score: 0.000

Transcripts:: ITPR2:ENST00000381340.8:c.2934+1419T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26782032ATG>* [-/1]

Variant score: 0.000

Transcripts:: ITPR2:ENST00000242737.5:c.163+8123_163+8125delCATins:p.(=); ITPR2:ENST00000381340.8:c.163+8123_163+8125delCATins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.26802568GATATAGATATAGATATATCTATATATAGATATAGATATAGATAT>* [-/1]

Variant score: 0.000

Transcripts:: ITPR2:ENST00000242737.5:c.93-12385_93-12341delATATCTATATCTATATCTATATATAGATATATCTATATCTATATCins:p.(=); ITPR2:ENST00000381340.8:c.93-12385_93-12341delATATCTATATCTATATCTATATATAGATATATCTATATCTATATCins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

YWHAQ

Exomiser Score: 0.093

Phenotype Score: 0.504

Variant Score: 0.629

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.093

Phenotype Score: 0.504

Variant Score: 0.629

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.9623063A>G [0/1] rs989883917 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: YWHAQ:ENST00000238081.8:c.294+7096T>C:p.(=); YWHAQ:ENST00000381844.8:c.294+7096T>C:p.(=)

Pathogenicity Data:: Best Score: 0.63008666; CADD: 0.630 (4.319)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.091

Phenotype Score: 0.504

Variant Score: 0.626

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.9623063A>G [0/1] rs989883917 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: YWHAQ:ENST00000238081.8:c.294+7096T>C:p.(=); YWHAQ:ENST00000381844.8:c.294+7096T>C:p.(=)

Pathogenicity Data:: Best Score: 0.63008666; CADD: 0.630 (4.319)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_NFE: 0.0133%

REGULATORY_REGION_VARIANT chr2:g.10013064G>T [0|1] rs796973306 (variation viewer)

Variant score: 0.624 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.62372965; CADD: 0.624 (4.245)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.9597985A>ATT [1/1] rs547582835 (variation viewer)

Variant score: 0.194

Transcripts:: YWHAQ:ENST00000238081.8:c.295-6471_295-6470insAA:p.(=); YWHAQ:ENST00000381844.8:c.295-6471_295-6470insAA:p.(=)

Pathogenicity Data:: Best Score: 0.19387943; CADD: 0.194 (0.936)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.9593923T>C [0/1] rs200469658 (variation viewer)

Variant score: 0.101

Transcripts:: YWHAQ:ENST00000238081.8:c.295-2408A>G:p.(=); YWHAQ:ENST00000381844.8:c.295-2408A>G:p.(=)

Pathogenicity Data:: Best Score: 0.100916564; CADD: 0.101 (0.462)

Frequency Data:: No frequency data

ADH1A

Exomiser Score: 0.093

Phenotype Score: 0.505

Variant Score: 0.628

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.093

Phenotype Score: 0.505

Variant Score: 0.628

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99288785G>A [0/1] rs898848734 (variation viewer)

Variant score: 0.628 CONTRIBUTING VARIANT

Transcripts:: ADH1A:ENST00000209668.3:c.19-1120C>T:p.(=)

Pathogenicity Data:: Best Score: 0.62786543; CADD: 0.628 (4.293)

Frequency Data:: No frequency data

Other passed variants:

COX7A2

Exomiser Score: 0.093

Phenotype Score: 0.503

Variant Score: 0.629

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.093

Phenotype Score: 0.503

Variant Score: 0.629

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.75231725G>A [0/1]

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: COX7A2:ENST00000370081.6::

Pathogenicity Data:: Best Score: 0.6294046; CADD: 0.629 (4.311)

Frequency Data:: No frequency data

Other passed variants:

CDH1

Exomiser Score: 0.092

Phenotype Score: 0.509

Variant Score: 0.622

Phenotype matches:

Proximity score 0.509 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:114480 Breast cancer, lobular (susceptibility); OMIM:119580 Blepharocheilodontic syndrome 1 - autosomal dominant; OMIM:137215 Gastric cancer, hereditary diffuse, with or without cleft lip and/or palate - autosomal dominant; OMIM:167000 Ovarian cancer, somatic - autosomal dominant; OMIM:176807 Prostate cancer, susceptibility to (susceptibility); OMIM:608089 Endometrial carcinoma, somatic - autosomal dominant; ORPHA:199306 Cleft lip/palate; ORPHA:1997 Blepharo-cheilo-odontic syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.092

Phenotype Score: 0.509

Variant Score: 0.622

Variants contributing to score:

INTERGENIC_VARIANT chr16:g.68731447C>T [0|1] rs1009731214 (variation viewer)

Variant score: 0.622 CONTRIBUTING VARIANT

Transcripts:: CDH1:ENST00000612417.4::; CDH1:ENST00000264012.9::

Pathogenicity Data:: Best Score: 0.6218188; CADD: 0.622 (4.223)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.014

Phenotype Score: 0.255

Variant Score: 0.699

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68814616A>G [0/1] rs148794150 (variation viewer)

Variant score: 0.777 CONTRIBUTING VARIANT

Transcripts:: CDH1:ENST00000261769.10:c.1321-899A>G:p.(=); CDH1:ENST00000422392.6:c.1138-899A>G:p.(=); CDH1:ENST00000611625.4:c.1384-899A>G:p.(=); CDH1:ENST00000612417.4:c.1321-899A>G:p.(=); CDH1:ENST00000621016.4:c.1321-899A>G:p.(=)

Pathogenicity Data:: Best Score: 0.824975; CADD: 0.825 (7.569)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.1035%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.3597%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1136%

INTERGENIC_VARIANT chr16:g.68731447C>T [0|1] rs1009731214 (variation viewer)

Variant score: 0.622 CONTRIBUTING VARIANT

Transcripts:: CDH1:ENST00000612417.4::; CDH1:ENST00000264012.9::

Pathogenicity Data:: Best Score: 0.6218188; CADD: 0.622 (4.223)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr16:g.68731423C>T [0|1] rs56313732 (variation viewer)

Variant score: 0.611

Transcripts:: CDH1:ENST00000612417.4::; CDH1:ENST00000264012.9::

Pathogenicity Data:: Best Score: 0.611313; CADD: 0.611 (4.104)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68804102CT>C [1/1] rs10563852 (variation viewer)

Variant score: 0.570

Transcripts:: CDH1:ENST00000261769.10:c.387+2210del:p.(=); CDH1:ENST00000422392.6:c.387+2210del:p.(=); CDH1:ENST00000611625.4:c.387+2210del:p.(=); CDH1:ENST00000612417.4:c.387+2210del:p.(=); CDH1:ENST00000621016.4:c.387+2210del:p.(=)

Pathogenicity Data:: Best Score: 0.56957257; CADD: 0.570 (3.661)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr16:g.68731421C>T [0|1] rs56065730 (variation viewer)

Variant score: 0.363

Transcripts:: CDH1:ENST00000612417.4::; CDH1:ENST00000264012.9::

Pathogenicity Data:: Best Score: 0.5976537; CADD: 0.598 (3.954)

Frequency Data:: gnomAD_G_AFR: 1.3605%; gnomAD_G_AMR: 1.1628%; gnomAD_G_EAS: 0.2976%; gnomAD_G_NFE: 1.1771%

INTERGENIC_VARIANT chr16:g.68718741T>A [0/1] rs144847760 (variation viewer)

Variant score: 0.352

Transcripts:: CDH1:ENST00000612417.4::; CDH1:ENST00000264012.9::

Pathogenicity Data:: Best Score: 0.5612673; CADD: 0.561 (3.578)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1171%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.0933%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68755282CAA>C [0/1] rs1188775959 (variation viewer)

Variant score: 0.257

Transcripts:: CDH1:ENST00000261769.10:c.163+16872_163+16873del:p.(=); CDH1:ENST00000422392.6:c.163+16872_163+16873del:p.(=); CDH1:ENST00000611625.4:c.163+16872_163+16873del:p.(=); CDH1:ENST00000612417.4:c.163+16872_163+16873del:p.(=); CDH1:ENST00000621016.4:c.163+16872_163+16873del:p.(=)

Pathogenicity Data:: Best Score: 0.25732297; CADD: 0.257 (1.292)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68777534C>CT [0/1] rs71148949 (variation viewer)

Variant score: 0.242

Transcripts:: CDH1:ENST00000261769.10:c.164-24136_164-24135insT:p.(=); CDH1:ENST00000422392.6:c.164-24136_164-24135insT:p.(=); CDH1:ENST00000611625.4:c.164-24136_164-24135insT:p.(=); CDH1:ENST00000612417.4:c.164-24136_164-24135insT:p.(=); CDH1:ENST00000621016.4:c.164-24136_164-24135insT:p.(=)

Pathogenicity Data:: Best Score: 0.24159706; CADD: 0.242 (1.201)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68762912CAAAA>C [1/1] rs55899466 (variation viewer)

Variant score: 0.111

Transcripts:: CDH1:ENST00000261769.10:c.163+24502_163+24505del:p.(=); CDH1:ENST00000422392.6:c.163+24502_163+24505del:p.(=); CDH1:ENST00000611625.4:c.163+24502_163+24505del:p.(=); CDH1:ENST00000612417.4:c.163+24502_163+24505del:p.(=); CDH1:ENST00000621016.4:c.163+24502_163+24505del:p.(=)

Pathogenicity Data:: Best Score: 0.11141288; CADD: 0.111 (0.513)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68745550A>AAATATATATATATATG [0/1] rs71253605 (variation viewer)

Variant score: 0.110

Transcripts:: CDH1:ENST00000261769.10:c.163+7139_163+7140insAATATATATATATATG:p.(=); CDH1:ENST00000422392.6:c.163+7139_163+7140insAATATATATATATATG:p.(=); CDH1:ENST00000611625.4:c.163+7139_163+7140insAATATATATATATATG:p.(=); CDH1:ENST00000612417.4:c.163+7139_163+7140insAATATATATATATATG:p.(=); CDH1:ENST00000621016.4:c.163+7139_163+7140insAATATATATATATATG:p.(=)

Pathogenicity Data:: Best Score: 0.10997951; CADD: 0.110 (0.506)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr16:g.68721814G>A [0/1] rs145091935 (variation viewer)

Variant score: 0.108

Transcripts:: CDH1:ENST00000612417.4::; CDH1:ENST00000264012.9::

Pathogenicity Data:: Best Score: 0.17262954; CADD: 0.173 (0.823)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.1163%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.0933%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.68758207CTTTTTTT>C [0/1] rs57413297 (variation viewer)

Variant score: 0.090

Transcripts:: CDH1:ENST00000261769.10:c.163+19797_163+19803del:p.(=); CDH1:ENST00000422392.6:c.163+19797_163+19803del:p.(=); CDH1:ENST00000611625.4:c.163+19797_163+19803del:p.(=); CDH1:ENST00000612417.4:c.163+19797_163+19803del:p.(=); CDH1:ENST00000621016.4:c.163+19797_163+19803del:p.(=)

Pathogenicity Data:: Best Score: 0.08987719; CADD: 0.090 (0.409)

Frequency Data:: No frequency data

PRKAR1B

Exomiser Score: 0.091

Phenotype Score: 0.507

Variant Score: 0.622

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.015

Phenotype Score: 0.507

Variant Score: 0.418

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.587516C>T [0/1] rs1185848590 (variation viewer)

Variant score: 0.418 CONTRIBUTING VARIANT

Transcripts:: PRKAR1B:ENST00000360274.8:c.709-2948G>A:p.(=); PRKAR1B:ENST00000403562.5:c.709-2948G>A:p.(=); PRKAR1B:ENST00000406797.5:c.709-2948G>A:p.(=); PRKAR1B:ENST00000537384.6:c.709-2948G>A:p.(=); PRKAR1B:ENST00000544935.5:c.709-2948G>A:p.(=)

Pathogenicity Data:: Best Score: 0.41789675; CADD: 0.418 (2.350)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.091

Phenotype Score: 0.507

Variant Score: 0.622

Variants contributing to score:

REGULATORY_REGION_VARIANT chr7:g.538246G>A [0/1] rs536875175 (variation viewer)

Variant score: 0.826 CONTRIBUTING VARIANT

Transcripts:: PRKAR1B:ENST00000544935.5::; PRKAR1B:ENST00000402802.7::

Pathogenicity Data:: Best Score: 0.87264967; CADD: 0.873 (8.950)

Frequency Data:: TOPMed: 0.0215%; gnomAD_G_AFR: 0.0694%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0135%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.587516C>T [0/1] rs1185848590 (variation viewer)

Variant score: 0.418 CONTRIBUTING VARIANT

Transcripts:: PRKAR1B:ENST00000360274.8:c.709-2948G>A:p.(=); PRKAR1B:ENST00000403562.5:c.709-2948G>A:p.(=); PRKAR1B:ENST00000406797.5:c.709-2948G>A:p.(=); PRKAR1B:ENST00000537384.6:c.709-2948G>A:p.(=); PRKAR1B:ENST00000544935.5:c.709-2948G>A:p.(=)

Pathogenicity Data:: Best Score: 0.41789675; CADD: 0.418 (2.350)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr7:g.547723A>G [0/1] rs182548244 (variation viewer)

Variant score: 0.332

Transcripts:: PRKAR1B:ENST00000544935.5::; PRKAR1B:ENST00000402802.7::

Pathogenicity Data:: Best Score: 0.5302141; CADD: 0.530 (3.281)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.7733%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1730%; gnomAD_G_AMR: 0.4902%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.7353%; gnomAD_G_NFE: 0.9987%; gnomAD_G_OTH: 0.8197%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.703999G>A [0/1]

Variant score: 0.255

Transcripts:: PRKAR1B:ENST00000360274.8:c.177+7330C>T:p.(=); PRKAR1B:ENST00000403562.5:c.177+7330C>T:p.(=); PRKAR1B:ENST00000406797.5:c.177+7330C>T:p.(=); PRKAR1B:ENST00000537384.6:c.177+7330C>T:p.(=); PRKAR1B:ENST00000544935.5:c.177+7330C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2547534; CADD: 0.255 (1.277)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.556118G>C [0/1] rs28649270 (variation viewer)

Variant score: 0.231

Transcripts:: PRKAR1B:ENST00000360274.8:c.892-4648C>G:p.(=); PRKAR1B:ENST00000403562.5:c.892-4648C>G:p.(=); PRKAR1B:ENST00000406797.5:c.892-4648C>G:p.(=); PRKAR1B:ENST00000537384.6:c.892-4648C>G:p.(=); PRKAR1B:ENST00000544935.5:c.892-4648C>G:p.(=)

Pathogenicity Data:: Best Score: 0.41883427; CADD: 0.419 (2.357)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.3393%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.1196%; gnomAD_G_FIN: 1.4605%; gnomAD_G_NFE: 0.6011%; gnomAD_G_OTH: 1.0204%

FIVE_PRIME_UTR_INTRON_VARIANT chr7:g.714149C>G [0/1] rs1057295395 (variation viewer)

Variant score: 0.202

Transcripts:: PRKAR1B:ENST00000403562.5:c.-22-2622G>C:p.(=); PRKAR1B:ENST00000537384.6:c.-22-2622G>C:p.(=)

Pathogenicity Data:: Best Score: 0.20163774; CADD: 0.202 (0.978)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.563282C>T [0/1] rs188846749 (variation viewer)

Variant score: 0.117

Transcripts:: PRKAR1B:ENST00000360274.8:c.892-11812G>A:p.(=); PRKAR1B:ENST00000403562.5:c.892-11812G>A:p.(=); PRKAR1B:ENST00000406797.5:c.892-11812G>A:p.(=); PRKAR1B:ENST00000537384.6:c.892-11812G>A:p.(=); PRKAR1B:ENST00000544935.5:c.892-11812G>A:p.(=)

Pathogenicity Data:: Best Score: 0.21222901; CADD: 0.212 (1.036)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.2811%; UK10K: 0.4099%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 1.4596%; gnomAD_G_NFE: 0.4937%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.706422A>ATTTTTTTTTTTTT [1/1] rs33963335 (variation viewer)

Variant score: 0.089

Transcripts:: PRKAR1B:ENST00000360274.8:c.177+4906_177+4907insAAAAAAAAAAAAA:p.(=); PRKAR1B:ENST00000403562.5:c.177+4906_177+4907insAAAAAAAAAAAAA:p.(=); PRKAR1B:ENST00000406797.5:c.177+4906_177+4907insAAAAAAAAAAAAA:p.(=); PRKAR1B:ENST00000537384.6:c.177+4906_177+4907insAAAAAAAAAAAAA:p.(=); PRKAR1B:ENST00000544935.5:c.177+4906_177+4907insAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.582132C>G [0/1] rs28439657 (variation viewer)

Variant score: 0.038

Transcripts:: PRKAR1B:ENST00000360274.8:c.769+2376G>C:p.(=); PRKAR1B:ENST00000403562.5:c.769+2376G>C:p.(=); PRKAR1B:ENST00000406797.5:c.769+2376G>C:p.(=); PRKAR1B:ENST00000537384.6:c.769+2376G>C:p.(=); PRKAR1B:ENST00000544935.5:c.769+2376G>C:p.(=)

Pathogenicity Data:: Best Score: 0.08588678; CADD: 0.086 (0.390)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.2724%; UK10K: 0.3570%; gnomAD_G_AFR: 0.0804%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 1.6342%; gnomAD_G_NFE: 0.4674%; gnomAD_G_OTH: 1.0183%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.566170T>TCACCATCATCACCATCACTATCACCATCACCATCCTCACCATCACCTTCATCATCACCATCTTCACCATATCATCATCACCTCCACCATCACCACCAC [0/1]

Variant score: 0.000

Transcripts:: PRKAR1B:ENST00000360274.8:c.891+13085_891+13086insGTGGTGGTGATGGTGGAGGTGATGATGATATGGTGAAGATGGTGATGATGAAGGTGATGGTGAGGATGGTGATGGTGATAGTGATGGTGATGATGGTG:p.(=); PRKAR1B:ENST00000403562.5:c.891+13085_891+13086insGTGGTGGTGATGGTGGAGGTGATGATGATATGGTGAAGATGGTGATGATGAAGGTGATGGTGAGGATGGTGATGGTGATAGTGATGGTGATGATGGTG:p.(=); PRKAR1B:ENST00000406797.5:c.891+13085_891+13086insGTGGTGGTGATGGTGGAGGTGATGATGATATGGTGAAGATGGTGATGATGAAGGTGATGGTGAGGATGGTGATGGTGATAGTGATGGTGATGATGGTG:p.(=); PRKAR1B:ENST00000537384.6:c.891+13085_891+13086insGTGGTGGTGATGGTGGAGGTGATGATGATATGGTGAAGATGGTGATGATGAAGGTGATGGTGAGGATGGTGATGGTGATAGTGATGGTGATGATGGTG:p.(=); PRKAR1B:ENST00000544935.5:c.891+13085_891+13086insGTGGTGGTGATGGTGGAGGTGATGATGATATGGTGAAGATGGTGATGATGAAGGTGATGGTGAGGATGGTGATGGTGATAGTGATGGTGATGATGGTG:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.640809G>* [-/1]

Variant score: 0.000

Transcripts:: PRKAR1B:ENST00000360274.8:c.441-33357C>:p.(=); PRKAR1B:ENST00000403562.5:c.441-33357C>:p.(=); PRKAR1B:ENST00000406797.5:c.441-33357C>:p.(=); PRKAR1B:ENST00000537384.6:c.441-33357C>:p.(=); PRKAR1B:ENST00000544935.5:c.441-33357C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CREBBP

Exomiser Score: 0.090

Phenotype Score: 0.515

Variant Score: 0.611

Phenotype matches:

Phenotypic similarity 0.515 to Rubinstein-Taybi syndrome 1 associated with CREBBP.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000756, Agoraphobia

Phenotypic similarity 0.436 to mouse mutant involving CREBBP.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:180849 Rubinstein-Taybi syndrome 1 - autosomal dominant; OMIM:618332 Menke-Hennekam syndrome 1 - autosomal dominant; ORPHA:353277 Rubinstein-Taybi syndrome due to CREBBP mutations; ORPHA:353281 Rubinstein-Taybi syndrome due to 16p13.3 microdeletion

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.090

Phenotype Score: 0.515

Variant Score: 0.611

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3823957A>AACACACACAC [-/1] rs57902688 (variation viewer)

Variant score: 0.611 CONTRIBUTING VARIANT

Transcripts:: CREBBP:ENST00000262367.10:c.799-13179_799-13178insGTGTGTGTGT:p.(=); CREBBP:ENST00000382070.7:c.799-13179_799-13178insGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.6114025; CADD: 0.611 (4.105)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.258

Variant Score: 0.584

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3823957A>AACACACACAC [-/1] rs57902688 (variation viewer)

Variant score: 0.611 CONTRIBUTING VARIANT

Transcripts:: CREBBP:ENST00000262367.10:c.799-13179_799-13178insGTGTGTGTGT:p.(=); CREBBP:ENST00000382070.7:c.799-13179_799-13178insGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.6114025; CADD: 0.611 (4.105)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3758176A>C [0/1] rs111436750 (variation viewer)

Variant score: 0.557 CONTRIBUTING VARIANT

Transcripts:: CREBBP:ENST00000262367.10:c.3370-128T>G:p.(=); CREBBP:ENST00000382070.7:c.3256-128T>G:p.(=)

Pathogenicity Data:: Best Score: 0.8889291; CADD: 0.889 (9.544)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.6944%; UK10K: 0.7538%; gnomAD_G_AFR: 0.4926%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 1.0507%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 0.5396%; gnomAD_G_OTH: 0.2037%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3859834C>T [0/1] rs117310981 (variation viewer)

Variant score: 0.457

Transcripts:: CREBBP:ENST00000262367.10:c.86-8825G>A:p.(=); CREBBP:ENST00000382070.7:c.86-8825G>A:p.(=)

Pathogenicity Data:: Best Score: 0.72991526; CADD: 0.730 (5.685)

Frequency Data:: 1000Genomes: 0.7388%; TOPMed: 0.6459%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1380%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 1.0533%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5404%; gnomAD_G_OTH: 0.3067%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3769110G>A [0/1]

Variant score: 0.446

Transcripts:: CREBBP:ENST00000262367.10:c.3060+64C>T:p.(=); CREBBP:ENST00000382070.7:c.2946+64C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4462675; CADD: 0.446 (2.567)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3834482G>A [0/1] rs374660224 (variation viewer)

Variant score: 0.443

Transcripts:: CREBBP:ENST00000262367.10:c.798+15815C>T:p.(=); CREBBP:ENST00000382070.7:c.798+15815C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7073827; CADD: 0.707 (5.337)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6299%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1374%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9877%; gnomAD_G_FIN: 0.2862%; gnomAD_G_NFE: 0.5264%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3870798C>T [0/1] rs76315434 (variation viewer)

Variant score: 0.438

Transcripts:: CREBBP:ENST00000262367.10:c.85+9034G>A:p.(=); CREBBP:ENST00000382070.7:c.85+9034G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6999456; CADD: 0.700 (5.228)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 0.6451%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9901%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5399%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3762016A>G [0/1] rs75897959 (variation viewer)

Variant score: 0.434

Transcripts:: CREBBP:ENST00000262367.10:c.3251-3044T>C:p.(=); CREBBP:ENST00000382070.7:c.3137-3044T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6934509; CADD: 0.693 (5.135)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.6212%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9248%; gnomAD_G_FIN: 0.2290%; gnomAD_G_NFE: 0.5462%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3803261GGGGA>G [1/1] rs200371758 (variation viewer)

Variant score: 0.369

Transcripts:: CREBBP:ENST00000262367.10:c.975+7338_975+7341del:p.(=); CREBBP:ENST00000382070.7:c.975+7338_975+7341del:p.(=)

Pathogenicity Data:: Best Score: 0.43049175; CADD: 0.430 (2.445)

Frequency Data:: gnomAD_G_AFR: 0.4630%; gnomAD_G_EAS: 0.7246%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3837074A>C [0/1] rs145323052 (variation viewer)

Variant score: 0.346

Transcripts:: CREBBP:ENST00000262367.10:c.798+13223T>G:p.(=); CREBBP:ENST00000382070.7:c.798+13223T>G:p.(=)

Pathogenicity Data:: Best Score: 0.55259585; CADD: 0.553 (3.493)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6252%; UK10K: 0.7802%; gnomAD_G_AFR: 0.1378%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2295%; gnomAD_G_NFE: 0.5203%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3868543T>TA [0/1] rs202165384 (variation viewer)

Variant score: 0.330

Transcripts:: CREBBP:ENST00000262367.10:c.85+11288_85+11289insT:p.(=); CREBBP:ENST00000382070.7:c.85+11288_85+11289insT:p.(=)

Pathogenicity Data:: Best Score: 0.5302141; CADD: 0.530 (3.281)

Frequency Data:: gnomAD_G_AFR: 0.5330%; gnomAD_G_AMR: 0.3667%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.9913%; gnomAD_G_FIN: 0.2138%; gnomAD_G_NFE: 0.5364%; gnomAD_G_OTH: 0.4184%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3864796G>C [0/1] rs146403620 (variation viewer)

Variant score: 0.326

Transcripts:: CREBBP:ENST00000262367.10:c.86-13787C>G:p.(=); CREBBP:ENST00000382070.7:c.86-13787C>G:p.(=)

Pathogenicity Data:: Best Score: 0.5211494; CADD: 0.521 (3.198)

Frequency Data:: 1000Genomes: 0.7588%; TOPMed: 0.6777%; UK10K: 0.8331%; gnomAD_G_AFR: 0.2404%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5399%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3835492C>T [0/1] rs78727550 (variation viewer)

Variant score: 0.324

Transcripts:: CREBBP:ENST00000262367.10:c.798+14805G>A:p.(=); CREBBP:ENST00000382070.7:c.798+14805G>A:p.(=)

Pathogenicity Data:: Best Score: 0.51749706; CADD: 0.517 (3.165)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.6236%; UK10K: 0.7802%; gnomAD_G_AFR: 0.1379%; gnomAD_G_AMR: 0.2415%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2380%; gnomAD_G_NFE: 0.5232%; gnomAD_G_OTH: 0.1031%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3851306TA>T [1|1] rs1160251196 (variation viewer)

Variant score: 0.320

Transcripts:: CREBBP:ENST00000262367.10:c.86-298del:p.(=); CREBBP:ENST00000382070.7:c.86-298del:p.(=)

Pathogenicity Data:: Best Score: 0.31985736; CADD: 0.320 (1.674)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3794331CAAAAAAAAAAAAAA>C [1/1] rs746656673 (variation viewer)

Variant score: 0.296

Transcripts:: CREBBP:ENST00000262367.10:c.976-719_976-706del:p.(=); CREBBP:ENST00000382070.7:c.976-719_976-706del:p.(=)

Pathogenicity Data:: Best Score: 0.29563135; CADD: 0.296 (1.522)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3730911C>T [0/1] rs574404451 (variation viewer)

Variant score: 0.263

Transcripts:: CREBBP:ENST00000262367.10:c.5172+281G>A:p.(=); CREBBP:ENST00000382070.7:c.5058+281G>A:p.(=)

Pathogenicity Data:: Best Score: 0.41950297; CADD: 0.420 (2.362)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0916%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_NFE: 0.0800%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3835576C>CT [0/1] rs1021938849 (variation viewer)

Variant score: 0.260

Transcripts:: CREBBP:ENST00000262367.10:c.798+14720_798+14721insA:p.(=); CREBBP:ENST00000382070.7:c.798+14720_798+14721insA:p.(=)

Pathogenicity Data:: Best Score: 0.25971323; CADD: 0.260 (1.306)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3859812T>C [0/1] rs74436605 (variation viewer)

Variant score: 0.256

Transcripts:: CREBBP:ENST00000262367.10:c.86-8803A>G:p.(=); CREBBP:ENST00000382070.7:c.86-8803A>G:p.(=)

Pathogenicity Data:: Best Score: 0.40871072; CADD: 0.409 (2.282)

Frequency Data:: 1000Genomes: 0.8187%; TOPMed: 0.7231%; UK10K: 0.8067%; gnomAD_G_AFR: 0.2955%; gnomAD_G_AMR: 0.2421%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 1.0787%; gnomAD_G_FIN: 0.2301%; gnomAD_G_NFE: 0.5523%; gnomAD_G_OTH: 0.3093%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3790366CTT>C [-/1] rs57582399 (variation viewer)

Variant score: 0.231

Transcripts:: CREBBP:ENST00000262367.10:c.1330+1613_1330+1614del:p.(=); CREBBP:ENST00000382070.7:c.1216+3018_1216+3019del:p.(=)

Pathogenicity Data:: Best Score: 0.23140067; CADD: 0.231 (1.143)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3866836T>C [0/1] rs137957606 (variation viewer)

Variant score: 0.230

Transcripts:: CREBBP:ENST00000262367.10:c.85+12996A>G:p.(=); CREBBP:ENST00000382070.7:c.85+12996A>G:p.(=)

Pathogenicity Data:: Best Score: 0.3674425; CADD: 0.367 (1.989)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 0.6514%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5329%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3790366CT>C [-/1] rs57582399 (variation viewer)

Variant score: 0.221

Transcripts:: CREBBP:ENST00000262367.10:c.1330+1614del:p.(=); CREBBP:ENST00000382070.7:c.1216+3019del:p.(=)

Pathogenicity Data:: Best Score: 0.22106719; CADD: 0.221 (1.085)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3859059A>AT [0/1] rs201630274 (variation viewer)

Variant score: 0.217

Transcripts:: CREBBP:ENST00000262367.10:c.86-8051_86-8050insA:p.(=); CREBBP:ENST00000382070.7:c.86-8051_86-8050insA:p.(=)

Pathogenicity Data:: Best Score: 0.35106683; CADD: 0.351 (1.878)

Frequency Data:: 1000Genomes: 0.8387%; gnomAD_G_AFR: 0.1402%; gnomAD_G_AMR: 0.2488%; gnomAD_G_ASJ: 1.3423%; gnomAD_G_EAS: 1.0652%; gnomAD_G_FIN: 0.2378%; gnomAD_G_NFE: 0.5425%; gnomAD_G_OTH: 0.3125%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3760243T>C [0/1] rs149877289 (variation viewer)

Variant score: 0.205

Transcripts:: CREBBP:ENST00000262367.10:c.3251-1271A>G:p.(=); CREBBP:ENST00000382070.7:c.3137-1271A>G:p.(=)

Pathogenicity Data:: Best Score: 0.3290348; CADD: 0.329 (1.733)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6252%; UK10K: 0.7934%; gnomAD_G_AFR: 0.1379%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.9305%; gnomAD_G_FIN: 0.2295%; gnomAD_G_NFE: 0.5417%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3803167A>T [0/1] rs573556516 (variation viewer)

Variant score: 0.182

Transcripts:: CREBBP:ENST00000262367.10:c.975+7436T>A:p.(=); CREBBP:ENST00000382070.7:c.975+7436T>A:p.(=)

Pathogenicity Data:: Best Score: 0.29335713; CADD: 0.293 (1.508)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0599%; gnomAD_G_AFR: 0.0235%; gnomAD_G_AMR: 0.2410%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_NFE: 0.1210%; gnomAD_G_OTH: 0.1031%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3829958C>G [0/1] rs139509207 (variation viewer)

Variant score: 0.170

Transcripts:: CREBBP:ENST00000262367.10:c.799-19179G>C:p.(=); CREBBP:ENST00000382070.7:c.799-19179G>C:p.(=)

Pathogenicity Data:: Best Score: 0.2720526; CADD: 0.272 (1.379)

Frequency Data:: 1000Genomes: 0.6390%; TOPMed: 0.6283%; UK10K: 0.8199%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.2398%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 1.1714%; gnomAD_G_FIN: 0.2298%; gnomAD_G_NFE: 0.5206%; gnomAD_G_OTH: 0.1025%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3736382G>T [0/1] rs139369782 (variation viewer)

Variant score: 0.162

Transcripts:: CREBBP:ENST00000262367.10:c.4561-179C>A:p.(=); CREBBP:ENST00000382070.7:c.4447-179C>A:p.(=)

Pathogenicity Data:: Best Score: 0.2578358; CADD: 0.258 (1.295)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.1997%; UK10K: 0.3835%; gnomAD_G_AFR: 0.0460%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.3623%; gnomAD_G_OTH: 0.2053%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3776106G>A [0/1] rs143325688 (variation viewer)

Variant score: 0.149

Transcripts:: CREBBP:ENST00000262367.10:c.2159-1413C>T:p.(=); CREBBP:ENST00000382070.7:c.2045-1413C>T:p.(=)

Pathogenicity Data:: Best Score: 0.23949862; CADD: 0.239 (1.189)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 0.6275%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1382%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.9889%; gnomAD_G_FIN: 0.2013%; gnomAD_G_NFE: 0.5296%; gnomAD_G_OTH: 0.2062%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3852153ATTTGTT>A [0/1] rs1269079703 (variation viewer)

Variant score: 0.147

Transcripts:: CREBBP:ENST00000262367.10:c.86-1150_86-1145del:p.(=); CREBBP:ENST00000382070.7:c.86-1150_86-1145del:p.(=)

Pathogenicity Data:: Best Score: 0.22464603; CADD: 0.225 (1.105)

Frequency Data:: gnomAD_G_AFR: 0.8556%; gnomAD_G_AMR: 0.2222%; gnomAD_G_ASJ: 1.2712%; gnomAD_G_EAS: 0.2101%; gnomAD_G_FIN: 0.1661%; gnomAD_G_NFE: 0.3407%; gnomAD_G_OTH: 0.5282%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3835256C>G [0/1] rs190417635 (variation viewer)

Variant score: 0.146

Transcripts:: CREBBP:ENST00000262367.10:c.798+15041G>C:p.(=); CREBBP:ENST00000382070.7:c.798+15041G>C:p.(=)

Pathogenicity Data:: Best Score: 0.2328152; CADD: 0.233 (1.151)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6252%; UK10K: 0.7934%; gnomAD_G_AFR: 0.1380%; gnomAD_G_AMR: 0.2404%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 1.0283%; gnomAD_G_FIN: 0.2024%; gnomAD_G_NFE: 0.5209%; gnomAD_G_OTH: 0.1025%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3759588C>CAAAAAAAAAAAAAAAAAA [0/1] rs879293877 (variation viewer)

Variant score: 0.144

Transcripts:: CREBBP:ENST00000262367.10:c.3251-617_3251-616insTTTTTTTTTTTTTTTTTT:p.(=); CREBBP:ENST00000382070.7:c.3137-617_3137-616insTTTTTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14355397; CADD: 0.144 (0.673)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3864985A>G [0/1] rs149167803 (variation viewer)

Variant score: 0.135

Transcripts:: CREBBP:ENST00000262367.10:c.86-13976T>C:p.(=); CREBBP:ENST00000382070.7:c.86-13976T>C:p.(=)

Pathogenicity Data:: Best Score: 0.21584845; CADD: 0.216 (1.056)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 0.6459%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2298%; gnomAD_G_NFE: 0.5405%; gnomAD_G_OTH: 0.3061%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3831772G>A [0/1] rs192450684 (variation viewer)

Variant score: 0.133

Transcripts:: CREBBP:ENST00000262367.10:c.798+18525C>T:p.(=); CREBBP:ENST00000382070.7:c.798+18525C>T:p.(=)

Pathogenicity Data:: Best Score: 0.21186614; CADD: 0.212 (1.034)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.6642%; UK10K: 0.8199%; gnomAD_G_AFR: 0.2063%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9877%; gnomAD_G_FIN: 0.2294%; gnomAD_G_NFE: 0.5741%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3772915CAA>C [0/1] rs144154476 (variation viewer)

Variant score: 0.126

Transcripts:: CREBBP:ENST00000262367.10:c.2463+834_2463+835del:p.(=); CREBBP:ENST00000382070.7:c.2349+834_2349+835del:p.(=)

Pathogenicity Data:: Best Score: 0.12642539; CADD: 0.126 (0.587)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3838857C>T [0/1] rs74805219 (variation viewer)

Variant score: 0.090

Transcripts:: CREBBP:ENST00000262367.10:c.798+11440G>A:p.(=); CREBBP:ENST00000382070.7:c.798+11440G>A:p.(=)

Pathogenicity Data:: Best Score: 0.14434242; CADD: 0.144 (0.677)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 0.6833%; UK10K: 0.7802%; gnomAD_G_AFR: 0.2751%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 1.0494%; gnomAD_G_FIN: 0.2292%; gnomAD_G_NFE: 0.5198%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3836919C>T [0/1] rs75889363 (variation viewer)

Variant score: 0.088

Transcripts:: CREBBP:ENST00000262367.10:c.798+13378G>A:p.(=); CREBBP:ENST00000382070.7:c.798+13378G>A:p.(=)

Pathogenicity Data:: Best Score: 0.14059079; CADD: 0.141 (0.658)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6236%; UK10K: 0.7934%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5194%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3859338G>A [0/1] rs140368884 (variation viewer)

Variant score: 0.078

Transcripts:: CREBBP:ENST00000262367.10:c.86-8329C>T:p.(=); CREBBP:ENST00000382070.7:c.86-8329C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12562042; CADD: 0.126 (0.583)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 0.7136%; UK10K: 0.8067%; gnomAD_G_AFR: 0.2982%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 1.0494%; gnomAD_G_FIN: 0.2299%; gnomAD_G_NFE: 0.5348%; gnomAD_G_OTH: 0.3067%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3849429GTGTGTGTGTGTGTGTGTGTGTGT>G [1/1] rs540528965 (variation viewer)

Variant score: 0.065

Transcripts:: CREBBP:ENST00000262367.10:c.798+845_798+867del:p.(=); CREBBP:ENST00000382070.7:c.798+845_798+867del:p.(=)

Pathogenicity Data:: Best Score: 0.106077254; CADD: 0.106 (0.487)

Frequency Data:: gnomAD_G_AFR: 0.2796%; gnomAD_G_FIN: 0.6024%; gnomAD_G_NFE: 1.3514%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3860993C>G [0/1] rs143752855 (variation viewer)

Variant score: 0.058

Transcripts:: CREBBP:ENST00000262367.10:c.86-9984G>C:p.(=); CREBBP:ENST00000382070.7:c.86-9984G>C:p.(=)

Pathogenicity Data:: Best Score: 0.09238851; CADD: 0.092 (0.421)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 0.6451%; UK10K: 0.8199%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5264%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.3869894C>G [0/1] rs79337017 (variation viewer)

Variant score: 0.007

Transcripts:: CREBBP:ENST00000262367.10:c.85+9938G>C:p.(=); CREBBP:ENST00000382070.7:c.85+9938G>C:p.(=)

Pathogenicity Data:: Best Score: 0.011446893; CADD: 0.011 (0.050)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.6419%; UK10K: 0.8067%; gnomAD_G_AFR: 0.1261%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.9864%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 0.5328%; gnomAD_G_OTH: 0.3055%

SGMS1

Exomiser Score: 0.088

Phenotype Score: 0.501

Variant Score: 0.625

Phenotype matches:

Proximity score 0.501 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.501

Variant Score: 0.155

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50400396CATATATATATAT>C [-/1] rs10524155 (variation viewer)

Variant score: 0.155 CONTRIBUTING VARIANT

Transcripts:: SGMS1:ENST00000361781.7:c.-232+33068_-232+33079del:p.(=); SGMS1:ENST00000429490.5:c.-232+33068_-232+33079del:p.(=); SGMS1:ENST00000619438.4:c.-232+33068_-232+33079del:p.(=)

Pathogenicity Data:: Best Score: 0.15472114; CADD: 0.155 (0.730)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.088

Phenotype Score: 0.501

Variant Score: 0.625

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50375272A>G [0/1] rs541992677 (variation viewer)

Variant score: 0.656 CONTRIBUTING VARIANT

Transcripts:: SGMS1:ENST00000361781.7:c.-231-30927T>C:p.(=); SGMS1:ENST00000429490.5:c.-231-30927T>C:p.(=); SGMS1:ENST00000619438.4:c.-231-30927T>C:p.(=)

Pathogenicity Data:: Best Score: 0.69260275; CADD: 0.693 (5.123)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1234%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0229%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1532%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50492831C>G [0/1] rs570615776 (variation viewer)

Variant score: 0.594 CONTRIBUTING VARIANT

Transcripts:: SGMS1:ENST00000361781.7:c.-497-25899G>C:p.(=); SGMS1:ENST00000429490.5:c.-497-25899G>C:p.(=); SGMS1:ENST00000619438.4:c.-497-25899G>C:p.(=)

Pathogenicity Data:: Best Score: 0.60608727; CADD: 0.606 (4.046)

Frequency Data:: TOPMed: 0.0836%; UK10K: 0.0793%; gnomAD_G_NFE: 0.1334%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50608772A>G [0/1] rs78309389 (variation viewer)

Variant score: 0.219

Transcripts:: SGMS1:ENST00000361781.7:c.-684+14935T>C:p.(=); SGMS1:ENST00000429490.5:c.-684+14935T>C:p.(=); SGMS1:ENST00000619438.4:c.-684+14935T>C:p.(=)

Pathogenicity Data:: Best Score: 0.22482455; CADD: 0.225 (1.106)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0900%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0229%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.1000%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50469627C>T [0/1] rs182059735 (variation viewer)

Variant score: 0.178

Transcripts:: SGMS1:ENST00000361781.7:c.-497-2695G>A:p.(=); SGMS1:ENST00000429490.5:c.-497-2695G>A:p.(=); SGMS1:ENST00000619438.4:c.-497-2695G>A:p.(=)

Pathogenicity Data:: Best Score: 0.18172365; CADD: 0.182 (0.871)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0892%; UK10K: 0.0793%; gnomAD_G_EAS: 0.0618%; gnomAD_G_NFE: 0.1333%; gnomAD_G_OTH: 0.1018%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50379440A>T [0/1] rs547206653 (variation viewer)

Variant score: 0.119

Transcripts:: SGMS1:ENST00000361781.7:c.-231-35095T>A:p.(=); SGMS1:ENST00000429490.5:c.-231-35095T>A:p.(=); SGMS1:ENST00000619438.4:c.-231-35095T>A:p.(=)

Pathogenicity Data:: Best Score: 0.126023; CADD: 0.126 (0.585)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.3393%; UK10K: 0.3174%; gnomAD_G_AFR: 0.1657%; gnomAD_G_AMR: 0.1359%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_NFE: 0.3633%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50347786T>C [0/1] rs141099634 (variation viewer)

Variant score: 0.044

Transcripts:: SGMS1:ENST00000361781.7:c.-231-3441A>G:p.(=); SGMS1:ENST00000429490.5:c.-231-3441A>G:p.(=); SGMS1:ENST00000619438.4:c.-231-3441A>G:p.(=)

Pathogenicity Data:: Best Score: 0.055286765; CADD: 0.055 (0.247)

Frequency Data:: 1000Genomes: 0.9385%; TOPMed: 0.3743%; UK10K: 0.2909%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 0.1233%; gnomAD_G_FIN: 0.3436%; gnomAD_G_NFE: 0.4733%; gnomAD_G_OTH: 0.7128%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50574963G>GTATATATATA [-/1] rs143713324 (variation viewer)

Variant score: 0.042

Transcripts:: SGMS1:ENST00000361781.7:c.-589+15189_-589+15190insTATATATATA:p.(=); SGMS1:ENST00000429490.5:c.-589+15189_-589+15190insTATATATATA:p.(=); SGMS1:ENST00000619438.4:c.-589+15189_-589+15190insTATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.042365015; CADD: 0.042 (0.188)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50574963G>GTATATATATATATATGTGTATATATATATATATATATA [-/1]

Variant score: 0.024

Transcripts:: SGMS1:ENST00000361781.7:c.-589+15189_-589+15190insTATATATATATATATATATACACATATATATATATATA:p.(=); SGMS1:ENST00000429490.5:c.-589+15189_-589+15190insTATATATATATATATATATACACATATATATATATATA:p.(=); SGMS1:ENST00000619438.4:c.-589+15189_-589+15190insTATATATATATATATATATACACATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.024111927; CADD: 0.024 (0.106)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.50346220T>C [0/1] rs565188532 (variation viewer)

Variant score: 0.009

Transcripts:: SGMS1:ENST00000361781.7:c.-231-1875A>G:p.(=); SGMS1:ENST00000429490.5:c.-231-1875A>G:p.(=); SGMS1:ENST00000619438.4:c.-231-1875A>G:p.(=)

Pathogenicity Data:: Best Score: 0.0103081465; CADD: 0.010 (0.045)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0382%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0400%

UGT2B17

Exomiser Score: 0.088

Phenotype Score: 0.505

Variant Score: 0.621

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.088

Phenotype Score: 0.505

Variant Score: 0.621

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.68564294A>T [1/1] rs74889273 (variation viewer)

Variant score: 0.621 CONTRIBUTING VARIANT

Transcripts:: UGT2B17:ENST00000317746.2:c.873+1278T>A:p.(=)

Pathogenicity Data:: Best Score: 0.6208596; CADD: 0.621 (4.212)

Frequency Data:: No frequency data

Other passed variants:

H4C8

Exomiser Score: 0.084

Phenotype Score: 0.502

Variant Score: 0.618

Phenotype matches:

Proximity score 0.502 in interactome to HIRA and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with HIRA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.084

Phenotype Score: 0.502

Variant Score: 0.618

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.26295551C>T [0/1]

Variant score: 0.618 CONTRIBUTING VARIANT

Transcripts:: H4C8:ENST00000635491.1::; H4C8:ENST00000404612.1::

Pathogenicity Data:: Best Score: 0.61840737; CADD: 0.618 (4.184)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.009

Phenotype Score: 0.502

Variant Score: 0.366

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.26295551C>T [0/1]

Variant score: 0.618 CONTRIBUTING VARIANT

Transcripts:: H4C8:ENST00000635491.1::; H4C8:ENST00000404612.1::

Pathogenicity Data:: Best Score: 0.61840737; CADD: 0.618 (4.184)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.26290331G>A [0/1] rs762832906 (variation viewer)

Variant score: 0.113 CONTRIBUTING VARIANT

Transcripts:: H4C8:ENST00000635491.1::; H4C8:ENST00000404612.1::

Pathogenicity Data:: Best Score: 0.11386478; CADD: 0.114 (0.525)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr6:g.26276547AGGTGAAAGAATATGAGAAGCATCGTGGGCAGGAAGGTCTCTCTGATTTTTCCCAACTCTTCTCCCCTGAAACAGGTCATAGGACCCTCATG>A [0/1]

Variant score: 0.000

Transcripts:: H4C8:ENST00000635491.1::; H4C8:ENST00000377733.3::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr6:g.26276572T>* [-/1]

Variant score: 0.000

Transcripts:: H4C8:ENST00000635491.1::; H4C8:ENST00000377733.3::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr6:g.26286612C>* [-/1]

Variant score: 0.000

Transcripts:: H4C8:ENST00000635491.1::; H4C8:ENST00000404612.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MAOB

Exomiser Score: 0.083

Phenotype Score: 0.505

Variant Score: 0.614

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.083

Phenotype Score: 0.505

Variant Score: 0.614

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43834309C>T [1/1]

Variant score: 0.614 CONTRIBUTING VARIANT

Transcripts:: MAOB:ENST00000378069.5:c.279+4559G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6138998; CADD: 0.614 (4.133)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.083

Phenotype Score: 0.505

Variant Score: 0.614

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43834309C>T [1/1]

Variant score: 0.614 CONTRIBUTING VARIANT

Transcripts:: MAOB:ENST00000378069.5:c.279+4559G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6138998; CADD: 0.614 (4.133)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43840478G>A [1/1] rs757887815 (variation viewer)

Variant score: 0.554

Transcripts:: MAOB:ENST00000378069.5:c.142-1473C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5692751; CADD: 0.569 (3.658)

Frequency Data:: 1000Genomes: 0.1854%; TOPMed: 0.0072%; UK10K: 0.0303%; gnomAD_G_AFR: 0.0171%; gnomAD_G_OTH: 0.1393%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43810899A>C [1/1] rs148151091 (variation viewer)

Variant score: 0.105

Transcripts:: MAOB:ENST00000378069.5:c.280-7495T>G:p.(=)

Pathogenicity Data:: Best Score: 0.14689988; CADD: 0.147 (0.690)

Frequency Data:: 1000Genomes: 0.2119%; TOPMed: 0.2254%; UK10K: 0.5609%; gnomAD_G_AFR: 0.0679%; gnomAD_G_FIN: 1.1407%; gnomAD_G_NFE: 0.3296%; gnomAD_G_OTH: 0.6916%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43857114TATAGAGAGAGAGAGAGAG>T [1/1] rs1211229523 (variation viewer)

Variant score: 0.085

Transcripts:: MAOB:ENST00000378069.5:c.47-13368_47-13351del:p.(=)

Pathogenicity Data:: Best Score: 0.08504444; CADD: 0.085 (0.386)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.43791822C>T [1/1] rs760423371 (variation viewer)

Variant score: 0.043

Transcripts:: MAOB:ENST00000378069.5:c.928+1597G>A:p.(=)

Pathogenicity Data:: Best Score: 0.060276687; CADD: 0.060 (0.270)

Frequency Data:: 1000Genomes: 0.2119%; TOPMed: 0.2222%; UK10K: 0.5609%; gnomAD_G_AFR: 0.0506%; gnomAD_G_FIN: 1.1310%; gnomAD_G_NFE: 0.3317%; gnomAD_G_OTH: 0.8345%

COPB2

Exomiser Score: 0.082

Phenotype Score: 0.505

Variant Score: 0.613

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617800 ?Microcephaly 19, primary, autosomal recessive (unconfirmed); ORPHA:2512 Autosomal recessive primary microcephaly

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.082

Phenotype Score: 0.505

Variant Score: 0.613

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.139377022T>C [0/1] rs560985288 (variation viewer)

Variant score: 0.739 CONTRIBUTING VARIANT

Transcripts:: COPB2:ENST00000333188.10:c.504+1019A>G:p.(=); COPB2:ENST00000507777.5:c.417+1019A>G:p.(=)

Pathogenicity Data:: Best Score: 0.7666542; CADD: 0.767 (6.320)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0072%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.0133%

DOWNSTREAM_GENE_VARIANT chr3:g.139357162G>A [0/1] rs536270749 (variation viewer)

Variant score: 0.487 CONTRIBUTING VARIANT

Transcripts:: COPB2:ENST00000333188.10::

Pathogenicity Data:: Best Score: 0.5059169; CADD: 0.506 (3.062)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0271%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.0400%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.139380003CTTTTTT>C [1/1] rs869062825 (variation viewer)

Variant score: 0.115

Transcripts:: COPB2:ENST00000333188.10:c.142-543_142-538del:p.(=); COPB2:ENST00000507777.5:c.55-543_55-538del:p.(=)

Pathogenicity Data:: Best Score: 0.11488438; CADD: 0.115 (0.530)

Frequency Data:: No frequency data

CDK2

Exomiser Score: 0.078

Phenotype Score: 0.510

Variant Score: 0.600

Phenotype matches:

Proximity score 0.510 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.078

Phenotype Score: 0.510

Variant Score: 0.600

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr12:g.55972298A>G [0/1] rs905571241 (variation viewer)

Variant score: 0.600 CONTRIBUTING VARIANT

Transcripts:: CDK2:ENST00000266970.9:c.*673A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6009751; CADD: 0.601 (3.990)

Frequency Data:: TOPMed: 0.0096%; gnomAD_G_NFE: 0.0133%

Other passed variants:

FAF1

Exomiser Score: 0.074

Phenotype Score: 0.505

Variant Score: 0.600

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.074

Phenotype Score: 0.505

Variant Score: 0.600

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50812033C>A [0/1] rs541164667 (variation viewer)

Variant score: 0.600 CONTRIBUTING VARIANT

Transcripts:: FAF1:ENST00000371778.5:c.91-10356G>T:p.(=); FAF1:ENST00000396153.7:c.115-10356G>T:p.(=)

Pathogenicity Data:: Best Score: 0.6009751; CADD: 0.601 (3.990)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.045

Phenotype Score: 0.505

Variant Score: 0.544

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50812033C>A [0/1] rs541164667 (variation viewer)

Variant score: 0.600 CONTRIBUTING VARIANT

Transcripts:: FAF1:ENST00000371778.5:c.91-10356G>T:p.(=); FAF1:ENST00000396153.7:c.115-10356G>T:p.(=)

Pathogenicity Data:: Best Score: 0.6009751; CADD: 0.601 (3.990)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50607766CCAGTGA>C [0/1] rs535203098 (variation viewer)

Variant score: 0.487 CONTRIBUTING VARIANT

Transcripts:: FAF1:ENST00000371778.5:c.539-24108_539-24103del:p.(=); FAF1:ENST00000396153.7:c.745-11556_745-11551del:p.(=)

Pathogenicity Data:: Best Score: 0.5326954; CADD: 0.533 (3.304)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3042%; UK10K: 0.4099%; gnomAD_G_AFR: 0.0458%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4868%; gnomAD_G_NFE: 0.3796%; gnomAD_G_OTH: 0.2037%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50723412A>T [0|1] rs550001910 (variation viewer)

Variant score: 0.443

Transcripts:: FAF1:ENST00000371778.5:c.527+15451T>A:p.(=); FAF1:ENST00000396153.7:c.551+15451T>A:p.(=)

Pathogenicity Data:: Best Score: 0.5976537; CADD: 0.598 (3.954)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1035%; gnomAD_G_AFR: 0.2069%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.0669%; gnomAD_G_NFE: 0.0603%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50769870G>A [0/1] rs188071745 (variation viewer)

Variant score: 0.184

Transcripts:: FAF1:ENST00000371778.5:c.343+18130C>T:p.(=); FAF1:ENST00000396153.7:c.367+18130C>T:p.(=)

Pathogenicity Data:: Best Score: 0.20567179; CADD: 0.206 (1.000)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3791%; UK10K: 0.5819%; gnomAD_G_AFR: 0.0573%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 0.5197%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50606489CTT>C [0/1] rs34498946 (variation viewer)

Variant score: 0.167

Transcripts:: FAF1:ENST00000371778.5:c.539-22827_539-22826del:p.(=); FAF1:ENST00000396153.7:c.745-10275_745-10274del:p.(=)

Pathogenicity Data:: Best Score: 0.16727811; CADD: 0.167 (0.795)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50541462A>G [0/1] rs534590430 (variation viewer)

Variant score: 0.156

Transcripts:: FAF1:ENST00000371778.5:c.789-1734T>C:p.(=); FAF1:ENST00000396153.7:c.1269-1734T>C:p.(=)

Pathogenicity Data:: Best Score: 0.16995811; CADD: 0.170 (0.809)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3018%; UK10K: 0.4232%; gnomAD_G_AFR: 0.0458%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 0.3801%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50457724C>CA [1/1] rs35479561 (variation viewer)

Variant score: 0.147

Transcripts:: FAF1:ENST00000371778.5:c.1390-16202_1390-16201insT:p.(=); FAF1:ENST00000396153.7:c.1870-16202_1870-16201insT:p.(=)

Pathogenicity Data:: Best Score: 0.14689988; CADD: 0.147 (0.690)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50551399T>C [0/1] rs556780909 (variation viewer)

Variant score: 0.144

Transcripts:: FAF1:ENST00000371778.5:c.789-11671A>G:p.(=); FAF1:ENST00000396153.7:c.1269-11671A>G:p.(=)

Pathogenicity Data:: Best Score: 0.14434242; CADD: 0.144 (0.677)

Frequency Data:: TOPMed: 0.0191%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50656971G>A [0/1] rs189638933 (variation viewer)

Variant score: 0.128

Transcripts:: FAF1:ENST00000371778.5:c.538+48910C>T:p.(=); FAF1:ENST00000396153.7:c.658-1443C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14493328; CADD: 0.145 (0.680)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.3783%; UK10K: 0.6215%; gnomAD_G_AFR: 0.0573%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4896%; gnomAD_G_NFE: 0.5132%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50729034C>A [0/1] rs10888705 (variation viewer)

Variant score: 0.108

Transcripts:: FAF1:ENST00000371778.5:c.527+9829G>T:p.(=); FAF1:ENST00000396153.7:c.551+9829G>T:p.(=)

Pathogenicity Data:: Best Score: 0.1081332; CADD: 0.108 (0.497)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50742153T>A [0/1] rs370481238 (variation viewer)

Variant score: 0.105

Transcripts:: FAF1:ENST00000371778.5:c.435+2531A>T:p.(=); FAF1:ENST00000396153.7:c.459+2531A>T:p.(=)

Pathogenicity Data:: Best Score: 0.1280331; CADD: 0.128 (0.595)

Frequency Data:: 1000Genomes: 0.8387%; TOPMed: 0.8387%; gnomAD_G_AFR: 0.4149%; gnomAD_G_AMR: 0.3745%; gnomAD_G_ASJ: 0.4065%; gnomAD_G_FIN: 0.4072%; gnomAD_G_NFE: 0.1050%; gnomAD_G_OTH: 0.1445%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50638070C>T [0/1] rs532876784 (variation viewer)

Variant score: 0.105

Transcripts:: FAF1:ENST00000371778.5:c.539-54406G>A:p.(=); FAF1:ENST00000396153.7:c.744+17372G>A:p.(=)

Pathogenicity Data:: Best Score: 0.115088165; CADD: 0.115 (0.531)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.3082%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4910%; gnomAD_G_NFE: 0.3801%; gnomAD_G_OTH: 0.2058%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50836170G>GTTTTTTTTTTT [0/1] rs36053491 (variation viewer)

Variant score: 0.087

Transcripts:: FAF1:ENST00000371778.5:c.90+21758_90+21759insAAAAAAAAAAA:p.(=); FAF1:ENST00000396153.7:c.114+21758_114+21759insAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.08735895; CADD: 0.087 (0.397)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50794868C>T [0/1] rs184732263 (variation viewer)

Variant score: 0.087

Transcripts:: FAF1:ENST00000371778.5:c.138-6663G>A:p.(=); FAF1:ENST00000396153.7:c.162-6663G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09468442; CADD: 0.095 (0.432)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3042%; gnomAD_G_AFR: 0.0461%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_FIN: 0.4930%; gnomAD_G_NFE: 0.3824%; gnomAD_G_OTH: 0.2045%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50718258G>A [0/1] rs190247930 (variation viewer)

Variant score: 0.086

Transcripts:: FAF1:ENST00000371778.5:c.528-12367C>T:p.(=); FAF1:ENST00000396153.7:c.552-12367C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12138218; CADD: 0.121 (0.562)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.6642%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1376%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.5457%; gnomAD_G_NFE: 1.1532%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50836951C>CT [0/1] rs528322924 (variation viewer)

Variant score: 0.083

Transcripts:: FAF1:ENST00000371778.5:c.90+20977_90+20978insA:p.(=); FAF1:ENST00000396153.7:c.114+20977_114+20978insA:p.(=)

Pathogenicity Data:: Best Score: 0.082724094; CADD: 0.083 (0.375)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50637681A>ATATGTGTGTGTG [0/1] rs1553123409 (variation viewer)

Variant score: 0.073

Transcripts:: FAF1:ENST00000371778.5:c.539-54018_539-54017insCACACACACATA:p.(=); FAF1:ENST00000396153.7:c.744+17760_744+17761insCACACACACATA:p.(=)

Pathogenicity Data:: Best Score: 0.07252973; CADD: 0.073 (0.327)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50636379CTT>C [0/1] rs1213567555 (variation viewer)

Variant score: 0.071

Transcripts:: FAF1:ENST00000371778.5:c.539-52717_539-52716del:p.(=); FAF1:ENST00000396153.7:c.744+19061_744+19062del:p.(=)

Pathogenicity Data:: Best Score: 0.0710336; CADD: 0.071 (0.320)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50724308C>CACAT [0/1] rs112568731 (variation viewer)

Variant score: 0.039

Transcripts:: FAF1:ENST00000371778.5:c.527+14554_527+14555insATGT:p.(=); FAF1:ENST00000396153.7:c.551+14554_551+14555insATGT:p.(=)

Pathogenicity Data:: Best Score: 0.07274324; CADD: 0.073 (0.328)

Frequency Data:: gnomAD_G_AFR: 1.4844%; gnomAD_G_AMR: 0.2618%; gnomAD_G_ASJ: 0.3846%; gnomAD_G_FIN: 0.4215%; gnomAD_G_NFE: 0.4190%; gnomAD_G_OTH: 0.3326%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50698075T>C [0/1] rs1179286897 (variation viewer)

Variant score: 0.031

Transcripts:: FAF1:ENST00000371778.5:c.538+7806A>G:p.(=); FAF1:ENST00000396153.7:c.657+7711A>G:p.(=)

Pathogenicity Data:: Best Score: 0.031276107; CADD: 0.031 (0.138)

Frequency Data:: TOPMed: 0.0048%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.50620262TA>T [0/1]

Variant score: 0.000

Transcripts:: FAF1:ENST00000371778.5:c.539-36599del:p.(=); FAF1:ENST00000396153.7:c.745-24047del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CHAF1B

Exomiser Score: 0.073

Phenotype Score: 0.525

Variant Score: 0.575

Phenotype matches:

Proximity score 0.525 in interactome to HIRA and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with HIRA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.039

Phenotype Score: 0.525

Variant Score: 0.505

Variants contributing to score:

INTERGENIC_VARIANT chr21:g.36436382CAA>C [0/1] rs71198810 (variation viewer)

Variant score: 0.505 CONTRIBUTING VARIANT

Transcripts:: CHAF1B:ENST00000314103.6::; CHAF1B:ENST00000399139.5::

Pathogenicity Data:: Best Score: 0.50489193; CADD: 0.505 (3.053)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.073

Phenotype Score: 0.525

Variant Score: 0.575

Variants contributing to score:

INTERGENIC_VARIANT chr21:g.36427865G>A [0/1] rs534909149 (variation viewer)

Variant score: 0.636 CONTRIBUTING VARIANT

Transcripts:: CHAF1B:ENST00000314103.6::; CHAF1B:ENST00000399139.5::

Pathogenicity Data:: Best Score: 0.64940965; CADD: 0.649 (4.552)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0828%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.1070%

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.36405810C>A [0/1] rs142646501 (variation viewer)

Variant score: 0.515 CONTRIBUTING VARIANT

Transcripts:: CHAF1B:ENST00000314103.6:c.758-2951C>A:p.(=)

Pathogenicity Data:: Best Score: 0.5899848; CADD: 0.590 (3.872)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0374%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0200%

Other passed variants:

INTERGENIC_VARIANT chr21:g.36378555G>A [0/1] rs867900812 (variation viewer)

Variant score: 0.375

Transcripts:: CHAF1B:ENST00000314103.6::

Pathogenicity Data:: Best Score: 0.42944175; CADD: 0.429 (2.437)

Frequency Data:: TOPMed: 0.0382%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0200%

INTERGENIC_VARIANT chr21:g.36379135CT>C [1/1] rs759766318 (variation viewer)

Variant score: 0.207

Transcripts:: CHAF1B:ENST00000314103.6::

Pathogenicity Data:: Best Score: 0.20713365; CADD: 0.207 (1.008)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.36396157T>G [0|1]

Variant score: 0.163

Transcripts:: CHAF1B:ENST00000314103.6:c.482-1258T>G:p.(=)

Pathogenicity Data:: Best Score: 0.16324174; CADD: 0.163 (0.774)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.36396149G>A [0|1] rs530517038 (variation viewer)

Variant score: 0.061

Transcripts:: CHAF1B:ENST00000314103.6:c.482-1266G>A:p.(=)

Pathogenicity Data:: Best Score: 0.061357975; CADD: 0.061 (0.275)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0016%

CODING_TRANSCRIPT_INTRON_VARIANT chr21:g.36415898G>A [0/1] rs147930595 (variation viewer)

Variant score: 0.060

Transcripts:: CHAF1B:ENST00000314103.6:c.1589-377G>A:p.(=)

Pathogenicity Data:: Best Score: 0.06824875; CADD: 0.068 (0.307)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0430%; gnomAD_E_AMR: 0.0842%; gnomAD_E_ASJ: 0.2160%; gnomAD_E_NFE: 0.0590%; gnomAD_E_SAS: 0.1869%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0201%

COPB1

Exomiser Score: 0.072

Phenotype Score: 0.504

Variant Score: 0.599

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.072

Phenotype Score: 0.504

Variant Score: 0.599

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.14458074A>AT [-/1] rs748562590 (variation viewer)

Variant score: 0.599 CONTRIBUTING VARIANT

Transcripts:: COPB1:ENST00000249923.7:c.2803-192_2803-191insA:p.(=); COPB1:ENST00000439561.6:c.2803-192_2803-191insA:p.(=)

Pathogenicity Data:: Best Score: 0.5986715; CADD: 0.599 (3.965)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.017

Phenotype Score: 0.504

Variant Score: 0.437

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.14458074A>AT [-/1] rs748562590 (variation viewer)

Variant score: 0.599 CONTRIBUTING VARIANT

Transcripts:: COPB1:ENST00000249923.7:c.2803-192_2803-191insA:p.(=); COPB1:ENST00000439561.6:c.2803-192_2803-191insA:p.(=)

Pathogenicity Data:: Best Score: 0.5986715; CADD: 0.599 (3.965)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.14479941G>A [0/1] rs117481850 (variation viewer)

Variant score: 0.276 CONTRIBUTING VARIANT

Transcripts:: COPB1:ENST00000249923.7:c.1213-227C>T:p.(=); COPB1:ENST00000439561.6:c.1213-227C>T:p.(=)

Pathogenicity Data:: Best Score: 0.39854932; CADD: 0.399 (2.208)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.5917%; UK10K: 1.0711%; gnomAD_G_AFR: 0.1833%; gnomAD_G_AMR: 0.1196%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.1433%; gnomAD_G_NFE: 1.1870%; gnomAD_G_OTH: 0.6110%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr11:g.14454637C>CAAAAAAAAAAAAAAA [-/1] rs57696251 (variation viewer)

Variant score: 0.130

Transcripts:: COPB1:ENST00000249923.7::; COPB1:ENST00000534211.1::

Pathogenicity Data:: Best Score: 0.13003856; CADD: 0.130 (0.605)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr11:g.14454637C>CAAAAAAAAAAAAAAAA [-/1] rs57696251 (variation viewer)

Variant score: 0.128

Transcripts:: COPB1:ENST00000249923.7::; COPB1:ENST00000534211.1::

Pathogenicity Data:: Best Score: 0.12763143; CADD: 0.128 (0.593)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr11:g.14454346A>* [-/1]

Variant score: 0.000

Transcripts:: COPB1:ENST00000249923.7::; COPB1:ENST00000534211.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MMP9

Exomiser Score: 0.072

Phenotype Score: 0.502

Variant Score: 0.601

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:613073 Metaphyseal anadysplasia 2 - autosomal recessive; ORPHA:1040 Metaphyseal anadysplasia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.313

Variants contributing to score:

INTERGENIC_VARIANT chr20:g.45991732GTTT>G [-/1] rs149092595 (variation viewer)

Variant score: 0.313 CONTRIBUTING VARIANT

Transcripts:: MMP9:ENST00000372330.3::; MMP9:ENST00000449155.1::

Pathogenicity Data:: Best Score: 0.3126151; CADD: 0.313 (1.628)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.072

Phenotype Score: 0.502

Variant Score: 0.601

Variants contributing to score:

INTERGENIC_VARIANT chr20:g.46002428CAA>C [1/1] rs71181880 (variation viewer)

Variant score: 0.601 CONTRIBUTING VARIANT

Transcripts:: MMP9:ENST00000372330.3::; MMP9:ENST00000449155.1::

Pathogenicity Data:: Best Score: 0.60115886; CADD: 0.601 (3.992)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr20:g.45991889C>T [0/1] rs945410097 (variation viewer)

Variant score: 0.223

Transcripts:: MMP9:ENST00000372330.3::; MMP9:ENST00000449155.1::

Pathogenicity Data:: Best Score: 0.22339535; CADD: 0.223 (1.098)

Frequency Data:: TOPMed: 0.0008%

INTERGENIC_VARIANT chr20:g.45991732GT>G [-/1] rs149092595 (variation viewer)

Variant score: 0.043

Transcripts:: MMP9:ENST00000372330.3::; MMP9:ENST00000449155.1::

Pathogenicity Data:: Best Score: 0.043466926; CADD: 0.043 (0.193)

Frequency Data:: No frequency data

REV3L

Exomiser Score: 0.072

Phenotype Score: 0.258

Variant Score: 0.877

Phenotype matches:

Proximity score 0.516 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:570 Moebius syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.516

Variant Score: 0.308

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111474988T>TATATAC [-/1] rs151075609 (variation viewer)

Variant score: 0.308 CONTRIBUTING VARIANT

Transcripts:: REV3L:ENST00000358835.7:c.139+7761_139+7762insGTATAT:p.(=); REV3L:ENST00000368802.8:c.139+7761_139+7762insGTATAT:p.(=); REV3L:ENST00000435970.5:c.-223-2849_-223-2848insGTATAT:p.(=)

Pathogenicity Data:: Best Score: 0.30832833; CADD: 0.308 (1.601)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.072

Phenotype Score: 0.258

Variant Score: 0.877

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111456456G>A [0/1] rs192371047 (variation viewer)

Variant score: 0.903 CONTRIBUTING VARIANT

Transcripts:: REV3L:ENST00000358835.7:c.139+26294C>T:p.(=); REV3L:ENST00000368802.8:c.139+26294C>T:p.(=); REV3L:ENST00000435970.5:c.-96+15557C>T:p.(=)

Pathogenicity Data:: Best Score: 0.91852957; CADD: 0.919 (10.890)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0183%; gnomAD_G_AFR: 0.0114%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111389270T>G [0/1] rs181531501 (variation viewer)

Variant score: 0.851 CONTRIBUTING VARIANT

Transcripts:: REV3L:ENST00000358835.7:c.758-60A>C:p.(=); REV3L:ENST00000368802.8:c.758-60A>C:p.(=); REV3L:ENST00000435970.5:c.524-60A>C:p.(=)

Pathogenicity Data:: Best Score: 0.865352; CADD: 0.865 (8.708)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0159%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1022%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111384392C>T [0/1] rs180944294 (variation viewer)

Variant score: 0.846

Transcripts:: REV3L:ENST00000358835.7:c.1097-2948G>A:p.(=); REV3L:ENST00000368802.8:c.1097-2948G>A:p.(=); REV3L:ENST00000435970.5:c.863-2948G>A:p.(=)

Pathogenicity Data:: Best Score: 0.86078054; CADD: 0.861 (8.563)

Frequency Data:: gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111366843T>C [0/1] rs184317369 (variation viewer)

Variant score: 0.839

Transcripts:: REV3L:ENST00000358835.7:c.6673+272A>G:p.(=); REV3L:ENST00000368802.8:c.6673+272A>G:p.(=); REV3L:ENST00000435970.5:c.6439+272A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8538159; CADD: 0.854 (8.351)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0159%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111301330T>C [0/1] rs188473715 (variation viewer)

Variant score: 0.832

Transcripts:: REV3L:ENST00000358835.7:c.9253-1174A>G:p.(=); REV3L:ENST00000368802.8:c.9253-1174A>G:p.(=); REV3L:ENST00000435970.5:c.9019-1174A>G:p.(=)

Pathogenicity Data:: Best Score: 0.84675014; CADD: 0.847 (8.146)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0159%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111407173A>C [0/1] rs185777871 (variation viewer)

Variant score: 0.786

Transcripts:: REV3L:ENST00000358835.7:c.405-1543T>G:p.(=); REV3L:ENST00000368802.8:c.405-1543T>G:p.(=); REV3L:ENST00000435970.5:c.171-1543T>G:p.(=)

Pathogenicity Data:: Best Score: 0.79982954; CADD: 0.800 (6.986)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0159%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111301254A>G [0/1] rs536144387 (variation viewer)

Variant score: 0.612

Transcripts:: REV3L:ENST00000358835.7:c.9253-1098T>C:p.(=); REV3L:ENST00000368802.8:c.9253-1098T>C:p.(=); REV3L:ENST00000435970.5:c.9019-1098T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6224278; CADD: 0.622 (4.230)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0159%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

DOWNSTREAM_GENE_VARIANT chr6:g.111297469G>A [0/1] rs185204687 (variation viewer)

Variant score: 0.277

Transcripts:: REV3L:ENST00000368802.8::; REV3L:ENST00000671876.2::

Pathogenicity Data:: Best Score: 0.2822057; CADD: 0.282 (1.440)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0159%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111422674ATATACG>A [0|1] rs1275806267 (variation viewer)

Variant score: 0.220

Transcripts:: REV3L:ENST00000358835.7:c.140-6208_140-6203del:p.(=); REV3L:ENST00000368802.8:c.140-6208_140-6203del:p.(=); REV3L:ENST00000435970.5:c.-95-6208_-95-6203del:p.(=)

Pathogenicity Data:: Best Score: 0.3072126; CADD: 0.307 (1.594)

Frequency Data:: gnomAD_G_AFR: 0.0571%; gnomAD_G_EAS: 0.3464%; gnomAD_G_NFE: 1.1301%; gnomAD_G_OTH: 0.7519%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111465745C>CAAA [1/1] rs376561912 (variation viewer)

Variant score: 0.203

Transcripts:: REV3L:ENST00000358835.7:c.139+17004_139+17005insTTT:p.(=); REV3L:ENST00000368802.8:c.139+17004_139+17005insTTT:p.(=); REV3L:ENST00000435970.5:c.-96+6267_-96+6268insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.20273995; CADD: 0.203 (0.984)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111338312CTTTTTTTTTTTTT>C [1/1] rs144497761 (variation viewer)

Variant score: 0.184

Transcripts:: REV3L:ENST00000358835.7:c.7539-2715_7539-2703del:p.(=); REV3L:ENST00000368802.8:c.7539-2715_7539-2703del:p.(=); REV3L:ENST00000435970.5:c.7305-2715_7305-2703del:p.(=)

Pathogenicity Data:: Best Score: 0.18360561; CADD: 0.184 (0.881)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111341327C>T [0/1] rs192192582 (variation viewer)

Variant score: 0.091

Transcripts:: REV3L:ENST00000358835.7:c.7538+2598G>A:p.(=); REV3L:ENST00000368802.8:c.7538+2598G>A:p.(=); REV3L:ENST00000435970.5:c.7304+2598G>A:p.(=)

Pathogenicity Data:: Best Score: 0.094475925; CADD: 0.094 (0.431)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0199%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111340462T>C [0/1] rs193244534 (variation viewer)

Variant score: 0.076

Transcripts:: REV3L:ENST00000358835.7:c.7538+3463A>G:p.(=); REV3L:ENST00000368802.8:c.7538+3463A>G:p.(=); REV3L:ENST00000435970.5:c.7304+3463A>G:p.(=)

Pathogenicity Data:: Best Score: 0.07764101; CADD: 0.078 (0.351)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0159%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111386717AT>A [-/1] rs67124715 (variation viewer)

Variant score: 0.074

Transcripts:: REV3L:ENST00000358835.7:c.1096+1047del:p.(=); REV3L:ENST00000368802.8:c.1096+1047del:p.(=); REV3L:ENST00000435970.5:c.862+1047del:p.(=)

Pathogenicity Data:: Best Score: 0.074023426; CADD: 0.074 (0.334)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111303165C>CTTTCTTTT [1/1] rs4038141 (variation viewer)

Variant score: 0.029

Transcripts:: REV3L:ENST00000358835.7:c.9253-3010_9253-3009insAAAAGAAA:p.(=); REV3L:ENST00000368802.8:c.9253-3010_9253-3009insAAAAGAAA:p.(=); REV3L:ENST00000435970.5:c.9019-3010_9019-3009insAAAAGAAA:p.(=)

Pathogenicity Data:: Best Score: 0.028595746; CADD: 0.029 (0.126)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111422615C>* [-/1]

Variant score: 0.000

Transcripts:: REV3L:ENST00000358835.7:c.140-6143G>:p.(=); REV3L:ENST00000368802.8:c.140-6143G>:p.(=); REV3L:ENST00000435970.5:c.-95-6143G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.111422663C>* [-/1]

Variant score: 0.000

Transcripts:: REV3L:ENST00000358835.7:c.140-6191G>:p.(=); REV3L:ENST00000368802.8:c.140-6191G>:p.(=); REV3L:ENST00000435970.5:c.-95-6191G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TRAF2

Exomiser Score: 0.071

Phenotype Score: 0.504

Variant Score: 0.596

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.071

Phenotype Score: 0.504

Variant Score: 0.596

Variants contributing to score:

REGULATORY_REGION_VARIANT chr9:g.137173488A>G [0/1] rs765358052 (variation viewer)

Variant score: 0.596 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.59848666; CADD: 0.598 (3.963)

Frequency Data:: TOPMed: 0.0072%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.504

Variant Score: 0.349

Variants contributing to score:

REGULATORY_REGION_VARIANT chr9:g.137173488A>G [0/1] rs765358052 (variation viewer)

Variant score: 0.596 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.59848666; CADD: 0.598 (3.963)

Frequency Data:: TOPMed: 0.0072%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136925198G>A [0/1] rs17250869 (variation viewer)

Variant score: 0.101 CONTRIBUTING VARIANT

Transcripts:: TRAF2:ENST00000247668.7:c.1288-485G>A:p.(=)

Pathogenicity Data:: Best Score: 0.24142241; CADD: 0.241 (1.200)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2580%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0574%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 1.6667%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.2733%; gnomAD_G_OTH: 0.5092%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136913295A>ATTTT [1/1] rs369765173 (variation viewer)

Variant score: 0.154

Transcripts:: TRAF2:ENST00000247668.7:c.604-3246_604-3245insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.15413707; CADD: 0.154 (0.727)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr9:g.136888777C>T [0/1] rs1042469230 (variation viewer)

Variant score: 0.059

Transcripts:: TRAF2:ENST00000247668.7:c.-29+2236C>T:p.(=)

Pathogenicity Data:: Best Score: 0.058977544; CADD: 0.059 (0.264)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136900183G>* [-/1]

Variant score: 0.000

Transcripts:: TRAF2:ENST00000247668.7:c.268-239G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CDH2

Exomiser Score: 0.070

Phenotype Score: 0.254

Variant Score: 0.878

Phenotype matches:

Phenotypic similarity 0.434 to Agenesis of corpus callosum, cardiac, ocular, and genital syndrome associated with CDH2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000739, Anxiety

Proximity score 0.508 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618920 Arrhythmogenic right ventricular dysplasia, familial, 14 - autosomal dominant; OMIM:618929 Agenesis of corpus callosum, cardiac, ocular, and genital syndrome - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.508

Variant Score: 0.244

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28131683G>GGTGTGTGTGTGT [-/1] rs33990872 (variation viewer)

Variant score: 0.244 CONTRIBUTING VARIANT

Transcripts:: CDH2:ENST00000269141.8:c.172+15989_172+15990insACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.24368972; CADD: 0.244 (1.213)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.070

Phenotype Score: 0.254

Variant Score: 0.878

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28101390C>CTTAATT [0/1] rs553426746 (variation viewer)

Variant score: 0.914 CONTRIBUTING VARIANT

Transcripts:: CDH2:ENST00000269141.8:c.172+46282_172+46283insAATTAA:p.(=)

Pathogenicity Data:: Best Score: 0.9482393; CADD: 0.948 (12.860)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1195%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.1268%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28003815C>A [0/1] rs184299691 (variation viewer)

Variant score: 0.841 CONTRIBUTING VARIANT

Transcripts:: CDH2:ENST00000269141.8:c.848-646G>T:p.(=); CDH2:ENST00000399380.7:c.755-646G>T:p.(=)

Pathogenicity Data:: Best Score: 0.93129313; CADD: 0.931 (11.630)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.1203%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1199%; gnomAD_G_OTH: 0.1020%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28101168T>C [0/1] rs139499133 (variation viewer)

Variant score: 0.426

Transcripts:: CDH2:ENST00000269141.8:c.172+46505A>G:p.(=)

Pathogenicity Data:: Best Score: 0.47131133; CADD: 0.471 (2.768)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.1258%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1133%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28077218C>T [0/1] rs45539939 (variation viewer)

Variant score: 0.300

Transcripts:: CDH2:ENST00000269141.8:c.173-63309G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3316561; CADD: 0.332 (1.750)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.1203%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1265%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28043890ATTTTTTTTTTTTTTTT>A [0/1] rs67532914 (variation viewer)

Variant score: 0.174

Transcripts:: CDH2:ENST00000269141.8:c.173-29997_173-29982del:p.(=)

Pathogenicity Data:: Best Score: 0.17358154; CADD: 0.174 (0.828)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.27999391A>T [0/1] rs117188523 (variation viewer)

Variant score: 0.159

Transcripts:: CDH2:ENST00000269141.8:c.1020+3606T>A:p.(=); CDH2:ENST00000399380.7:c.927+3606T>A:p.(=)

Pathogenicity Data:: Best Score: 0.7024225; CADD: 0.702 (5.264)

Frequency Data:: 1000Genomes: 0.8786%; TOPMed: 1.0500%; UK10K: 1.9043%; gnomAD_G_AFR: 0.2635%; gnomAD_G_AMR: 0.5981%; gnomAD_G_FIN: 1.1168%; gnomAD_G_NFE: 1.6065%; gnomAD_G_OTH: 1.1202%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28043461AATAT>A [0|1] rs1158754890 (variation viewer)

Variant score: 0.119

Transcripts:: CDH2:ENST00000269141.8:c.173-29556_173-29553del:p.(=)

Pathogenicity Data:: Best Score: 0.11915398; CADD: 0.119 (0.551)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28028371G>A [0/1] rs11664087 (variation viewer)

Variant score: 0.099

Transcripts:: CDH2:ENST00000269141.8:c.173-14462C>T:p.(=); CDH2:ENST00000399380.7:c.79+8099C>T:p.(=)

Pathogenicity Data:: Best Score: 0.45912117; CADD: 0.459 (2.669)

Frequency Data:: 1000Genomes: 0.8786%; TOPMed: 1.0580%; UK10K: 1.9175%; gnomAD_G_AFR: 0.2633%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 1.1181%; gnomAD_G_NFE: 1.6286%; gnomAD_G_OTH: 1.1202%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28007165AAT>A [0/1] rs1555632742 (variation viewer)

Variant score: 0.092

Transcripts:: CDH2:ENST00000269141.8:c.703-1174_703-1173del:p.(=); CDH2:ENST00000399380.7:c.610-1174_610-1173del:p.(=)

Pathogenicity Data:: Best Score: 0.09155214; CADD: 0.092 (0.417)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28166149C>CATATATATAT [-/1] rs35562216 (variation viewer)

Variant score: 0.063

Transcripts:: CDH2:ENST00000269141.8:c.60+10813_60+10814insATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.06308544; CADD: 0.063 (0.283)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28089438G>A [0/1] rs11660408 (variation viewer)

Variant score: 0.060

Transcripts:: CDH2:ENST00000269141.8:c.172+58235C>T:p.(=)

Pathogenicity Data:: Best Score: 0.26345378; CADD: 0.263 (1.328)

Frequency Data:: 1000Genomes: 0.8187%; TOPMed: 1.0600%; UK10K: 1.9043%; gnomAD_G_AFR: 0.2637%; gnomAD_G_AMR: 0.5981%; gnomAD_G_FIN: 1.1474%; gnomAD_G_NFE: 1.6602%; gnomAD_G_OTH: 1.1224%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28166149C>CATATATATATATATAT [-/1] rs35562216 (variation viewer)

Variant score: 0.056

Transcripts:: CDH2:ENST00000269141.8:c.60+10813_60+10814insATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.055939138; CADD: 0.056 (0.250)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28166176C>A [0|1] rs1941388 (variation viewer)

Variant score: 0.042

Transcripts:: CDH2:ENST00000269141.8:c.60+10787G>T:p.(=)

Pathogenicity Data:: Best Score: 0.042365015; CADD: 0.042 (0.188)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28052687T>C [0/1] rs181444172 (variation viewer)

Variant score: 0.034

Transcripts:: CDH2:ENST00000269141.8:c.173-38778A>G:p.(=)

Pathogenicity Data:: Best Score: 0.038609087; CADD: 0.039 (0.171)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.2126%; UK10K: 0.5819%; gnomAD_G_AFR: 0.0573%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.2666%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28007167T>* [-/1]

Variant score: 0.000

Transcripts:: CDH2:ENST00000269141.8:c.703-1174A>:p.(=); CDH2:ENST00000399380.7:c.610-1174A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.28043464AT>* [-/1]

Variant score: 0.000

Transcripts:: CDH2:ENST00000269141.8:c.173-29556_173-29555delATins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PRKCI

Exomiser Score: 0.068

Phenotype Score: 0.501

Variant Score: 0.594

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.010

Phenotype Score: 0.501

Variant Score: 0.382

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.170312571G>A [0/1] rs771843060 (variation viewer)

Variant score: 0.382 CONTRIBUTING VARIANT

Transcripts:: PRKCI:ENST00000295797.5::

Pathogenicity Data:: Best Score: 0.38283682; CADD: 0.383 (2.096)

Frequency Data:: TOPMed: 0.0111%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.068

Phenotype Score: 0.501

Variant Score: 0.594

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.170319615TA>T [0|1] rs1264411879 (variation viewer)

Variant score: 0.631 CONTRIBUTING VARIANT

Transcripts:: PRKCI:ENST00000295797.5::

Pathogenicity Data:: Best Score: 0.6684874; CADD: 0.668 (4.795)

Frequency Data:: gnomAD_G_AFR: 0.0850%; gnomAD_G_ASJ: 0.3472%; gnomAD_G_FIN: 0.1217%; gnomAD_G_NFE: 0.0628%; gnomAD_G_OTH: 0.1089%

INTERGENIC_VARIANT chr3:g.170319611C>CA [0|1] rs1309893504 (variation viewer)

Variant score: 0.557 CONTRIBUTING VARIANT

Transcripts:: PRKCI:ENST00000295797.5::

Pathogenicity Data:: Best Score: 0.59215045; CADD: 0.592 (3.895)

Frequency Data:: gnomAD_G_AFR: 0.0985%; gnomAD_G_ASJ: 0.3650%; gnomAD_G_FIN: 0.0954%; gnomAD_G_NFE: 0.0538%; gnomAD_G_OTH: 0.1176%

Other passed variants:

INTERGENIC_VARIANT chr3:g.170319645C>CCCGG [0|1] rs1356801896 (variation viewer)

Variant score: 0.375

Transcripts:: PRKCI:ENST00000295797.5::

Pathogenicity Data:: Best Score: 0.62597555; CADD: 0.626 (4.271)

Frequency Data:: gnomAD_G_AFR: 1.2430%; gnomAD_G_AMR: 1.0145%; gnomAD_G_EAS: 0.5216%; gnomAD_G_FIN: 1.2414%; gnomAD_G_NFE: 0.7676%; gnomAD_G_OTH: 1.3774%

INTERGENIC_VARIANT chr3:g.170203115C>T [0/1]

Variant score: 0.197

Transcripts:: PRKCI:ENST00000295797.5::; PRKCI:ENST00000467570.5::

Pathogenicity Data:: Best Score: 0.19702876; CADD: 0.197 (0.953)

Frequency Data:: No frequency data

NME7

Exomiser Score: 0.067

Phenotype Score: 0.504

Variant Score: 0.590

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.276

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169156154C>CAAAAAAAAAAAAA [0/1] rs71121729 (variation viewer)

Variant score: 0.276 CONTRIBUTING VARIANT

Transcripts:: NME7:ENST00000367811.8:c.1098+13292_1098+13293insTTTTTTTTTTTTT:p.(=); NME7:ENST00000472647.5:c.990+13292_990+13293insTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.276231; CADD: 0.276 (1.404)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.067

Phenotype Score: 0.504

Variant Score: 0.590

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169234499AAAC>A [0/1] rs569416719 (variation viewer)

Variant score: 0.759 CONTRIBUTING VARIANT

Transcripts:: NME7:ENST00000367811.8:c.888+629_888+631del:p.(=); NME7:ENST00000472647.5:c.780+629_780+631del:p.(=)

Pathogenicity Data:: Best Score: 0.7768484; CADD: 0.777 (6.514)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.0223%; gnomAD_G_AFR: 0.0231%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0134%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169236698C>T [0/1] rs186782305 (variation viewer)

Variant score: 0.420 CONTRIBUTING VARIANT

Transcripts:: NME7:ENST00000367811.8:c.819+925G>A:p.(=); NME7:ENST00000472647.5:c.711+925G>A:p.(=)

Pathogenicity Data:: Best Score: 0.54804; CADD: 0.548 (3.449)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.5105%; UK10K: 0.9654%; gnomAD_G_AFR: 0.2238%; gnomAD_G_AMR: 0.2725%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2231%; gnomAD_G_NFE: 1.0008%; gnomAD_G_OTH: 0.6397%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275887T>C [1/1] rs1327329254 (variation viewer)

Variant score: 0.556

Transcripts:: NME7:ENST00000367811.8:c.754+11416A>G:p.(=); NME7:ENST00000472647.5:c.646+11416A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5678843; CADD: 0.568 (3.644)

Frequency Data:: gnomAD_G_AFR: 0.0401%; gnomAD_G_AMR: 0.1425%; gnomAD_G_FIN: 0.0757%; gnomAD_G_NFE: 0.0277%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275873T>C [1|1] rs1401431530 (variation viewer)

Variant score: 0.538

Transcripts:: NME7:ENST00000367811.8:c.754+11430A>G:p.(=); NME7:ENST00000472647.5:c.646+11430A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5606607; CADD: 0.561 (3.572)

Frequency Data:: gnomAD_G_AFR: 0.0808%; gnomAD_G_AMR: 0.1416%; gnomAD_G_EAS: 0.0683%; gnomAD_G_FIN: 0.1511%; gnomAD_G_NFE: 0.0370%; gnomAD_G_OTH: 0.2660%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275870A>C [1|1] rs1325831373 (variation viewer)

Variant score: 0.515

Transcripts:: NME7:ENST00000367811.8:c.754+11433T>G:p.(=); NME7:ENST00000472647.5:c.646+11433T>G:p.(=)

Pathogenicity Data:: Best Score: 0.525321; CADD: 0.525 (3.236)

Frequency Data:: gnomAD_G_AFR: 0.0527%; gnomAD_G_EAS: 0.0677%; gnomAD_G_FIN: 0.1121%; gnomAD_G_NFE: 0.0270%; gnomAD_G_OTH: 0.1312%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275858C>T [1|1]

Variant score: 0.409

Transcripts:: NME7:ENST00000367811.8:c.754+11445G>A:p.(=); NME7:ENST00000472647.5:c.646+11445G>A:p.(=)

Pathogenicity Data:: Best Score: 0.40898293; CADD: 0.409 (2.284)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169218659AT>A [1/1] rs34342694 (variation viewer)

Variant score: 0.387

Transcripts:: NME7:ENST00000367811.8:c.990+12058del:p.(=); NME7:ENST00000472647.5:c.882+12058del:p.(=)

Pathogenicity Data:: Best Score: 0.38680303; CADD: 0.387 (2.124)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275850G>A [1|1] rs1411075203 (variation viewer)

Variant score: 0.349

Transcripts:: NME7:ENST00000367811.8:c.754+11453C>T:p.(=); NME7:ENST00000472647.5:c.646+11453C>T:p.(=)

Pathogenicity Data:: Best Score: 0.35597903; CADD: 0.356 (1.911)

Frequency Data:: gnomAD_G_AFR: 0.0665%; gnomAD_G_EAS: 0.0683%; gnomAD_G_FIN: 0.1131%; gnomAD_G_NFE: 0.0090%; gnomAD_G_OTH: 0.1285%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275898G>A [1/1] rs1258660714 (variation viewer)

Variant score: 0.347

Transcripts:: NME7:ENST00000367811.8:c.754+11405C>T:p.(=); NME7:ENST00000472647.5:c.646+11405C>T:p.(=)

Pathogenicity Data:: Best Score: 0.34686947; CADD: 0.347 (1.850)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169148799C>T [0/1] rs140703025 (variation viewer)

Variant score: 0.270

Transcripts:: NME7:ENST00000367811.8:c.1099-15982G>A:p.(=); NME7:ENST00000472647.5:c.991-15982G>A:p.(=)

Pathogenicity Data:: Best Score: 0.27789563; CADD: 0.278 (1.414)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1011%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0458%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.1066%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169308274T>C [0/1] rs181623889 (variation viewer)

Variant score: 0.176

Transcripts:: NME7:ENST00000367811.8:c.389+1696A>G:p.(=); NME7:ENST00000472647.5:c.281+1696A>G:p.(=)

Pathogenicity Data:: Best Score: 0.18153518; CADD: 0.182 (0.870)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.0255%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169286953C>CAAAAAA [1/1] rs71121752 (variation viewer)

Variant score: 0.147

Transcripts:: NME7:ENST00000367811.8:c.754+349_754+350insTTTTTT:p.(=); NME7:ENST00000472647.5:c.646+349_646+350insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14670342; CADD: 0.147 (0.689)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169275968GT>G [1/1] rs1164773842 (variation viewer)

Variant score: 0.138

Transcripts:: NME7:ENST00000367811.8:c.754+11334del:p.(=); NME7:ENST00000472647.5:c.646+11334del:p.(=)

Pathogenicity Data:: Best Score: 0.1403929; CADD: 0.140 (0.657)

Frequency Data:: gnomAD_G_AFR: 0.0129%; gnomAD_G_NFE: 0.0179%; gnomAD_G_OTH: 0.1266%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169352758T>C [1/1] rs146307544 (variation viewer)

Variant score: 0.137

Transcripts:: NME7:ENST00000367811.8:c.3+14950A>G:p.(=); NME7:ENST00000472647.5:c.-75+14950A>G:p.(=)

Pathogenicity Data:: Best Score: 0.42838973; CADD: 0.428 (2.429)

Frequency Data:: 1000Genomes: 0.8986%; TOPMed: 1.1860%; UK10K: 1.7059%; gnomAD_G_AFR: 0.4582%; gnomAD_G_AMR: 1.5513%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.1181%; gnomAD_G_NFE: 1.7952%; gnomAD_G_OTH: 1.1224%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169350245A>AGAAGGAAGGAAGGAAG [1/1] rs762821980 (variation viewer)

Variant score: 0.119

Transcripts:: NME7:ENST00000367811.8:c.3+17462_3+17463insCTTCCTTCCTTCCTTC:p.(=); NME7:ENST00000472647.5:c.-75+17462_-75+17463insCTTCCTTCCTTCCTTC:p.(=)

Pathogenicity Data:: Best Score: 0.11895114; CADD: 0.119 (0.550)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169212058G>A [0/1] rs879516012 (variation viewer)

Variant score: 0.113

Transcripts:: NME7:ENST00000367811.8:c.990+18660C>T:p.(=); NME7:ENST00000472647.5:c.882+18660C>T:p.(=)

Pathogenicity Data:: Best Score: 0.11284399; CADD: 0.113 (0.520)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_AFR: 0.0115%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169232912CTT>C [1/1] rs10545228 (variation viewer)

Variant score: 0.085

Transcripts:: NME7:ENST00000367811.8:c.889-2095_889-2094del:p.(=); NME7:ENST00000472647.5:c.781-2095_781-2094del:p.(=)

Pathogenicity Data:: Best Score: 0.08504444; CADD: 0.085 (0.386)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169367143T>TAA [-/1] rs571898192 (variation viewer)

Variant score: 0.083

Transcripts:: NME7:ENST00000367811.8:c.3+564_3+565insTT:p.(=); NME7:ENST00000472647.5:c.-75+564_-75+565insTT:p.(=)

Pathogenicity Data:: Best Score: 0.5999632; CADD: 0.600 (3.979)

Frequency Data:: UK10K: 1.9968%; gnomAD_G_AFR: 0.4475%; gnomAD_G_AMR: 1.7442%; gnomAD_G_ASJ: 0.6897%; gnomAD_G_FIN: 1.2788%; gnomAD_G_NFE: 1.7450%; gnomAD_G_OTH: 0.9852%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.169354769TTA>T [0/1] rs199517087 (variation viewer)

Variant score: 0.061

Transcripts:: NME7:ENST00000367811.8:c.3+12937_3+12938del:p.(=); NME7:ENST00000472647.5:c.-75+12937_-75+12938del:p.(=)

Pathogenicity Data:: Best Score: 0.083990455; CADD: 0.084 (0.381)

Frequency Data:: gnomAD_G_AFR: 0.5836%; gnomAD_G_AMR: 0.3106%; gnomAD_G_ASJ: 0.3788%; gnomAD_G_EAS: 0.1277%; gnomAD_G_FIN: 0.6266%; gnomAD_G_NFE: 1.1146%; gnomAD_G_OTH: 0.5650%

GRB2

Exomiser Score: 0.066

Phenotype Score: 0.505

Variant Score: 0.587

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.211

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.75346578C>CT [0/1] rs775027742 (variation viewer)

Variant score: 0.211 CONTRIBUTING VARIANT

Transcripts:: GRB2:ENST00000316615.9:c.79-13782_79-13781insA:p.(=); GRB2:ENST00000316804.10:c.79-13782_79-13781insA:p.(=); GRB2:ENST00000392562.5:c.79-13782_79-13781insA:p.(=); GRB2:ENST00000392563.5:c.79-13782_79-13781insA:p.(=); GRB2:ENST00000392564.5:c.79-13782_79-13781insA:p.(=); GRB2:ENST00000578961.5:c.79-13782_79-13781insA:p.(=)

Pathogenicity Data:: Best Score: 0.21059477; CADD: 0.211 (1.027)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.066

Phenotype Score: 0.505

Variant Score: 0.587

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.75335936T>C [0/1] rs190445414 (variation viewer)

Variant score: 0.771 CONTRIBUTING VARIANT

Transcripts:: GRB2:ENST00000316615.9:c.79-3139A>G:p.(=); GRB2:ENST00000316804.10:c.79-3139A>G:p.(=); GRB2:ENST00000392562.5:c.79-3139A>G:p.(=); GRB2:ENST00000392563.5:c.79-3139A>G:p.(=); GRB2:ENST00000392564.5:c.79-3139A>G:p.(=); GRB2:ENST00000578961.5:c.79-3139A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8831308; CADD: 0.883 (9.323)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1362%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.1399%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.75339558G>T [0/1] rs117932757 (variation viewer)

Variant score: 0.404 CONTRIBUTING VARIANT

Transcripts:: GRB2:ENST00000316615.9:c.79-6761C>A:p.(=); GRB2:ENST00000316804.10:c.79-6761C>A:p.(=); GRB2:ENST00000392562.5:c.79-6761C>A:p.(=); GRB2:ENST00000392563.5:c.79-6761C>A:p.(=); GRB2:ENST00000392564.5:c.79-6761C>A:p.(=); GRB2:ENST00000578961.5:c.79-6761C>A:p.(=)

Pathogenicity Data:: Best Score: 0.90383875; CADD: 0.904 (10.170)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.9071%; UK10K: 1.6266%; gnomAD_G_AFR: 0.2651%; gnomAD_G_AMR: 0.8516%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.0161%; gnomAD_G_NFE: 1.3064%; gnomAD_G_OTH: 0.9454%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.75331001C>T [0/1] rs61764608 (variation viewer)

Variant score: 0.266

Transcripts:: GRB2:ENST00000316615.9:c.176+1699G>A:p.(=); GRB2:ENST00000316804.10:c.176+1699G>A:p.(=); GRB2:ENST00000392562.5:c.176+1699G>A:p.(=); GRB2:ENST00000392563.5:c.176+1699G>A:p.(=); GRB2:ENST00000392564.5:c.176+1699G>A:p.(=); GRB2:ENST00000578961.5:c.176+1699G>A:p.(=)

Pathogenicity Data:: Best Score: 0.27456254; CADD: 0.275 (1.394)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0956%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0230%; gnomAD_G_NFE: 0.0733%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.75357679G>C [0/1] rs56295711 (variation viewer)

Variant score: 0.165

Transcripts:: GRB2:ENST00000316615.9:c.79-24882C>G:p.(=); GRB2:ENST00000316804.10:c.79-24882C>G:p.(=); GRB2:ENST00000392562.5:c.79-24882C>G:p.(=); GRB2:ENST00000392563.5:c.79-24882C>G:p.(=); GRB2:ENST00000392564.5:c.79-24882C>G:p.(=); GRB2:ENST00000578961.5:c.79-24882C>G:p.(=)

Pathogenicity Data:: Best Score: 0.33026963; CADD: 0.330 (1.741)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.9047%; UK10K: 1.5472%; gnomAD_G_AFR: 0.2636%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.0023%; gnomAD_G_NFE: 1.3054%; gnomAD_G_OTH: 1.0204%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.75324507GTTTTTTTT>G [1|1] rs767194304 (variation viewer)

Variant score: 0.125

Transcripts:: GRB2:ENST00000316615.9:c.177-2688_177-2681del:p.(=); GRB2:ENST00000316804.10:c.299+1383_299+1390del:p.(=); GRB2:ENST00000392562.5:c.299+1383_299+1390del:p.(=); GRB2:ENST00000392563.5:c.177-2688_177-2681del:p.(=); GRB2:ENST00000392564.5:c.299+1383_299+1390del:p.(=); GRB2:ENST00000578961.5:c.299+1383_299+1390del:p.(=)

Pathogenicity Data:: Best Score: 0.12481475; CADD: 0.125 (0.579)

Frequency Data:: No frequency data

TIMM13

Exomiser Score: 0.066

Phenotype Score: 0.520

Variant Score: 0.570

Phenotype matches:

Phenotypic similarity 0.454 to mouse mutant involving TIMM13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0020420, abnormal freezing behavior

Proximity score 0.520 in interactome to SLC25A13 and phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.066

Phenotype Score: 0.520

Variant Score: 0.570

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr19:g.2426200G>GGGTCATGGGCATGCATTTTGGTACCACCCTTTGTTCCAA [0/1] rs372398591 (variation viewer)

Variant score: 0.570 CONTRIBUTING VARIANT

Transcripts:: TIMM13:ENST00000215570.8:c.*747_*748insTTGGAACAAAGGGTGGTACCAAAATGCATGCCCATGACC:p.(=); TIMM13:ENST00000648592.1:c.*112_*113insGGTCATGGGCATGCATTTTGGTACCACCCTTTGTTCCAA:p.(=); TIMM13:ENST00000649857.1:c.*112_*113insGGTCATGGGCATGCATTTTGGTACCACCCTTTGTTCCAA:p.(=)

Pathogenicity Data:: Best Score: 0.5701667; CADD: 0.570 (3.667)

Frequency Data:: No frequency data

Other passed variants:

PPCDC

Exomiser Score: 0.066

Phenotype Score: 0.502

Variant Score: 0.590

Phenotype matches:

Proximity score 0.502 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.066

Phenotype Score: 0.502

Variant Score: 0.590

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr15:g.75023305C>CA [-/1] rs71140129 (variation viewer)

Variant score: 0.590 CONTRIBUTING VARIANT

Transcripts:: PPCDC:ENST00000564923.5::; PPCDC:ENST00000565251.2::

Pathogenicity Data:: Best Score: 0.5897014; CADD: 0.590 (3.869)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.056

Phenotype Score: 0.502

Variant Score: 0.571

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr15:g.75023305C>CA [-/1] rs71140129 (variation viewer)

Variant score: 0.590 CONTRIBUTING VARIANT

Transcripts:: PPCDC:ENST00000564923.5::; PPCDC:ENST00000565251.2::

Pathogenicity Data:: Best Score: 0.5897014; CADD: 0.590 (3.869)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr15:g.75049780C>T [0/1] rs899949671 (variation viewer)

Variant score: 0.553 CONTRIBUTING VARIANT

Transcripts:: PPCDC:ENST00000342932.8:c.*545C>T:p.(=)

Pathogenicity Data:: Best Score: 0.55352205; CADD: 0.554 (3.502)

Frequency Data:: TOPMed: 0.0135%

Other passed variants:

UBQLN2

Exomiser Score: 0.065

Phenotype Score: 0.504

Variant Score: 0.586

Phenotype matches:

Phenotypic similarity 0.473 to Amyotrophic lateral sclerosis associated with UBQLN2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300857 Amyotrophic lateral sclerosis 15, with or without frontotemporal dementia - X-linked dominant; ORPHA:803 Amyotrophic lateral sclerosis

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.252

Variant Score: 0.586

Variants contributing to score:

INTERGENIC_VARIANT chr23:g.56581494T>A [1/1] rs1294152716 (variation viewer)

Variant score: 0.586 CONTRIBUTING VARIANT

Transcripts:: UBQLN2:ENST00000338222.6::; UBQLN2:ENST00000637096.1::

Pathogenicity Data:: Best Score: 0.5871427; CADD: 0.587 (3.842)

Frequency Data:: gnomAD_G_NFE: 0.0095%

X_DOMINANT

Exomiser Score: 0.065

Phenotype Score: 0.504

Variant Score: 0.586

Variants contributing to score:

INTERGENIC_VARIANT chr23:g.56581494T>A [1/1] rs1294152716 (variation viewer)

Variant score: 0.586 CONTRIBUTING VARIANT

Transcripts:: UBQLN2:ENST00000338222.6::; UBQLN2:ENST00000637096.1::

Pathogenicity Data:: Best Score: 0.5871427; CADD: 0.587 (3.842)

Frequency Data:: gnomAD_G_NFE: 0.0095%

Other passed variants:

MARK4

Exomiser Score: 0.065

Phenotype Score: 0.501

Variant Score: 0.589

Phenotype matches:

Phenotypic similarity 0.389 to mouse mutant involving MARK4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001433, polyphagia

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.501

Variant Score: 0.219

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.45290688T>C [0/1]

Variant score: 0.219 CONTRIBUTING VARIANT

Transcripts:: MARK4:ENST00000262891.9:c.1494+3024T>C:p.(=); MARK4:ENST00000300843.8:c.1494+3024T>C:p.(=); MARK4:ENST00000620044.4:c.*187-7197T>C:p.(=)

Pathogenicity Data:: Best Score: 0.21873206; CADD: 0.219 (1.072)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.065

Phenotype Score: 0.501

Variant Score: 0.589

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.45251657C>G [0/1] rs755800891 (variation viewer)

Variant score: 0.959 CONTRIBUTING VARIANT

Transcripts:: MARK4:ENST00000262891.9:c.51+18C>G:p.(=); MARK4:ENST00000300843.8:c.51+18C>G:p.(=); MARK4:ENST00000620044.4:c.51+18C>G:p.(=)

Pathogenicity Data:: Best Score: 0.9838192; CADD: 0.984 (17.910)

Frequency Data:: TOPMed: 0.0088%; ExAC NFE: 0.0217%; gnomAD_E_AMR: 0.0052%; gnomAD_E_NFE: 0.0096%; gnomAD_E_OTH: 0.1719%; gnomAD_G_NFE: 0.0204%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.45290688T>C [0/1]

Variant score: 0.219 CONTRIBUTING VARIANT

Transcripts:: MARK4:ENST00000262891.9:c.1494+3024T>C:p.(=); MARK4:ENST00000300843.8:c.1494+3024T>C:p.(=); MARK4:ENST00000620044.4:c.*187-7197T>C:p.(=)

Pathogenicity Data:: Best Score: 0.21873206; CADD: 0.219 (1.072)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.45301557C>CAAA [0/1] rs10630193 (variation viewer)

Variant score: 0.116

Transcripts:: MARK4:ENST00000262891.9:c.1923-817_1923-816insAAA:p.(=); MARK4:ENST00000300843.8:c.2003-817_2003-816insAAA:p.(=); MARK4:ENST00000622871.1:c.-97-817_-97-816insAAA:p.(=); MARK4:ENST00000620044.4:c.*302-817_*302-816insAAA:p.(=)

Pathogenicity Data:: Best Score: 0.11590284; CADD: 0.116 (0.535)

Frequency Data:: No frequency data

UBE2I

Exomiser Score: 0.063

Phenotype Score: 0.505

Variant Score: 0.582

Phenotype matches:

Proximity score 0.505 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.063

Phenotype Score: 0.505

Variant Score: 0.582

Variants contributing to score:

INTERGENIC_VARIANT chr16:g.1294839A>AT [1/1] rs34409910 (variation viewer)

Variant score: 0.582 CONTRIBUTING VARIANT

Transcripts:: UBE2I:ENST00000355803.8::; UBE2I:ENST00000561760.1::

Pathogenicity Data:: Best Score: 0.58216965; CADD: 0.582 (3.790)

Frequency Data:: No frequency data

Other passed variants:

NDUFS1

Exomiser Score: 0.062

Phenotype Score: 0.504

Variant Score: 0.579

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFS1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618226 Mitochondrial complex I deficiency, nuclear type 5 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.266

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.206142592G>A [0/1] rs769004242 (variation viewer)

Variant score: 0.266 CONTRIBUTING VARIANT

Transcripts:: NDUFS1:ENST00000233190.11:c.1133+94C>T:p.(=); NDUFS1:ENST00000423725.5:c.962+94C>T:p.(=); NDUFS1:ENST00000432169.5:c.800+94C>T:p.(=); NDUFS1:ENST00000440274.5:c.1025+94C>T:p.(=); NDUFS1:ENST00000449699.5:c.1133+94C>T:p.(=); NDUFS1:ENST00000455934.6:c.1175+94C>T:p.(=); NDUFS1:ENST00000457011.5:c.785+94C>T:p.(=)

Pathogenicity Data:: Best Score: 0.26650017; CADD: 0.267 (1.346)

Frequency Data:: UK10K: 0.0132%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.062

Phenotype Score: 0.504

Variant Score: 0.579

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr2:g.206122629C>CAAAAAAAAAAA [1/1] rs71034409 (variation viewer)

Variant score: 0.579 CONTRIBUTING VARIANT

Transcripts:: NDUFS1:ENST00000233190.11:c.*1545_*1555dup:p.(=)

Pathogenicity Data:: Best Score: 0.57946706; CADD: 0.579 (3.762)

Frequency Data:: No frequency data

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr2:g.206121634G>A [0/1] rs144279255 (variation viewer)

Variant score: 0.568

Transcripts:: NDUFS1:ENST00000233190.11:c.*2551C>T:p.(=)

Pathogenicity Data:: Best Score: 0.7626441; CADD: 0.763 (6.246)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.4109%; UK10K: 0.7009%; gnomAD_G_AFR: 0.1146%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.0602%; gnomAD_G_NFE: 0.7268%; gnomAD_G_OTH: 0.5092%

DOWNSTREAM_GENE_VARIANT chr2:g.206114137C>T [0/1] rs530074330 (variation viewer)

Variant score: 0.280

Transcripts:: NDUFS1:ENST00000233190.11::; NDUFS1:ENST00000403263.6::

Pathogenicity Data:: Best Score: 0.29579353; CADD: 0.296 (1.523)

Frequency Data:: TOPMed: 0.0542%; UK10K: 0.0661%; gnomAD_G_ASJ: 0.3356%; gnomAD_G_NFE: 0.0336%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.206145999C>G [0/1] rs143026673 (variation viewer)

Variant score: 0.244

Transcripts:: NDUFS1:ENST00000233190.11:c.737+904G>C:p.(=); NDUFS1:ENST00000423725.5:c.566+904G>C:p.(=); NDUFS1:ENST00000432169.5:c.404+904G>C:p.(=); NDUFS1:ENST00000440274.5:c.629+904G>C:p.(=); NDUFS1:ENST00000449699.5:c.737+904G>C:p.(=); NDUFS1:ENST00000455934.6:c.779+904G>C:p.(=); NDUFS1:ENST00000457011.5:c.389+904G>C:p.(=)

Pathogenicity Data:: Best Score: 0.32702333; CADD: 0.327 (1.720)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.3313%; UK10K: 0.4628%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.0590%; gnomAD_G_NFE: 0.6461%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.206125335G>A [0|1] rs565905265 (variation viewer)

Variant score: 0.234

Transcripts:: NDUFS1:ENST00000233190.11:c.2093-1059C>T:p.(=); NDUFS1:ENST00000423725.5:c.1922-1059C>T:p.(=); NDUFS1:ENST00000432169.5:c.1760-1059C>T:p.(=); NDUFS1:ENST00000440274.5:c.1985-1059C>T:p.(=); NDUFS1:ENST00000449699.5:c.2093-1059C>T:p.(=); NDUFS1:ENST00000455934.6:c.2135-1059C>T:p.(=); NDUFS1:ENST00000457011.5:c.1745-1059C>T:p.(=)

Pathogenicity Data:: Best Score: 0.24716467; CADD: 0.247 (1.233)

Frequency Data:: TOPMed: 0.0438%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.206139871TA>T [1/1] rs35564839 (variation viewer)

Variant score: 0.229

Transcripts:: NDUFS1:ENST00000233190.11:c.1263-1258del:p.(=); NDUFS1:ENST00000423725.5:c.1092-1258del:p.(=); NDUFS1:ENST00000432169.5:c.930-1258del:p.(=); NDUFS1:ENST00000440274.5:c.1155-1258del:p.(=); NDUFS1:ENST00000449699.5:c.1263-1258del:p.(=); NDUFS1:ENST00000455934.6:c.1305-1258del:p.(=); NDUFS1:ENST00000457011.5:c.915-1258del:p.(=)

Pathogenicity Data:: Best Score: 0.22909653; CADD: 0.229 (1.130)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.206140943T>TATATACACACACACACACAC [-/1] rs367723817 (variation viewer)

Variant score: 0.045

Transcripts:: NDUFS1:ENST00000233190.11:c.1262+997_1262+998insGTGTGTGTGTGTGTGTATAT:p.(=); NDUFS1:ENST00000423725.5:c.1091+997_1091+998insGTGTGTGTGTGTGTGTATAT:p.(=); NDUFS1:ENST00000432169.5:c.929+997_929+998insGTGTGTGTGTGTGTGTATAT:p.(=); NDUFS1:ENST00000440274.5:c.1154+997_1154+998insGTGTGTGTGTGTGTGTATAT:p.(=); NDUFS1:ENST00000449699.5:c.1262+997_1262+998insGTGTGTGTGTGTGTGTATAT:p.(=); NDUFS1:ENST00000455934.6:c.1304+997_1304+998insGTGTGTGTGTGTGTGTATAT:p.(=); NDUFS1:ENST00000457011.5:c.914+997_914+998insGTGTGTGTGTGTGTGTATAT:p.(=)

Pathogenicity Data:: Best Score: 0.044567525; CADD: 0.045 (0.198)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.206140943T>TATATATATATATACACACACAC [-/1] rs367723817 (variation viewer)

Variant score: 0.043

Transcripts:: NDUFS1:ENST00000233190.11:c.1262+997_1262+998insGTGTGTGTGTATATATATATAT:p.(=); NDUFS1:ENST00000423725.5:c.1091+997_1091+998insGTGTGTGTGTATATATATATAT:p.(=); NDUFS1:ENST00000432169.5:c.929+997_929+998insGTGTGTGTGTATATATATATAT:p.(=); NDUFS1:ENST00000440274.5:c.1154+997_1154+998insGTGTGTGTGTATATATATATAT:p.(=); NDUFS1:ENST00000449699.5:c.1262+997_1262+998insGTGTGTGTGTATATATATATAT:p.(=); NDUFS1:ENST00000455934.6:c.1304+997_1304+998insGTGTGTGTGTATATATATATAT:p.(=); NDUFS1:ENST00000457011.5:c.914+997_914+998insGTGTGTGTGTATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.04280591; CADD: 0.043 (0.190)

Frequency Data:: No frequency data

NDUFB4

Exomiser Score: 0.060

Phenotype Score: 0.504

Variant Score: 0.576

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.005

Phenotype Score: 0.504

Variant Score: 0.293

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.120617108G>A [0|1] rs1364008203 (variation viewer)

Variant score: 0.293 CONTRIBUTING VARIANT

Transcripts:: NDUFB4:ENST00000184266.3::; NDUFB4:ENST00000283871.10::

Pathogenicity Data:: Best Score: 0.29303163; CADD: 0.293 (1.506)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.060

Phenotype Score: 0.504

Variant Score: 0.576

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr3:g.120594440C>T [0/1] rs371132423 (variation viewer)

Variant score: 0.859 CONTRIBUTING VARIANT

Transcripts:: NDUFB4:ENST00000485064.1::; NDUFB4:ENST00000496098.1::

Pathogenicity Data:: Best Score: 0.9140986; CADD: 0.914 (10.660)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.2166%; UK10K: 0.3703%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.1147%; gnomAD_G_NFE: 0.2399%; gnomAD_G_OTH: 0.3061%

INTERGENIC_VARIANT chr3:g.120617108G>A [0|1] rs1364008203 (variation viewer)

Variant score: 0.293 CONTRIBUTING VARIANT

Transcripts:: NDUFB4:ENST00000184266.3::; NDUFB4:ENST00000283871.10::

Pathogenicity Data:: Best Score: 0.29303163; CADD: 0.293 (1.506)

Frequency Data:: TOPMed: 0.0008%; gnomAD_G_NFE: 0.0067%

Other passed variants:

INTERGENIC_VARIANT chr3:g.120580762G>GA [0/1] rs79562478 (variation viewer)

Variant score: 0.198

Transcripts:: NDUFB4:ENST00000485064.1::; NDUFB4:ENST00000496098.1::

Pathogenicity Data:: Best Score: 0.19776797; CADD: 0.198 (0.957)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.120597069T>G [0|1] rs796103581 (variation viewer)

Variant score: 0.176

Transcripts:: NDUFB4:ENST00000184266.3:c.180+530T>G:p.(=); NDUFB4:ENST00000485064.1:c.180+530T>G:p.(=); NDUFB4:ENST00000492739.1:c.180+530T>G:p.(=)

Pathogenicity Data:: Best Score: 0.18040371; CADD: 0.180 (0.864)

Frequency Data:: gnomAD_G_AFR: 0.0122%; gnomAD_G_NFE: 0.1563%

TMED3

Exomiser Score: 0.056

Phenotype Score: 0.504

Variant Score: 0.570

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.79353263T>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: TMED3:ENST00000424155.6:c.417+39258T>*:p.(=); TMED3:ENST00000536821.5:c.418-29705T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.056

Phenotype Score: 0.504

Variant Score: 0.570

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.79331664A>T [0/1] rs147496716 (variation viewer)

Variant score: 0.746 CONTRIBUTING VARIANT

Transcripts:: TMED3:ENST00000424155.6:c.417+17659A>T:p.(=); TMED3:ENST00000536821.5:c.417+17659A>T:p.(=)

Pathogenicity Data:: Best Score: 0.8549559; CADD: 0.855 (8.385)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0175%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.79407078T>C [0/1] rs547237187 (variation viewer)

Variant score: 0.393 CONTRIBUTING VARIANT

Transcripts:: TMED3:ENST00000424155.6:c.418-4322T>C:p.(=)

Pathogenicity Data:: Best Score: 0.39854932; CADD: 0.399 (2.208)

Frequency Data:: TOPMed: 0.0486%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.79331542CAAA>C [1/1] rs71451761 (variation viewer)

Variant score: 0.142

Transcripts:: TMED3:ENST00000424155.6:c.417+17538_417+17540del:p.(=); TMED3:ENST00000536821.5:c.417+17538_417+17540del:p.(=)

Pathogenicity Data:: Best Score: 0.14157963; CADD: 0.142 (0.663)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.79319806A>AAG [0/1] rs1263646086 (variation viewer)

Variant score: 0.055

Transcripts:: TMED3:ENST00000299705.10:c.418-2172_418-2171insAG:p.(=); TMED3:ENST00000424155.6:c.417+5801_417+5802insAG:p.(=); TMED3:ENST00000536821.5:c.417+5801_417+5802insAG:p.(=)

Pathogenicity Data:: Best Score: 0.06286967; CADD: 0.063 (0.282)

Frequency Data:: TOPMed: 0.0327%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.0334%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.79353298TTATATATATTATATATATAA>* [-/1]

Variant score: 0.000

Transcripts:: TMED3:ENST00000424155.6:c.417+39293_417+39313delTTATATATATTATATATATAAins*:p.(=); TMED3:ENST00000536821.5:c.418-29670_418-29650delTTATATATATTATATATATAAins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

RGS4

Exomiser Score: 0.056

Phenotype Score: 0.507

Variant Score: 0.566

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.056

Phenotype Score: 0.507

Variant Score: 0.566

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.163057310T>A [0/1] rs774096403 (variation viewer)

Variant score: 0.566 CONTRIBUTING VARIANT

Transcripts:: RGS4:ENST00000421743.6::; RGS4:ENST00000434394.1::

Pathogenicity Data:: Best Score: 0.5668882; CADD: 0.567 (3.634)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.507

Variant Score: 0.368

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.163057310T>A [0/1] rs774096403 (variation viewer)

Variant score: 0.566 CONTRIBUTING VARIANT

Transcripts:: RGS4:ENST00000421743.6::; RGS4:ENST00000434394.1::

Pathogenicity Data:: Best Score: 0.5668882; CADD: 0.567 (3.634)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%

INTERGENIC_VARIANT chr1:g.163059183T>TATATATATATATATATAC [0/1] rs1485962490 (variation viewer)

Variant score: 0.171 CONTRIBUTING VARIANT

Transcripts:: RGS4:ENST00000421743.6::; RGS4:ENST00000434394.1::

Pathogenicity Data:: Best Score: 0.17110407; CADD: 0.171 (0.815)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.163071866C>CG [1/1] rs552070932 (variation viewer)

Variant score: 0.257

Transcripts:: RGS4:ENST00000367908.8:c.45-529_45-528insG:p.(=); RGS4:ENST00000367909.10:c.45-529_45-528insG:p.(=); RGS4:ENST00000421743.6:c.336-529_336-528insG:p.(=); RGS4:ENST00000531057.5:c.45-529_45-528insG:p.(=); RGS4:ENST00000527809.5:c.-10-529_-10-528insG:p.(=)

Pathogenicity Data:: Best Score: 0.25698084; CADD: 0.257 (1.290)

Frequency Data:: No frequency data

DGUOK

Exomiser Score: 0.056

Phenotype Score: 0.517

Variant Score: 0.554

Phenotype matches:

Phenotypic similarity 0.479 to Adult-onset multiple mitochondrial DNA deletion syndrome due to DGUOK deficiency associated with DGUOK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.517 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:251880 Mitochondrial DNA depletion syndrome 3 (hepatocerebral type) - autosomal recessive; OMIM:617068 Portal hypertension, noncirrhotic - autosomal recessive; OMIM:617070 Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 4 - autosomal recessive; ORPHA:329314 Adult-onset multiple mitochondrial DNA deletion syndrome due to DGUOK deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.056

Phenotype Score: 0.517

Variant Score: 0.554

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.73953719C>CTT [1/1] rs386390474 (variation viewer)

Variant score: 0.554 CONTRIBUTING VARIANT

Transcripts:: DGUOK:ENST00000264093.9:c.591+2987_591+2988insTT:p.(=); DGUOK:ENST00000348222.3:c.444-4427_444-4426insTT:p.(=); DGUOK:ENST00000629438.2:c.*208+2987_*208+2988insTT:p.(=)

Pathogenicity Data:: Best Score: 0.55393314; CADD: 0.554 (3.506)

Frequency Data:: No frequency data

Other passed variants:

SLN

Exomiser Score: 0.055

Phenotype Score: 0.507

Variant Score: 0.564

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.055

Phenotype Score: 0.507

Variant Score: 0.564

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.107701363A>C [0/1] rs553242037 (variation viewer)

Variant score: 0.564 CONTRIBUTING VARIANT

Transcripts:: SLN:ENST00000305991.3::

Pathogenicity Data:: Best Score: 0.5720432; CADD: 0.572 (3.686)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0111%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.025

Phenotype Score: 0.507

Variant Score: 0.476

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.107701363A>C [0/1] rs553242037 (variation viewer)

Variant score: 0.564 CONTRIBUTING VARIANT

Transcripts:: SLN:ENST00000305991.3::

Pathogenicity Data:: Best Score: 0.5720432; CADD: 0.572 (3.686)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0111%; gnomAD_G_NFE: 0.0200%

REGULATORY_REGION_VARIANT chr11:g.108648464G>A [0/1] rs1435947610 (variation viewer)

Variant score: 0.387 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.38722646; CADD: 0.387 (2.127)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

EHD4

Exomiser Score: 0.053

Phenotype Score: 0.513

Variant Score: 0.553

Phenotype matches:

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.036

Phenotype Score: 0.513

Variant Score: 0.509

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41902241C>CTCCATCCATCCA [-/1] rs56023420 (variation viewer)

Variant score: 0.509 CONTRIBUTING VARIANT

Transcripts:: EHD4:ENST00000220325.9:c.1090-1061_1090-1060insTGGATGGATGGA:p.(=)

Pathogenicity Data:: Best Score: 0.5089791; CADD: 0.509 (3.089)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.053

Phenotype Score: 0.513

Variant Score: 0.553

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41915504C>T [0/1] rs374948444 (variation viewer)

Variant score: 0.597 CONTRIBUTING VARIANT

Transcripts:: EHD4:ENST00000220325.9:c.924+3706G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9533341; CADD: 0.953 (13.310)

Frequency Data:: 1000Genomes: 0.7987%; TOPMed: 0.1656%; UK10K: 0.2116%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.1865%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41902241C>CTCCATCCATCCA [-/1] rs56023420 (variation viewer)

Variant score: 0.509 CONTRIBUTING VARIANT

Transcripts:: EHD4:ENST00000220325.9:c.1090-1061_1090-1060insTGGATGGATGGA:p.(=)

Pathogenicity Data:: Best Score: 0.5089791; CADD: 0.509 (3.089)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41914785A>AT [-/1] rs10713712 (variation viewer)

Variant score: 0.481

Transcripts:: EHD4:ENST00000220325.9:c.924+4424_924+4425insA:p.(=)

Pathogenicity Data:: Best Score: 0.54354286; CADD: 0.544 (3.406)

Frequency Data:: gnomAD_G_AFR: 0.6120%; gnomAD_G_FIN: 0.2286%; gnomAD_G_NFE: 0.0806%; gnomAD_G_OTH: 0.1558%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41918240ACACG>A [0/1] rs553008345 (variation viewer)

Variant score: 0.114

Transcripts:: EHD4:ENST00000220325.9:c.924+966_924+969del:p.(=)

Pathogenicity Data:: Best Score: 0.18134671; CADD: 0.181 (0.869)

Frequency Data:: gnomAD_G_AFR: 0.4053%; gnomAD_G_AMR: 0.3623%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0633%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.1753%; gnomAD_G_OTH: 0.4115%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41904550A>T [0/1] rs553435310 (variation viewer)

Variant score: 0.007

Transcripts:: EHD4:ENST00000220325.9:c.1090-3369T>A:p.(=)

Pathogenicity Data:: Best Score: 0.006883979; CADD: 0.007 (0.030)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0215%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0467%; gnomAD_G_OTH: 0.1018%

PTEN

Exomiser Score: 0.052

Phenotype Score: 0.516

Variant Score: 0.547

Phenotype matches:

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.516 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases:: OMIM:158350 Cowden syndrome 1 - autosomal dominant; OMIM:176807 Prostate cancer, somatic - autosomal dominant; OMIM:605309 Macrocephaly/autism syndrome - autosomal dominant; OMIM:607174 Meningioma (susceptibility); ORPHA:109 Bannayan-Riley-Ruvalcaba syndrome; ORPHA:145 Hereditary breast and ovarian cancer syndrome; ORPHA:201 Cowden syndrome; ORPHA:2969 Proteus-like syndrome; ORPHA:65285 Lhermitte-Duclos disease; ORPHA:744 Proteus syndrome; ORPHA:79076 Juvenile polyposis of infancy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.052

Phenotype Score: 0.516

Variant Score: 0.547

Variants contributing to score:

INTERGENIC_VARIANT chr10:g.87991841A>G [0/1] rs748028692 (variation viewer)

Variant score: 0.547 CONTRIBUTING VARIANT

Transcripts:: PTEN:ENST00000371953.8::; PTEN:ENST00000439659.1::

Pathogenicity Data:: Best Score: 0.54783183; CADD: 0.548 (3.447)

Frequency Data:: TOPMed: 0.0056%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.258

Variant Score: 0.585

Variants contributing to score:

REGULATORY_REGION_VARIANT chr10:g.88062623C>T [0/1] rs145052648 (variation viewer)

Variant score: 0.623 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.98465383; CADD: 0.985 (18.140)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.6594%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1947%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.8586%; gnomAD_G_NFE: 1.1657%; gnomAD_G_OTH: 0.2037%

INTERGENIC_VARIANT chr10:g.87991841A>G [0/1] rs748028692 (variation viewer)

Variant score: 0.547 CONTRIBUTING VARIANT

Transcripts:: PTEN:ENST00000371953.8::; PTEN:ENST00000439659.1::

Pathogenicity Data:: Best Score: 0.54783183; CADD: 0.548 (3.447)

Frequency Data:: TOPMed: 0.0056%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.87876919C>CT [0/1] rs60047601 (variation viewer)

Variant score: 0.404

Transcripts:: PTEN:ENST00000371953.8:c.79+12371_79+12372insT:p.(=)

Pathogenicity Data:: Best Score: 0.40433782; CADD: 0.404 (2.250)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.87958601C>T [0/1] rs114699831 (variation viewer)

Variant score: 0.296

Transcripts:: PTEN:ENST00000371953.8:c.801+582C>T:p.(=)

Pathogenicity Data:: Best Score: 0.29773664; CADD: 0.298 (1.535)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0175%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.87946391A>T [0/1] rs35581475 (variation viewer)

Variant score: 0.265

Transcripts:: PTEN:ENST00000371953.8:c.493-5727A>T:p.(=)

Pathogenicity Data:: Best Score: 0.5131446; CADD: 0.513 (3.126)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.6713%; UK10K: 1.5208%; gnomAD_G_AFR: 0.2409%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.1431%; gnomAD_G_NFE: 0.9864%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.87957157G>C [0/1] rs34513359 (variation viewer)

ClinVar: LIKELY_BENIGN (no_assertion_criteria_provided)

Variant score: 0.115

Transcripts:: PTEN:ENST00000371953.8:c.635-696G>C:p.(=)

Pathogenicity Data:: Best Score: 0.26902926; CADD: 0.269 (1.361)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.6522%; UK10K: 0.8860%; gnomAD_G_AFR: 0.1833%; gnomAD_G_AMR: 1.3221%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.7454%; gnomAD_G_NFE: 1.0151%; gnomAD_G_OTH: 0.2045%

NOS1

Exomiser Score: 0.052

Phenotype Score: 0.503

Variant Score: 0.562

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving NOS1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.503 in interactome to MT-CO1 and phenotypic similarity 0.864 to MELAS associated with MT-CO1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:930 Idiopathic achalasia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.124

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.117256284G>GTTTTTTTT [0/1] rs57047376 (variation viewer)

Variant score: 0.124 CONTRIBUTING VARIANT

Transcripts:: NOS1:ENST00000317775.11:c.2531+2112_2531+2113insAAAAAAAA:p.(=); NOS1:ENST00000338101.8:c.2532-248_2532-247insAAAAAAAA:p.(=); NOS1:ENST00000344089.4:c.2528+2112_2528+2113insAAAAAAAA:p.(=); NOS1:ENST00000618760.4:c.2532-248_2532-247insAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.123806536; CADD: 0.124 (0.574)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.052

Phenotype Score: 0.503

Variant Score: 0.562

Variants contributing to score:

MISSENSE_VARIANT chr12:g.117253695C>T [0/1] rs9658445 (variation viewer)

ClinVar: LIKELY_BENIGN (criteria_provided,_single_submitter)

Variant score: 0.825 CONTRIBUTING VARIANT

Transcripts:: NOS1:ENST00000317775.11:c.2591G>A:p.(Gly864Asp); NOS1:ENST00000338101.8:c.2693G>A:p.(Gly898Asp); NOS1:ENST00000344089.4:c.2588G>A:p.(Gly863Asp); NOS1:ENST00000618760.4:c.2693G>A:p.(Gly898Asp)

Pathogenicity Data:: Best Score: 1.0; Polyphen2: 0.297 (B); Mutation Taster: 1.000 (P); SIFT: 0.311 (T); CADD: 0.993 (21.400)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3560%; UK10K: 0.4893%; ESP AA: 0.1857%; ESP EA: 0.4810%; ESP All: 0.3819%; ExAC AFR: 0.1224%; ExAC AMR: 0.3715%; ExAC FIN: 0.5897%; ExAC NFE: 0.6160%; ExAC OTH: 0.6667%; ExAC SAS: 0.0242%; gnomAD_E_AFR: 0.1047%; gnomAD_E_AMR: 0.4229%; gnomAD_E_ASJ: 0.0102%; gnomAD_E_EAS: 0.0058%; gnomAD_E_FIN: 0.7489%; gnomAD_E_NFE: 0.6306%; gnomAD_E_OTH: 0.4927%; gnomAD_E_SAS: 0.0325%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.8300%; gnomAD_G_NFE: 0.6404%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.117275909C>T [0/1] rs138224617 (variation viewer)

Variant score: 0.300 CONTRIBUTING VARIANT

Transcripts:: NOS1:ENST00000317775.11:c.1664+2050G>A:p.(=); NOS1:ENST00000338101.8:c.1664+2050G>A:p.(=); NOS1:ENST00000344089.4:c.1661+2050G>A:p.(=); NOS1:ENST00000618760.4:c.1664+2050G>A:p.(=)

Pathogenicity Data:: Best Score: 0.36320448; CADD: 0.363 (1.960)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.3289%; UK10K: 0.3967%; gnomAD_G_AFR: 0.0573%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.8300%; gnomAD_G_NFE: 0.5995%; gnomAD_G_OTH: 0.5102%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr12:g.117359876TTA>T [1/1] rs56787288 (variation viewer)

Variant score: 0.501

Transcripts:: NOS1:ENST00000317775.11:c.-421+1634_-421+1635del:p.(=); NOS1:ENST00000618760.4:c.-421+1634_-421+1635del:p.(=)

Pathogenicity Data:: Best Score: 0.5008857; CADD: 0.501 (3.018)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.117283855C>CAAA [1/1] rs61448842 (variation viewer)

Variant score: 0.461

Transcripts:: NOS1:ENST00000317775.11:c.1382+1385_1382+1386insTTT:p.(=); NOS1:ENST00000338101.8:c.1382+1385_1382+1386insTTT:p.(=); NOS1:ENST00000344089.4:c.1379+1385_1379+1386insTTT:p.(=); NOS1:ENST00000618760.4:c.1382+1385_1382+1386insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.4606136; CADD: 0.461 (2.681)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.117321992C>T [1|1] rs12319599 (variation viewer)

Variant score: 0.309

Transcripts:: NOS1:ENST00000317775.11:c.725+8353G>A:p.(=); NOS1:ENST00000338101.8:c.725+8353G>A:p.(=); NOS1:ENST00000344089.4:c.722+8353G>A:p.(=); NOS1:ENST00000618760.4:c.725+8353G>A:p.(=)

Pathogenicity Data:: Best Score: 0.49370927; CADD: 0.494 (2.956)

Frequency Data:: gnomAD_G_AFR: 0.4009%; gnomAD_G_AMR: 0.2882%; gnomAD_G_ASJ: 1.3274%; gnomAD_G_EAS: 0.3436%; gnomAD_G_FIN: 0.3485%; gnomAD_G_NFE: 0.5075%; gnomAD_G_OTH: 0.6906%

FIVE_PRIME_UTR_INTRON_VARIANT chr12:g.117335729T>TGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA [1/1]

Variant score: 0.148

Transcripts:: NOS1:ENST00000317775.11:c.-420-4241_-420-4240insTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC:p.(=); NOS1:ENST00000618760.4:c.-420-4241_-420-4240insTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC:p.(=)

Pathogenicity Data:: Best Score: 0.14788151; CADD: 0.148 (0.695)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.117215869CTT>C [0/1] rs34665031 (variation viewer)

Variant score: 0.124

Transcripts:: NOS1:ENST00000317775.11:c.4290-547_4290-546del:p.(=); NOS1:ENST00000338101.8:c.4392-547_4392-546del:p.(=); NOS1:ENST00000344089.4:c.4287-547_4287-546del:p.(=); NOS1:ENST00000618760.4:c.4392-547_4392-546del:p.(=)

Pathogenicity Data:: Best Score: 0.123604774; CADD: 0.124 (0.573)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.117321998C>T [1|1] rs12319601 (variation viewer)

Variant score: 0.113

Transcripts:: NOS1:ENST00000317775.11:c.725+8347G>A:p.(=); NOS1:ENST00000338101.8:c.725+8347G>A:p.(=); NOS1:ENST00000344089.4:c.722+8347G>A:p.(=); NOS1:ENST00000618760.4:c.725+8347G>A:p.(=)

Pathogenicity Data:: Best Score: 0.14138198; CADD: 0.141 (0.662)

Frequency Data:: gnomAD_G_AFR: 0.2873%; gnomAD_G_AMR: 0.2874%; gnomAD_G_ASJ: 0.9009%; gnomAD_G_EAS: 0.1727%; gnomAD_G_FIN: 0.2845%; gnomAD_G_NFE: 0.4820%; gnomAD_G_OTH: 0.6868%

ATP2B2

Exomiser Score: 0.052

Phenotype Score: 0.511

Variant Score: 0.553

Phenotype matches:

Proximity score 0.511 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.511 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:601386 Deafness, autosomal recessive 12, modifier of (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.255

Variant Score: 0.551

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10527773G>A [0/1] rs374163000 (variation viewer)

Variant score: 0.551 CONTRIBUTING VARIANT

Transcripts:: ATP2B2:ENST00000646379.1:c.-320+6266C>T:p.(=)

Pathogenicity Data:: Best Score: 0.55063426; CADD: 0.551 (3.474)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.052

Phenotype Score: 0.511

Variant Score: 0.553

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10524002G>C [0/1] rs74975137 (variation viewer)

Variant score: 0.556 CONTRIBUTING VARIANT

Transcripts:: ATP2B2:ENST00000646379.1:c.-320+10037C>G:p.(=)

Pathogenicity Data:: Best Score: 0.97213876; CADD: 0.972 (15.550)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.4914%; UK10K: 0.8331%; gnomAD_G_AFR: 0.0572%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.2041%; gnomAD_G_NFE: 0.9130%; gnomAD_G_OTH: 1.4257%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10527773G>A [0/1] rs374163000 (variation viewer)

Variant score: 0.551 CONTRIBUTING VARIANT

Transcripts:: ATP2B2:ENST00000646379.1:c.-320+6266C>T:p.(=)

Pathogenicity Data:: Best Score: 0.55063426; CADD: 0.551 (3.474)

Frequency Data:: TOPMed: 0.0016%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10565207C>A [0/1] rs746288883 (variation viewer)

Variant score: 0.393

Transcripts:: ATP2B2:ENST00000646379.1:c.-414-31074G>T:p.(=)

Pathogenicity Data:: Best Score: 0.40830213; CADD: 0.408 (2.279)

Frequency Data:: TOPMed: 0.0924%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.2387%; gnomAD_G_NFE: 0.1133%; gnomAD_G_OTH: 0.1018%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10686043C>CT [0/1] rs34073958 (variation viewer)

Variant score: 0.352

Transcripts:: ATP2B2:ENST00000646379.1:c.-460+21871_-460+21872insA:p.(=)

Pathogenicity Data:: Best Score: 0.35151494; CADD: 0.352 (1.881)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10512464GCACACA>G [0/1] rs6147706 (variation viewer)

Variant score: 0.180

Transcripts:: ATP2B2:ENST00000646379.1:c.-320+21569_-320+21574del:p.(=)

Pathogenicity Data:: Best Score: 0.18021494; CADD: 0.180 (0.863)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10485326C>T [0/1] rs746792541 (variation viewer)

Variant score: 0.078

Transcripts:: ATP2B2:ENST00000360273.7:c.-320+20139G>A:p.(=); ATP2B2:ENST00000397077.6:c.-320+20139G>A:p.(=); ATP2B2:ENST00000643662.1:c.-320+20139G>A:p.(=); ATP2B2:ENST00000646379.1:c.-319-35464G>A:p.(=)

Pathogenicity Data:: Best Score: 0.078277886; CADD: 0.078 (0.354)

Frequency Data:: TOPMed: 0.0064%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0133%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10683760G>GTGTA [-/1] rs1446781892 (variation viewer)

Variant score: 0.065

Transcripts:: ATP2B2:ENST00000646379.1:c.-460+24154_-460+24155insTACA:p.(=)

Pathogenicity Data:: Best Score: 0.06480968; CADD: 0.065 (0.291)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10653604C>T [0/1] rs545077107 (variation viewer)

Variant score: 0.064

Transcripts:: ATP2B2:ENST00000646379.1:c.-459-33643G>A:p.(=)

Pathogenicity Data:: Best Score: 0.065240264; CADD: 0.065 (0.293)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0175%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0200%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10683760G>GTGTATA [-/1] rs1446781892 (variation viewer)

Variant score: 0.062

Transcripts:: ATP2B2:ENST00000646379.1:c.-460+24154_-460+24155insTATACA:p.(=)

Pathogenicity Data:: Best Score: 0.062222064; CADD: 0.062 (0.279)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.10471364C>CTGAGTGTGTGTG [1/1] rs1221371075 (variation viewer)

Variant score: 0.041

Transcripts:: ATP2B2:ENST00000360273.7:c.-319-21503_-319-21502insCACACACACTCA:p.(=); ATP2B2:ENST00000397077.6:c.-319-21503_-319-21502insCACACACACTCA:p.(=); ATP2B2:ENST00000643662.1:c.-319-21503_-319-21502insCACACACACTCA:p.(=); ATP2B2:ENST00000646379.1:c.-319-21503_-319-21502insCACACACACTCA:p.(=)

Pathogenicity Data:: Best Score: 0.041482627; CADD: 0.041 (0.184)

Frequency Data:: No frequency data

RABEP1

Exomiser Score: 0.051

Phenotype Score: 0.513

Variant Score: 0.548

Phenotype matches:

Proximity score 0.513 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.051

Phenotype Score: 0.513

Variant Score: 0.548

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5323819A>AAT [0|1] rs200561684 (variation viewer)

Variant score: 0.548 CONTRIBUTING VARIANT

Transcripts:: RABEP1:ENST00000341923.10:c.164-8130_164-8129insAT:p.(=); RABEP1:ENST00000537505.6:c.164-8130_164-8129insAT:p.(=)

Pathogenicity Data:: Best Score: 0.54814404; CADD: 0.548 (3.450)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.042

Phenotype Score: 0.513

Variant Score: 0.526

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5323819A>AAT [0|1] rs200561684 (variation viewer)

Variant score: 0.548 CONTRIBUTING VARIANT

Transcripts:: RABEP1:ENST00000341923.10:c.164-8130_164-8129insAT:p.(=); RABEP1:ENST00000537505.6:c.164-8130_164-8129insAT:p.(=)

Pathogenicity Data:: Best Score: 0.54814404; CADD: 0.548 (3.450)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5351335A>G [0/1] rs191643631 (variation viewer)

Variant score: 0.503 CONTRIBUTING VARIANT

Transcripts:: RABEP1:ENST00000341923.10:c.963+706A>G:p.(=); RABEP1:ENST00000537505.6:c.963+706A>G:p.(=)

Pathogenicity Data:: Best Score: 0.6554915; CADD: 0.655 (4.628)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.3926%; UK10K: 0.4364%; gnomAD_G_AFR: 0.1032%; gnomAD_G_AMR: 0.2404%; gnomAD_G_ASJ: 1.0000%; gnomAD_G_FIN: 0.4376%; gnomAD_G_NFE: 0.5396%; gnomAD_G_OTH: 0.5102%

Other passed variants:

INTERGENIC_VARIANT chr17:g.5267739T>C [0/1]

Variant score: 0.488

Transcripts:: RABEP1:ENST00000537505.6::; RABEP1:ENST00000574297.1::

Pathogenicity Data:: Best Score: 0.48808247; CADD: 0.488 (2.908)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5294633CTTT>C [1/1] rs1185209680 (variation viewer)

Variant score: 0.443

Transcripts:: RABEP1:ENST00000341923.10:c.34+12114_34+12116del:p.(=); RABEP1:ENST00000537505.6:c.34+12114_34+12116del:p.(=)

Pathogenicity Data:: Best Score: 0.4433272; CADD: 0.443 (2.544)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5308556C>A [0/1] rs1048913655 (variation viewer)

Variant score: 0.355

Transcripts:: RABEP1:ENST00000341923.10:c.35-138C>A:p.(=); RABEP1:ENST00000537505.6:c.35-138C>A:p.(=)

Pathogenicity Data:: Best Score: 0.3553856; CADD: 0.355 (1.907)

Frequency Data:: TOPMed: 0.0008%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5302067GT>G [0|1] rs528943326 (variation viewer)

Variant score: 0.321

Transcripts:: RABEP1:ENST00000341923.10:c.35-6626del:p.(=); RABEP1:ENST00000537505.6:c.35-6626del:p.(=)

Pathogenicity Data:: Best Score: 0.41709203; CADD: 0.417 (2.344)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3910%; UK10K: 0.4232%; gnomAD_G_AFR: 0.1033%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.4590%; gnomAD_G_NFE: 0.5333%; gnomAD_G_OTH: 0.5112%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5375710T>TA [0/1] rs957884366 (variation viewer)

Variant score: 0.223

Transcripts:: RABEP1:ENST00000341923.10:c.2026-1406_2026-1405insA:p.(=); RABEP1:ENST00000537505.6:c.2026-1406_2026-1405insA:p.(=)

Pathogenicity Data:: Best Score: 0.23844725; CADD: 0.238 (1.183)

Frequency Data:: gnomAD_G_AFR: 0.3812%; gnomAD_G_AMR: 0.3497%; gnomAD_G_EAS: 0.1285%; gnomAD_G_FIN: 0.2203%; gnomAD_G_NFE: 0.0159%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5373693AACACACACACAC>A [-/1] rs55736303 (variation viewer)

Variant score: 0.215

Transcripts:: RABEP1:ENST00000341923.10:c.2025+240_2025+251del:p.(=); RABEP1:ENST00000537505.6:c.2025+240_2025+251del:p.(=)

Pathogenicity Data:: Best Score: 0.21512592; CADD: 0.215 (1.052)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5302072G>T [0|1] rs182607864 (variation viewer)

Variant score: 0.156

Transcripts:: RABEP1:ENST00000341923.10:c.35-6622G>T:p.(=); RABEP1:ENST00000537505.6:c.35-6622G>T:p.(=)

Pathogenicity Data:: Best Score: 0.20237273; CADD: 0.202 (0.982)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.3918%; UK10K: 0.4099%; gnomAD_G_AFR: 0.1033%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.4595%; gnomAD_G_NFE: 0.5398%; gnomAD_G_OTH: 0.5112%

INTERGENIC_VARIANT chr17:g.5271732C>T [0/1] rs563958472 (variation viewer)

Variant score: 0.138

Transcripts:: RABEP1:ENST00000537505.6::; RABEP1:ENST00000574297.1::

Pathogenicity Data:: Best Score: 0.14296216; CADD: 0.143 (0.670)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0223%; UK10K: 0.0132%; gnomAD_G_AMR: 0.1199%; gnomAD_G_EAS: 0.2478%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5323839A>AATATATATATATATCTAGGAATAT [0|1] rs369734347 (variation viewer)

Variant score: 0.114

Transcripts:: RABEP1:ENST00000341923.10:c.164-8110_164-8109insATATATATATATATCTAGGAATAT:p.(=); RABEP1:ENST00000537505.6:c.164-8110_164-8109insATATATATATATATCTAGGAATAT:p.(=)

Pathogenicity Data:: Best Score: 0.20822823; CADD: 0.208 (1.014)

Frequency Data:: gnomAD_G_AFR: 0.1126%; gnomAD_G_ASJ: 1.4706%; gnomAD_G_NFE: 0.1829%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5320421C>CA [1/1] rs60202531 (variation viewer)

Variant score: 0.103

Transcripts:: RABEP1:ENST00000341923.10:c.164-11528_164-11527insA:p.(=); RABEP1:ENST00000537505.6:c.164-11528_164-11527insA:p.(=)

Pathogenicity Data:: Best Score: 0.10339737; CADD: 0.103 (0.474)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5316832CA>C [-/1] rs55890740 (variation viewer)

Variant score: 0.100

Transcripts:: RABEP1:ENST00000341923.10:c.163+8011del:p.(=); RABEP1:ENST00000537505.6:c.163+8011del:p.(=)

Pathogenicity Data:: Best Score: 0.09967357; CADD: 0.100 (0.456)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5316832CAA>C [-/1] rs55890740 (variation viewer)

Variant score: 0.098

Transcripts:: RABEP1:ENST00000341923.10:c.163+8011_163+8012del:p.(=); RABEP1:ENST00000537505.6:c.163+8011_163+8012del:p.(=)

Pathogenicity Data:: Best Score: 0.097598135; CADD: 0.098 (0.446)

Frequency Data:: No frequency data

MYO15A

Exomiser Score: 0.051

Phenotype Score: 0.512

Variant Score: 0.549

Phenotype matches:

Proximity score 0.512 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.512 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:600316 Deafness, autosomal recessive 3 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.256

Variant Score: 0.117

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.18155746G>A [0/1]

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: MYO15A:ENST00000418233.7:c.251+314G>A:p.(=); MYO15A:ENST00000615845.4:c.8459+314G>A:p.(=); MYO15A:ENST00000644795.1:c.251+314G>A:p.(=); MYO15A:ENST00000647165.2:c.8459+314G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11651331; CADD: 0.117 (0.538)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.051

Phenotype Score: 0.512

Variant Score: 0.549

Variants contributing to score:

MISSENSE_VARIANT chr17:g.18122003G>T [0/1] rs189061214 (variation viewer)

ClinVar: CONFLICTING_PATHOGENICITY_INTERPRETATIONS (criteria_provided,_conflicting_interpretations)

Variant score: 0.981 CONTRIBUTING VARIANT

Transcripts:: MYO15A:ENST00000615845.4:c.3203G>T:p.(Cys1068Phe); MYO15A:ENST00000647165.2:c.3203G>T:p.(Cys1068Phe)

Pathogenicity Data:: Best Score: 0.999; Polyphen2: 0.014 (B); SIFT: 0.001 (D); CADD: 0.794 (6.862)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0414%; UK10K: 0.0529%; ESP AA: 0.0503%; ESP EA: 0.0600%; ESP All: 0.0568%; ExAC AFR: 0.0206%; ExAC AMR: 0.1211%; ExAC NFE: 0.0696%; ExAC SAS: 0.0061%; gnomAD_E_AFR: 0.0327%; gnomAD_E_AMR: 0.0685%; gnomAD_E_ASJ: 0.0102%; gnomAD_E_NFE: 0.0708%; gnomAD_E_OTH: 0.1278%; gnomAD_E_SAS: 0.0032%; gnomAD_G_NFE: 0.0401%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.18155746G>A [0/1]

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: MYO15A:ENST00000418233.7:c.251+314G>A:p.(=); MYO15A:ENST00000615845.4:c.8459+314G>A:p.(=); MYO15A:ENST00000644795.1:c.251+314G>A:p.(=); MYO15A:ENST00000647165.2:c.8459+314G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11651331; CADD: 0.117 (0.538)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.18176541CT>C [1/1] rs35105114 (variation viewer)

Variant score: 0.092

Transcripts:: MYO15A:ENST00000418233.7:c.2284-2175del:p.(=); MYO15A:ENST00000615845.4:c.10492-2227del:p.(=); MYO15A:ENST00000644795.1:c.2093-2227del:p.(=); MYO15A:ENST00000647165.2:c.10492-2227del:p.(=)

Pathogenicity Data:: Best Score: 0.09238851; CADD: 0.092 (0.421)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.18112855TA>* [-/1]

Variant score: 0.000

Transcripts:: MYO15A:ENST00000615845.4:c.-220+4031_-220+4032delTAins*:p.(=); MYO15A:ENST00000647165.2:c.-220+4031_-220+4032delTAins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TIMM23

Exomiser Score: 0.050

Phenotype Score: 0.518

Variant Score: 0.541

Phenotype matches:

Proximity score 0.518 in interactome to SLC25A13 and phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.042

Phenotype Score: 0.518

Variant Score: 0.519

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45973810AT>A [0/1] rs35822209 (variation viewer)

Variant score: 0.519 CONTRIBUTING VARIANT

Transcripts:: TIMM23:ENST00000580018.4:c.106+1081del:p.(=)

Pathogenicity Data:: Best Score: 0.5192714; CADD: 0.519 (3.181)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.050

Phenotype Score: 0.518

Variant Score: 0.541

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45973184A>AAT [1/1] rs1397854800 (variation viewer)

Variant score: 0.541 CONTRIBUTING VARIANT

Transcripts:: TIMM23:ENST00000580018.4:c.106+454_106+455insAT:p.(=)

Pathogenicity Data:: Best Score: 0.54133034; CADD: 0.541 (3.385)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45994533A>G [1/1] rs71501484 (variation viewer)

Variant score: 0.501

Transcripts:: TIMM23:ENST00000580018.4:c.514+5686A>G:p.(=)

Pathogenicity Data:: Best Score: 0.50146; CADD: 0.501 (3.023)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45976512G>A [0/1] rs1554913138 (variation viewer)

Variant score: 0.489

Transcripts:: TIMM23:ENST00000580018.4:c.165+1000G>A:p.(=)

Pathogenicity Data:: Best Score: 0.48890692; CADD: 0.489 (2.915)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45979466C>CT [0/1] rs782211474 (variation viewer)

Variant score: 0.444

Transcripts:: TIMM23:ENST00000580018.4:c.166-3057_166-3056insT:p.(=)

Pathogenicity Data:: Best Score: 0.44396776; CADD: 0.444 (2.549)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45972814G>GT [0/1] rs71026290 (variation viewer)

Variant score: 0.436

Transcripts:: TIMM23:ENST00000580018.4:c.106+84_106+85insT:p.(=)

Pathogenicity Data:: Best Score: 0.5778177; CADD: 0.578 (3.745)

Frequency Data:: gnomAD_G_FIN: 1.0363%; gnomAD_G_NFE: 0.1316%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45987832A>G [1/1] rs111423220 (variation viewer)

Variant score: 0.335

Transcripts:: TIMM23:ENST00000580018.4:c.404-905A>G:p.(=)

Pathogenicity Data:: Best Score: 0.33457363; CADD: 0.335 (1.769)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45976432A>G [1/1] rs9732801 (variation viewer)

Variant score: 0.316

Transcripts:: TIMM23:ENST00000580018.4:c.165+920A>G:p.(=)

Pathogenicity Data:: Best Score: 0.31593084; CADD: 0.316 (1.649)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45990116ATT>A [0/1] rs782791725 (variation viewer)

Variant score: 0.297

Transcripts:: TIMM23:ENST00000580018.4:c.514+1270_514+1271del:p.(=)

Pathogenicity Data:: Best Score: 0.2967658; CADD: 0.297 (1.529)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr10:g.46004318G>GTTTTTTT [-/1] rs5784814 (variation viewer)

Variant score: 0.277

Transcripts:: TIMM23:ENST00000580018.4::; TIMM23:ENST00000585132.5::

Pathogenicity Data:: Best Score: 0.27739662; CADD: 0.277 (1.411)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45996317A>G [0/1] rs371001435 (variation viewer)

Variant score: 0.258

Transcripts:: TIMM23:ENST00000580018.4:c.515-6886A>G:p.(=)

Pathogenicity Data:: Best Score: 0.29123867; CADD: 0.291 (1.495)

Frequency Data:: gnomAD_G_AFR: 0.1342%; gnomAD_G_AMR: 0.2488%; gnomAD_G_ASJ: 0.6173%; gnomAD_G_FIN: 0.1585%; gnomAD_G_NFE: 0.0869%

DOWNSTREAM_GENE_VARIANT chr10:g.46004318GT>G [-/1] rs5784814 (variation viewer)

Variant score: 0.241

Transcripts:: TIMM23:ENST00000580018.4::; TIMM23:ENST00000585132.5::

Pathogenicity Data:: Best Score: 0.24072343; CADD: 0.241 (1.196)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45987233G>GA [0/1] rs782220947 (variation viewer)

Variant score: 0.209

Transcripts:: TIMM23:ENST00000580018.4:c.404-1504_404-1503insA:p.(=)

Pathogenicity Data:: Best Score: 0.20913929; CADD: 0.209 (1.019)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45995794G>A [0/1] rs1554916603 (variation viewer)

Variant score: 0.188

Transcripts:: TIMM23:ENST00000580018.4:c.514+6947G>A:p.(=)

Pathogenicity Data:: Best Score: 0.19998157; CADD: 0.200 (0.969)

Frequency Data:: gnomAD_G_AFR: 0.3715%; gnomAD_G_EAS: 0.0988%; gnomAD_G_NFE: 0.0386%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45996968C>A [0|1] rs1554916821 (variation viewer)

Variant score: 0.180

Transcripts:: TIMM23:ENST00000580018.4:c.515-6235C>A:p.(=)

Pathogenicity Data:: Best Score: 0.18021494; CADD: 0.180 (0.863)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45978782C>T [0/1] rs1341240229 (variation viewer)

Variant score: 0.175

Transcripts:: TIMM23:ENST00000580018.4:c.165+3270C>T:p.(=)

Pathogenicity Data:: Best Score: 0.17453247; CADD: 0.175 (0.833)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45987615ATT>A [1/1] rs781826848 (variation viewer)

Variant score: 0.129

Transcripts:: TIMM23:ENST00000580018.4:c.404-1121_404-1120del:p.(=)

Pathogenicity Data:: Best Score: 0.12943739; CADD: 0.129 (0.602)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45974162G>GT [0/1] rs1554912463 (variation viewer)

Variant score: 0.129

Transcripts:: TIMM23:ENST00000580018.4:c.107-1292_107-1291insT:p.(=)

Pathogenicity Data:: Best Score: 0.12863523; CADD: 0.129 (0.598)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45996964C>CAA [0|1] rs1467134430 (variation viewer)

Variant score: 0.089

Transcripts:: TIMM23:ENST00000580018.4:c.515-6239_515-6238insAA:p.(=)

Pathogenicity Data:: Best Score: 0.088618934; CADD: 0.089 (0.403)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45998831CT>C [0/1] rs35752006 (variation viewer)

Variant score: 0.086

Transcripts:: TIMM23:ENST00000580018.4:c.515-4371del:p.(=)

Pathogenicity Data:: Best Score: 0.08588678; CADD: 0.086 (0.390)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45995413A>T [1/1] rs1228039533 (variation viewer)

Variant score: 0.084

Transcripts:: TIMM23:ENST00000580018.4:c.514+6566A>T:p.(=)

Pathogenicity Data:: Best Score: 0.08483374; CADD: 0.085 (0.385)

Frequency Data:: gnomAD_G_AFR: 0.0617%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45986804C>CGT [0/1] rs1161990914 (variation viewer)

Variant score: 0.071

Transcripts:: TIMM23:ENST00000580018.4:c.403+1363_403+1364insGT:p.(=)

Pathogenicity Data:: Best Score: 0.07146132; CADD: 0.071 (0.322)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45979606CT>C [1/1] rs1171770886 (variation viewer)

Variant score: 0.067

Transcripts:: TIMM23:ENST00000580018.4:c.166-2916del:p.(=)

Pathogenicity Data:: Best Score: 0.067390144; CADD: 0.067 (0.303)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45981261A>G [1/1] rs78385682 (variation viewer)

Variant score: 0.066

Transcripts:: TIMM23:ENST00000580018.4:c.166-1262A>G:p.(=)

Pathogenicity Data:: Best Score: 0.06567061; CADD: 0.066 (0.295)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.45974862G>C [0/1] rs797028063 (variation viewer)

Variant score: 0.029

Transcripts:: TIMM23:ENST00000580018.4:c.107-592G>C:p.(=)

Pathogenicity Data:: Best Score: 0.029043019; CADD: 0.029 (0.128)

Frequency Data:: gnomAD_G_AFR: 0.0720%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.46002810A>ATTT [0/1] rs386371331 (variation viewer)

Variant score: 0.022

Transcripts:: TIMM23:ENST00000580018.4:c.515-393_515-392insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.021637022; CADD: 0.022 (0.095)

Frequency Data:: No frequency data

PDPN

Exomiser Score: 0.050

Phenotype Score: 0.517

Variant Score: 0.542

Phenotype matches:

Proximity score 0.517 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.517 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.517

Variant Score: 0.231

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.13599241C>A [0/1]

Variant score: 0.231 CONTRIBUTING VARIANT

Transcripts:: PDPN:ENST00000294489.10:c.296-7932C>A:p.(=); PDPN:ENST00000376057.8:c.296-7932C>A:p.(=); PDPN:ENST00000509009.5:c.53-7932C>A:p.(=); PDPN:ENST00000510906.5:c.68-7932C>A:p.(=); PDPN:ENST00000617617.4:c.296-7932C>A:p.(=); PDPN:ENST00000621990.4:c.68-7932C>A:p.(=); PDPN:ENST00000376061.8:c.-59-7932C>A:p.(=); PDPN:ENST00000475043.5:c.-59-7932C>A:p.(=); PDPN:ENST00000487038.5:c.-59-7932C>A:p.(=); PDPN:ENST00000513143.5:c.-60+3257C>A:p.(=)

Pathogenicity Data:: Best Score: 0.23086953; CADD: 0.231 (1.140)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.050

Phenotype Score: 0.517

Variant Score: 0.542

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.13587474G>GGGA [0/1] rs531647187 (variation viewer)

Variant score: 0.853 CONTRIBUTING VARIANT

Transcripts:: PDPN:ENST00000294489.10:c.295+3374_295+3375insGGA:p.(=); PDPN:ENST00000376057.8:c.295+3374_295+3375insGGA:p.(=); PDPN:ENST00000509009.5:c.52+3286_52+3287insGGA:p.(=); PDPN:ENST00000510906.5:c.67+3374_67+3375insGGA:p.(=); PDPN:ENST00000617617.4:c.295+3374_295+3375insGGA:p.(=); PDPN:ENST00000621990.4:c.67+3374_67+3375insGGA:p.(=); PDPN:ENST00000376061.8:c.-60+3133_-60+3134insGGA:p.(=); PDPN:ENST00000475043.5:c.-60+1906_-60+1907insGGA:p.(=); PDPN:ENST00000487038.5:c.-60+1835_-60+1836insGGA:p.(=); PDPN:ENST00000513143.5:c.-218+3133_-218+3134insGGA:p.(=)

Pathogenicity Data:: Best Score: 0.94138616; CADD: 0.941 (12.320)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0799%; UK10K: 0.5290%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2398%; gnomAD_G_FIN: 0.1153%; gnomAD_G_NFE: 0.3867%; gnomAD_G_OTH: 0.2049%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.13599241C>A [0/1]

Variant score: 0.231 CONTRIBUTING VARIANT

Transcripts:: PDPN:ENST00000294489.10:c.296-7932C>A:p.(=); PDPN:ENST00000376057.8:c.296-7932C>A:p.(=); PDPN:ENST00000509009.5:c.53-7932C>A:p.(=); PDPN:ENST00000510906.5:c.68-7932C>A:p.(=); PDPN:ENST00000617617.4:c.296-7932C>A:p.(=); PDPN:ENST00000621990.4:c.68-7932C>A:p.(=); PDPN:ENST00000376061.8:c.-59-7932C>A:p.(=); PDPN:ENST00000475043.5:c.-59-7932C>A:p.(=); PDPN:ENST00000487038.5:c.-59-7932C>A:p.(=); PDPN:ENST00000513143.5:c.-60+3257C>A:p.(=)

Pathogenicity Data:: Best Score: 0.23086953; CADD: 0.231 (1.140)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.13592543AT>A [0/1] rs34176163 (variation viewer)

Variant score: 0.218

Transcripts:: PDPN:ENST00000294489.10:c.295+8444del:p.(=); PDPN:ENST00000376057.8:c.295+8444del:p.(=); PDPN:ENST00000509009.5:c.52+8356del:p.(=); PDPN:ENST00000510906.5:c.67+8444del:p.(=); PDPN:ENST00000617617.4:c.295+8444del:p.(=); PDPN:ENST00000621990.4:c.67+8444del:p.(=); PDPN:ENST00000376061.8:c.-60+8203del:p.(=); PDPN:ENST00000475043.5:c.-60+6976del:p.(=); PDPN:ENST00000487038.5:c.-60+6905del:p.(=); PDPN:ENST00000513143.5:c.-217-3283del:p.(=)

Pathogenicity Data:: Best Score: 0.21765196; CADD: 0.218 (1.066)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr1:g.13564291C>G [0/1] rs185747458 (variation viewer)

Variant score: 0.174

Transcripts:: PDPN:ENST00000294489.10::; PDPN:ENST00000401091.2::

Pathogenicity Data:: Best Score: 0.192765; CADD: 0.193 (0.930)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.2365%; UK10K: 0.5422%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.3733%; gnomAD_G_OTH: 0.1018%

RYR1

Exomiser Score: 0.050

Phenotype Score: 0.507

Variant Score: 0.552

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:117000 Central core disease - autosomal dominant/recessive; OMIM:145600 King-Denborough syndrome - autosomal dominant; OMIM:145600 Malignant hyperthermia susceptibility 1 (susceptibility); OMIM:255320 Minicore myopathy with external ophthalmoplegia - autosomal recessive; ORPHA:169186 Autosomal recessive centronuclear myopathy; ORPHA:169189 Autosomal dominant centronuclear myopathy; ORPHA:178145 Moderate multiminicore disease with hand involvement; ORPHA:423 Malignant hyperthermia of anesthesia; ORPHA:597 Central core disease; ORPHA:98905 Congenital multicore myopathy with external ophthalmoplegia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.507

Variant Score: 0.226

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38555929T>C [0/1] rs984048379 (variation viewer)

Variant score: 0.226 CONTRIBUTING VARIANT

Transcripts:: RYR1:ENST00000355481.8:c.12268-5184T>C:p.(=); RYR1:ENST00000359596.8:c.12283-5184T>C:p.(=)

Pathogenicity Data:: Best Score: 0.22625118; CADD: 0.226 (1.114)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.050

Phenotype Score: 0.507

Variant Score: 0.552

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38438616C>CT [1/1] rs71165544 (variation viewer)

Variant score: 0.552 CONTRIBUTING VARIANT

Transcripts:: RYR1:ENST00000355481.8:c.46-2129_46-2128insT:p.(=); RYR1:ENST00000359596.8:c.46-2129_46-2128insT:p.(=)

Pathogenicity Data:: Best Score: 0.55187416; CADD: 0.552 (3.486)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38435035T>C [0/1] rs559190529 (variation viewer)

Variant score: 0.459

Transcripts:: RYR1:ENST00000355481.8:c.45+1161T>C:p.(=); RYR1:ENST00000359596.8:c.45+1161T>C:p.(=)

Pathogenicity Data:: Best Score: 0.50065583; CADD: 0.501 (3.016)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1736%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.2673%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38529448C>T [0/1] rs191030752 (variation viewer)

Variant score: 0.379

Transcripts:: RYR1:ENST00000355481.8:c.11126+391C>T:p.(=); RYR1:ENST00000359596.8:c.11141+391C>T:p.(=)

Pathogenicity Data:: Best Score: 0.47482985; CADD: 0.475 (2.797)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.4874%; UK10K: 0.9125%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.3723%; gnomAD_G_NFE: 0.6269%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38574151T>G [0/1] rs532885680 (variation viewer)

Variant score: 0.301

Transcripts:: RYR1:ENST00000355481.8:c.14114+844T>G:p.(=); RYR1:ENST00000359596.8:c.14129+844T>G:p.(=)

Pathogenicity Data:: Best Score: 0.34067434; CADD: 0.341 (1.809)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.2548%; UK10K: 0.6215%; gnomAD_G_AFR: 0.0232%; gnomAD_G_AMR: 0.1202%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0295%; gnomAD_G_NFE: 0.3110%; gnomAD_G_OTH: 0.2083%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38457046C>A [1/1] rs11673389 (variation viewer)

Variant score: 0.201

Transcripts:: RYR1:ENST00000355481.8:c.1792-451C>A:p.(=); RYR1:ENST00000359596.8:c.1792-451C>A:p.(=)

Pathogenicity Data:: Best Score: 0.20053399; CADD: 0.201 (0.972)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38457045C>CAAAA [1/1] rs35088425 (variation viewer)

Variant score: 0.175

Transcripts:: RYR1:ENST00000355481.8:c.1792-452_1792-451insAAAA:p.(=); RYR1:ENST00000359596.8:c.1792-452_1792-451insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.17548227; CADD: 0.175 (0.838)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38530179C>T [0/1] rs374713243 (variation viewer)

Variant score: 0.141

Transcripts:: RYR1:ENST00000355481.8:c.11126+1122C>T:p.(=); RYR1:ENST00000359596.8:c.11141+1122C>T:p.(=)

Pathogenicity Data:: Best Score: 0.16092652; CADD: 0.161 (0.762)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4149%; UK10K: 0.6480%; gnomAD_G_AFR: 0.1604%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2006%; gnomAD_G_NFE: 0.5467%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38462891C>CTTT [1/1] rs553168266 (variation viewer)

Variant score: 0.120

Transcripts:: RYR1:ENST00000355481.8:c.2578-532_2578-531insTTT:p.(=); RYR1:ENST00000359596.8:c.2578-532_2578-531insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.120167494; CADD: 0.120 (0.556)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38520693CAAAA>C [0/1] rs71165555 (variation viewer)

Variant score: 0.119

Transcripts:: RYR1:ENST00000355481.8:c.10259+1240_10259+1243del:p.(=); RYR1:ENST00000359596.8:c.10259+1240_10259+1243del:p.(=)

Pathogenicity Data:: Best Score: 0.11895114; CADD: 0.119 (0.550)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38509456T>A [0/1] rs868173760 (variation viewer)

Variant score: 0.119

Transcripts:: RYR1:ENST00000355481.8:c.8933-1042T>A:p.(=); RYR1:ENST00000359596.8:c.8933-1042T>A:p.(=)

Pathogenicity Data:: Best Score: 0.1707223; CADD: 0.171 (0.813)

Frequency Data:: gnomAD_G_AFR: 0.1992%; gnomAD_G_ASJ: 0.4425%; gnomAD_G_EAS: 1.1806%; gnomAD_G_NFE: 0.2062%; gnomAD_G_OTH: 0.3623%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38549698CT>C [0/1] rs71165559 (variation viewer)

Variant score: 0.095

Transcripts:: RYR1:ENST00000355481.8:c.12267+1279del:p.(=); RYR1:ENST00000359596.8:c.12282+1279del:p.(=)

Pathogenicity Data:: Best Score: 0.095309556; CADD: 0.095 (0.435)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38541603CT>C [0|1] rs370476011 (variation viewer)

Variant score: 0.079

Transcripts:: RYR1:ENST00000355481.8:c.11675-1743del:p.(=); RYR1:ENST00000359596.8:c.11690-1743del:p.(=)

Pathogenicity Data:: Best Score: 0.120167494; CADD: 0.120 (0.556)

Frequency Data:: gnomAD_G_AFR: 0.9850%; gnomAD_G_AMR: 1.2640%; gnomAD_G_ASJ: 0.3788%; gnomAD_G_EAS: 1.0432%; gnomAD_G_FIN: 0.8101%; gnomAD_G_NFE: 0.3976%; gnomAD_G_OTH: 0.7919%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38544979C>T [0/1] rs776723537 (variation viewer)

Variant score: 0.068

Transcripts:: RYR1:ENST00000355481.8:c.11997+1104C>T:p.(=); RYR1:ENST00000359596.8:c.12012+1104C>T:p.(=)

Pathogenicity Data:: Best Score: 0.06803417; CADD: 0.068 (0.306)

Frequency Data:: TOPMed: 0.0127%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38530987CT>C [0/1] rs59244176 (variation viewer)

Variant score: 0.018

Transcripts:: RYR1:ENST00000355481.8:c.11127-1502del:p.(=); RYR1:ENST00000359596.8:c.11142-1502del:p.(=)

Pathogenicity Data:: Best Score: 0.017573655; CADD: 0.018 (0.077)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.38537516G>C [0/1] rs568926591 (variation viewer)

Variant score: 0.011

Transcripts:: RYR1:ENST00000355481.8:c.11594-364G>C:p.(=); RYR1:ENST00000359596.8:c.11609-364G>C:p.(=)

Pathogenicity Data:: Best Score: 0.010763824; CADD: 0.011 (0.047)

Frequency Data:: TOPMed: 0.0120%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0133%

VWF

Exomiser Score: 0.050

Phenotype Score: 0.508

Variant Score: 0.550

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:193400 von Willebrand disease, type 1 - autosomal dominant; OMIM:277480 von Willebrand disease, type 3 - autosomal recessive; OMIM:613554 von Willebrand disease, types 2A, 2B, 2M, and 2N - autosomal dominant/recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.508

Variant Score: 0.271

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.5998495AAAAATATATATATATATATATATATAT>A [0/1]

Variant score: 0.271 CONTRIBUTING VARIANT

Transcripts:: VWF:ENST00000261405.9:c.5843-2300_5843-2274del:p.(=)

Pathogenicity Data:: Best Score: 0.271214; CADD: 0.271 (1.374)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.050

Phenotype Score: 0.508

Variant Score: 0.550

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6058081G>A [0/1] rs572236291 (variation viewer)

Variant score: 0.600 CONTRIBUTING VARIANT

Transcripts:: VWF:ENST00000261405.9:c.1534-37C>T:p.(=)

Pathogenicity Data:: Best Score: 0.64420485; CADD: 0.644 (4.488)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0040%; ExAC EAS: 0.0242%; ExAC NFE: 0.0032%; ExAC SAS: 0.4023%; gnomAD_E_EAS: 0.0118%; gnomAD_E_NFE: 0.0028%; gnomAD_E_OTH: 0.0186%; gnomAD_E_SAS: 0.4074%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1025%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6083353T>A [0/1] rs186117029 (variation viewer)

Variant score: 0.499 CONTRIBUTING VARIANT

Transcripts:: VWF:ENST00000261405.9:c.658-7802A>T:p.(=)

Pathogenicity Data:: Best Score: 0.796577; CADD: 0.797 (6.916)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.3329%; UK10K: 0.3835%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.4398%; gnomAD_G_OTH: 0.5092%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6092620T>A [1|1] rs147129737 (variation viewer)

Variant score: 0.472

Transcripts:: VWF:ENST00000261405.9:c.657+2840A>T:p.(=)

Pathogenicity Data:: Best Score: 0.47204125; CADD: 0.472 (2.774)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6041740C>G [0/1] rs574123803 (variation viewer)

Variant score: 0.281

Transcripts:: VWF:ENST00000261405.9:c.2442+2551G>C:p.(=)

Pathogenicity Data:: Best Score: 0.3223585; CADD: 0.322 (1.690)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.0661%; gnomAD_G_AFR: 0.0229%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6092614T>TGAGTGA [-/1] rs71064187 (variation viewer)

Variant score: 0.177

Transcripts:: VWF:ENST00000261405.9:c.657+2845_657+2846insTCACTC:p.(=)

Pathogenicity Data:: Best Score: 0.17718917; CADD: 0.177 (0.847)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6092614T>TGAGTGAGAGA [-/1] rs71064187 (variation viewer)

Variant score: 0.165

Transcripts:: VWF:ENST00000261405.9:c.657+2845_657+2846insTCTCTCACTC:p.(=)

Pathogenicity Data:: Best Score: 0.16458935; CADD: 0.165 (0.781)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.5980212TAGGG>T [0/1] rs1226435022 (variation viewer)

Variant score: 0.127

Transcripts:: VWF:ENST00000261405.9:c.7287+1570_7287+1573del:p.(=)

Pathogenicity Data:: Best Score: 0.12662655; CADD: 0.127 (0.588)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.6108334T>TATACACACACAC [1/1] rs374693235 (variation viewer)

Variant score: 0.105

Transcripts:: VWF:ENST00000261405.9:c.532+2039_532+2040insGTGTGTGTGTAT:p.(=)

Pathogenicity Data:: Best Score: 0.10525352; CADD: 0.105 (0.483)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.5964051C>CA [0/1] rs541793303 (variation viewer)

Variant score: 0.078

Transcripts:: VWF:ENST00000261405.9:c.7887+3434_7887+3435insT:p.(=)

Pathogenicity Data:: Best Score: 0.09572607; CADD: 0.096 (0.437)

Frequency Data:: gnomAD_G_AFR: 0.8471%; gnomAD_G_AMR: 0.1199%; gnomAD_G_EAS: 0.1861%; gnomAD_G_FIN: 0.0598%; gnomAD_G_NFE: 0.1234%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.5983401G>GGATA [-/1] rs58264371 (variation viewer)

Variant score: 0.028

Transcripts:: VWF:ENST00000261405.9:c.6977-148_6977-147insTATC:p.(=)

Pathogenicity Data:: Best Score: 0.17510247; CADD: 0.175 (0.836)

Frequency Data:: 1000Genomes: 1.9770%; TOPMed: 1.9770%

RIPK1

Exomiser Score: 0.049

Phenotype Score: 0.504

Variant Score: 0.554

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618108 Immunodeficiency 57 with autoinflammation - autosomal recessive; OMIM:618852 Autoinflammation with episodic fever and lymphadenopathy - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.255

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr6:g.3076699C>CATATATATATATAT [0|1] rs10526418 (variation viewer)

Variant score: 0.255 CONTRIBUTING VARIANT

Transcripts:: RIPK1:ENST00000259808.9:c.-60-65_-60-64insATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.2547534; CADD: 0.255 (1.277)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.049

Phenotype Score: 0.504

Variant Score: 0.554

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.3054256CAAA>C [1/1] rs35936166 (variation viewer)

Variant score: 0.554 CONTRIBUTING VARIANT

Transcripts:: RIPK1:ENST00000259808.9::; RIPK1:ENST00000401898.2::

Pathogenicity Data:: Best Score: 0.5540358; CADD: 0.554 (3.507)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.3081860TAAAAAAA>T [-/1] rs58330257 (variation viewer)

Variant score: 0.125

Transcripts:: RIPK1:ENST00000259808.9:c.459+745_459+751del:p.(=); RIPK1:ENST00000380409.2:c.459+745_459+751del:p.(=)

Pathogenicity Data:: Best Score: 0.12541908; CADD: 0.125 (0.582)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.3090856T>TACCTACCTGCCGCACCTAGTAACCGCAGAGTACCTACCTGCCGCACCTAGTAACCGCAGCGC [1/1]

Variant score: 0.000

Transcripts:: RIPK1:ENST00000259808.9:c.915+1199_915+1200insACCTACCTGCCGCACCTAGTAACCGCAGAGTACCTACCTGCCGCACCTAGTAACCGCAGCGC:p.(=); RIPK1:ENST00000380409.2:c.915+1199_915+1200insACCTACCTGCCGCACCTAGTAACCGCAGAGTACCTACCTGCCGCACCTAGTAACCGCAGCGC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NDUFA4

Exomiser Score: 0.048

Phenotype Score: 0.252

Variant Score: 0.837

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFA4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: ORPHA:255241 Leigh syndrome with leukodystrophy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.048

Phenotype Score: 0.252

Variant Score: 0.837

Variants contributing to score:

INTERGENIC_VARIANT chr7:g.10923694TACAC>T [0/1] rs36095837 (variation viewer)

Variant score: 0.837 CONTRIBUTING VARIANT

Transcripts:: NDUFA4:ENST00000339600.6::; NDUFA4:ENST00000453188.1::

Pathogenicity Data:: Best Score: 0.83680755; CADD: 0.837 (7.873)

Frequency Data:: No frequency data

Other passed variants:

OTUB1

Exomiser Score: 0.048

Phenotype Score: 0.505

Variant Score: 0.549

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.048

Phenotype Score: 0.505

Variant Score: 0.549

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.63990597A>AAAAT [1/1] rs71039698 (variation viewer)

Variant score: 0.549 CONTRIBUTING VARIANT

Transcripts:: OTUB1:ENST00000422031.6:c.219+1845_219+1846insAAAT:p.(=); OTUB1:ENST00000428192.6:c.219+1845_219+1846insAAAT:p.(=); OTUB1:ENST00000535715.5:c.219+1845_219+1846insAAAT:p.(=); OTUB1:ENST00000538426.5:c.219+1845_219+1846insAAAT:p.(=); OTUB1:ENST00000541478.5:c.120+2199_120+2200insAAAT:p.(=); OTUB1:ENST00000543004.5:c.246+1845_246+1846insAAAT:p.(=); OTUB1:ENST00000543988.1:c.129+1845_129+1846insAAAT:p.(=)

Pathogenicity Data:: Best Score: 0.5491833; CADD: 0.549 (3.460)

Frequency Data:: No frequency data

Other passed variants:

PTGES

Exomiser Score: 0.048

Phenotype Score: 0.503

Variant Score: 0.552

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.048

Phenotype Score: 0.503

Variant Score: 0.552

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.129750181C>T [0/1] rs957170306 (variation viewer)

Variant score: 0.552 CONTRIBUTING VARIANT

Transcripts:: PTGES:ENST00000340607.5:c.127-1444G>A:p.(=)

Pathogenicity Data:: Best Score: 0.55321354; CADD: 0.553 (3.499)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.016

Phenotype Score: 0.503

Variant Score: 0.431

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.129750181C>T [0/1] rs957170306 (variation viewer)

Variant score: 0.552 CONTRIBUTING VARIANT

Transcripts:: PTGES:ENST00000340607.5:c.127-1444G>A:p.(=)

Pathogenicity Data:: Best Score: 0.55321354; CADD: 0.553 (3.499)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0200%

UPSTREAM_GENE_VARIANT chr9:g.129754734G>T [0/1] rs1311134172 (variation viewer)

Variant score: 0.310 CONTRIBUTING VARIANT

Transcripts:: PTGES:ENST00000340607.5::; PTGES:ENST00000425374.1::

Pathogenicity Data:: Best Score: 0.30960125; CADD: 0.310 (1.609)

Frequency Data:: TOPMed: 0.0016%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.129746456C>T [0/1] rs117319270 (variation viewer)

Variant score: 0.032

Transcripts:: PTGES:ENST00000340607.5:c.209+2199G>A:p.(=)

Pathogenicity Data:: Best Score: 0.055286765; CADD: 0.055 (0.247)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.8681%; UK10K: 1.4282%; gnomAD_G_AFR: 0.1606%; gnomAD_G_AMR: 0.7177%; gnomAD_G_FIN: 0.3723%; gnomAD_G_NFE: 1.1862%; gnomAD_G_OTH: 1.2220%

LFNG

Exomiser Score: 0.047

Phenotype Score: 0.507

Variant Score: 0.546

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:609813 Spondylocostal dysostosis 3, autosomal recessive - autosomal recessive; ORPHA:2311 Autosomal recessive spondylocostal dysostosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.008

Phenotype Score: 0.254

Variant Score: 0.629

Variants contributing to score:

INTERGENIC_VARIANT chr7:g.2535105A>G [0/1] rs1473501001 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: LFNG:ENST00000359574.7::

Pathogenicity Data:: Best Score: 0.6339841; CADD: 0.634 (4.365)

Frequency Data:: gnomAD_G_AFR: 0.0604%; gnomAD_G_FIN: 0.0313%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.047

Phenotype Score: 0.507

Variant Score: 0.546

Variants contributing to score:

INTERGENIC_VARIANT chr7:g.2535105A>G [0/1] rs1473501001 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: LFNG:ENST00000359574.7::

Pathogenicity Data:: Best Score: 0.6339841; CADD: 0.634 (4.365)

Frequency Data:: gnomAD_G_AFR: 0.0604%; gnomAD_G_FIN: 0.0313%

INTERGENIC_VARIANT chr7:g.2536072G>A [0/1] rs28668123 (variation viewer)

Variant score: 0.463 CONTRIBUTING VARIANT

Transcripts:: LFNG:ENST00000359574.7::

Pathogenicity Data:: Best Score: 0.46333903; CADD: 0.463 (2.703)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr7:g.2497081A>G [0/1] rs62444241 (variation viewer)

Variant score: 0.381

Transcripts:: LFNG:ENST00000402506.5::; LFNG:ENST00000614228.1::

Pathogenicity Data:: Best Score: 0.6079874; CADD: 0.608 (4.067)

Frequency Data:: 1000Genomes: 0.7388%; TOPMed: 0.6506%; UK10K: 0.8992%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 1.1808%; gnomAD_G_OTH: 0.8147%

POLG

Exomiser Score: 0.047

Phenotype Score: 0.864

Variant Score: 0.140

Phenotype matches:

Phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.521 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:157640 Progressive external ophthalmoplegia, autosomal dominant 1 - autosomal dominant; OMIM:203700 Mitochondrial DNA depletion syndrome 4A (Alpers type) - autosomal recessive; OMIM:258450 Progressive external ophthalmoplegia, autosomal recessive 1 - autosomal recessive; OMIM:607459 Mitochondrial recessive ataxia syndrome (includes SANDO and SCAE) - autosomal recessive; OMIM:613662 Mitochondrial DNA depletion syndrome 4B (MNGIE type) - autosomal recessive; ORPHA:254886 Autosomal recessive progressive external ophthalmoplegia; ORPHA:254892 Autosomal dominant progressive external ophthalmoplegia; ORPHA:298 Mitochondrial neurogastrointestinal encephalomyopathy; ORPHA:70595 Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome; ORPHA:726 Alpers-Huttenlocher syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.047

Phenotype Score: 0.864

Variant Score: 0.140

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.89325090G>A [0|1] rs1424943007 (variation viewer)

Variant score: 0.244 CONTRIBUTING VARIANT

Transcripts:: POLG:ENST00000268124.10:c.1949+360C>T:p.(=); POLG:ENST00000442287.6:c.1949+360C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4201709; CADD: 0.420 (2.367)

Frequency Data:: gnomAD_G_AFR: 0.1768%; gnomAD_G_AMR: 0.4854%; gnomAD_G_ASJ: 1.4085%; gnomAD_G_EAS: 0.3529%; gnomAD_G_FIN: 0.9182%; gnomAD_G_NFE: 1.2789%; gnomAD_G_OTH: 0.5263%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.89328381G>A [0/1] rs147036984 (variation viewer)

Variant score: 0.036 CONTRIBUTING VARIANT

Transcripts:: POLG:ENST00000268124.10:c.1250+75C>T:p.(=); POLG:ENST00000442287.6:c.1250+75C>T:p.(=)

Pathogenicity Data:: Best Score: 0.036392868; CADD: 0.036 (0.161)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0406%; UK10K: 0.0264%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0334%; gnomAD_G_OTH: 0.1018%

Other passed variants:

PSEN1

Exomiser Score: 0.046

Phenotype Score: 0.507

Variant Score: 0.543

Phenotype matches:

Phenotypic similarity 0.473 to Behavioral variant of frontotemporal dementia associated with PSEN1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000719, Inappropriate behavior

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:172700 Pick disease - autosomal dominant; OMIM:600274 Dementia, frontotemporal - autosomal dominant; OMIM:607822 Alzheimer disease, type 3, with spastic paraparesis and unusual plaques - autosomal dominant; OMIM:613694 Cardiomyopathy, dilated, 1U - autosomal dominant; OMIM:613737 ?Acne inversa, familial, 3 (unconfirmed); ORPHA:100069 Semantic dementia; ORPHA:100069 Semantic dementia; ORPHA:100070 Progressive non-fluent aphasia; ORPHA:100070 Progressive non-fluent aphasia; ORPHA:1020 Early-onset autosomal dominant Alzheimer disease; ORPHA:154 Familial isolated dilated cardiomyopathy; ORPHA:275864 Behavioral variant of frontotemporal dementia; ORPHA:275864 Behavioral variant of frontotemporal dementia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.046

Phenotype Score: 0.507

Variant Score: 0.543

Variants contributing to score:

INTERGENIC_VARIANT chr14:g.73130718G>A [0/1]

Variant score: 0.543 CONTRIBUTING VARIANT

Transcripts:: PSEN1:ENST00000394157.7::; PSEN1:ENST00000261973.12::

Pathogenicity Data:: Best Score: 0.543017; CADD: 0.543 (3.401)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.253

Variant Score: 0.347

Variants contributing to score:

INTERGENIC_VARIANT chr14:g.73130718G>A [0/1]

Variant score: 0.543 CONTRIBUTING VARIANT

Transcripts:: PSEN1:ENST00000394157.7::; PSEN1:ENST00000261973.12::

Pathogenicity Data:: Best Score: 0.543017; CADD: 0.543 (3.401)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.73188498AAATT>A [0/1] rs1034764443 (variation viewer)

Variant score: 0.151 CONTRIBUTING VARIANT

Transcripts:: PSEN1:ENST00000324501.10:c.548+1579_548+1582del:p.(=); PSEN1:ENST00000357710.8:c.536+1579_536+1582del:p.(=); PSEN1:ENST00000394164.5:c.536+1579_536+1582del:p.(=); PSEN1:ENST00000406768.1:c.272+1579_272+1582del:p.(=); PSEN1:ENST00000557511.5:c.548+1579_548+1582del:p.(=)

Pathogenicity Data:: Best Score: 0.15101504; CADD: 0.151 (0.711)

Frequency Data:: TOPMed: 0.0048%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.73202450ATATATATATATAT>A [1/1]

Variant score: 0.121

Transcripts:: PSEN1:ENST00000324501.10:c.869-3935_869-3923del:p.(=); PSEN1:ENST00000357710.8:c.857-3935_857-3923del:p.(=); PSEN1:ENST00000394164.5:c.857-3935_857-3923del:p.(=); PSEN1:ENST00000406768.1:c.593-3935_593-3923del:p.(=); PSEN1:ENST00000557511.5:c.869-3935_869-3923del:p.(=)

Pathogenicity Data:: Best Score: 0.12117988; CADD: 0.121 (0.561)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.73196252G>GTAC [0/1] rs138852262 (variation viewer)

Variant score: 0.108

Transcripts:: PSEN1:ENST00000324501.10:c.770-1779_770-1778insTAC:p.(=); PSEN1:ENST00000357710.8:c.758-1779_758-1778insTAC:p.(=); PSEN1:ENST00000394164.5:c.758-1779_758-1778insTAC:p.(=); PSEN1:ENST00000406768.1:c.494-1779_494-1778insTAC:p.(=); PSEN1:ENST00000557511.5:c.770-1779_770-1778insTAC:p.(=)

Pathogenicity Data:: Best Score: 0.8001059; CADD: 0.800 (6.992)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 1.0540%; UK10K: 1.2298%; gnomAD_G_AFR: 0.2867%; gnomAD_G_AMR: 1.5588%; gnomAD_G_ASJ: 2.0000%; gnomAD_G_FIN: 1.7981%; gnomAD_G_NFE: 1.8728%; gnomAD_G_OTH: 1.8405%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.73151878TTA>T [1/1] rs768963474 (variation viewer)

Variant score: 0.108

Transcripts:: PSEN1:ENST00000324501.10:c.87+3773_87+3774del:p.(=); PSEN1:ENST00000357710.8:c.75+3785_75+3786del:p.(=); PSEN1:ENST00000394157.7:c.87+3773_87+3774del:p.(=); PSEN1:ENST00000394164.5:c.75+3785_75+3786del:p.(=); PSEN1:ENST00000557511.5:c.87+3773_87+3774del:p.(=)

Pathogenicity Data:: Best Score: 0.1077224; CADD: 0.108 (0.495)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.73201173C>T [0/1] rs188247683 (variation viewer)

Variant score: 0.051

Transcripts:: PSEN1:ENST00000324501.10:c.868+3044C>T:p.(=); PSEN1:ENST00000357710.8:c.856+3044C>T:p.(=); PSEN1:ENST00000394164.5:c.856+3044C>T:p.(=); PSEN1:ENST00000406768.1:c.592+3044C>T:p.(=); PSEN1:ENST00000557511.5:c.868+3044C>T:p.(=)

Pathogenicity Data:: Best Score: 0.37640882; CADD: 0.376 (2.051)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.9182%; UK10K: 1.1637%; gnomAD_G_AFR: 0.2754%; gnomAD_G_AMR: 1.4320%; gnomAD_G_ASJ: 2.0000%; gnomAD_G_FIN: 1.8603%; gnomAD_G_NFE: 1.6825%; gnomAD_G_OTH: 1.7312%

SMARCA2

Exomiser Score: 0.046

Phenotype Score: 0.515

Variant Score: 0.532

Phenotype matches:

Proximity score 0.515 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.515 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Known diseases:: OMIM:601358 Nicolaides-Baraitser syndrome - autosomal dominant; ORPHA:3051 Intellectual disability-sparse hair-brachydactyly syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.046

Phenotype Score: 0.515

Variant Score: 0.532

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.2005175C>CAAAAAAAAA [0/1] rs201526008 (variation viewer)

Variant score: 0.532 CONTRIBUTING VARIANT

Transcripts:: SMARCA2:ENST00000357248.8::; SMARCA2:ENST00000436102.1::

Pathogenicity Data:: Best Score: 0.53237253; CADD: 0.532 (3.301)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.258

Variant Score: 0.426

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.2005175C>CAAAAAAAAA [0/1] rs201526008 (variation viewer)

Variant score: 0.532 CONTRIBUTING VARIANT

Transcripts:: SMARCA2:ENST00000357248.8::; SMARCA2:ENST00000436102.1::

Pathogenicity Data:: Best Score: 0.53237253; CADD: 0.532 (3.301)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.2005471T>C [0/1]

Variant score: 0.319 CONTRIBUTING VARIANT

Transcripts:: SMARCA2:ENST00000357248.8::; SMARCA2:ENST00000436102.1::

Pathogenicity Data:: Best Score: 0.31876022; CADD: 0.319 (1.667)

Frequency Data:: No frequency data

Other passed variants:

REGULATORY_REGION_VARIANT chr9:g.1665315T>TAAAAAA [0/1] rs570282901 (variation viewer)

Variant score: 0.309

Transcripts:

Pathogenicity Data:: Best Score: 0.30864674; CADD: 0.309 (1.603)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.2211280C>CTTTTTTTTTTTTTTTT [1/1] rs551091009 (variation viewer)

Variant score: 0.170

Transcripts:: SMARCA2:ENST00000302401.8::; SMARCA2:ENST00000382100.8::

Pathogenicity Data:: Best Score: 0.1701492; CADD: 0.170 (0.810)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.2206159CTTTT>C [1|1] rs57374994 (variation viewer)

Variant score: 0.115

Transcripts:: SMARCA2:ENST00000302401.8::; SMARCA2:ENST00000382100.8::

Pathogenicity Data:: Best Score: 0.11529189; CADD: 0.115 (0.532)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.2077896T>C [0/1] rs1261082086 (variation viewer)

Variant score: 0.019

Transcripts:: SMARCA2:ENST00000349721.8:c.2184+120T>C:p.(=); SMARCA2:ENST00000357248.8:c.2184+120T>C:p.(=); SMARCA2:ENST00000382194.6:c.2184+120T>C:p.(=); SMARCA2:ENST00000382203.5:c.2184+120T>C:p.(=); SMARCA2:ENST00000450198.6:c.2184+120T>C:p.(=)

Pathogenicity Data:: Best Score: 0.01915586; CADD: 0.019 (0.084)

Frequency Data:: gnomAD_G_NFE: 0.0067%

COMT

Exomiser Score: 0.045

Phenotype Score: 0.864

Variant Score: 0.137

Phenotype matches:

Phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Phenotypic similarity 0.454 to mouse mutant involving COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:167870 Panic disorder, susceptibility to (susceptibility); OMIM:181500 Schizophrenia, susceptibility to (susceptibility); ORPHA:567 22q11.2 deletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.045

Phenotype Score: 0.864

Variant Score: 0.137

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.19950261T>TTTTG [0/1] rs763598655 (variation viewer)

Variant score: 0.137 CONTRIBUTING VARIANT

Transcripts:: COMT:ENST00000361682.11:c.-92+8364_-92+8365insTTTG:p.(=); COMT:ENST00000403184.5:c.-92+8364_-92+8365insTTTG:p.(=); COMT:ENST00000403710.5:c.-386+8364_-386+8365insTTTG:p.(=); COMT:ENST00000407537.5:c.-270+8364_-270+8365insTTTG:p.(=)

Pathogenicity Data:: Best Score: 0.1368227; CADD: 0.137 (0.639)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.432

Variant Score: 0.378

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.19947489A>G [0/1] rs568691813 (variation viewer)

Variant score: 0.618 CONTRIBUTING VARIANT

Transcripts:: COMT:ENST00000361682.11:c.-92+5592A>G:p.(=); COMT:ENST00000403184.5:c.-92+5592A>G:p.(=); COMT:ENST00000403710.5:c.-386+5592A>G:p.(=); COMT:ENST00000407537.5:c.-270+5592A>G:p.(=)

Pathogenicity Data:: Best Score: 0.67408824; CADD: 0.674 (4.869)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0581%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.4773%; gnomAD_G_NFE: 0.0866%

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.19950261T>TTTTG [0/1] rs763598655 (variation viewer)

Variant score: 0.137 CONTRIBUTING VARIANT

Transcripts:: COMT:ENST00000361682.11:c.-92+8364_-92+8365insTTTG:p.(=); COMT:ENST00000403184.5:c.-92+8364_-92+8365insTTTG:p.(=); COMT:ENST00000403710.5:c.-386+8364_-386+8365insTTTG:p.(=); COMT:ENST00000407537.5:c.-270+8364_-270+8365insTTTG:p.(=)

Pathogenicity Data:: Best Score: 0.1368227; CADD: 0.137 (0.639)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.19956137CTT>C [1|1] rs71186638 (variation viewer)

Variant score: 0.115

Transcripts:: COMT:ENST00000361682.11:c.-91-5061_-91-5060del:p.(=); COMT:ENST00000403184.5:c.-91-5061_-91-5060del:p.(=); COMT:ENST00000403710.5:c.-385-5061_-385-5060del:p.(=); COMT:ENST00000406520.7:c.-92+4484_-92+4485del:p.(=); COMT:ENST00000407537.5:c.-269-5061_-269-5060del:p.(=)

Pathogenicity Data:: Best Score: 0.11529189; CADD: 0.115 (0.532)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.19946910GT>G [0|1] rs35689277 (variation viewer)

Variant score: 0.088

Transcripts:: COMT:ENST00000361682.11:c.-92+5014del:p.(=); COMT:ENST00000403184.5:c.-92+5014del:p.(=); COMT:ENST00000403710.5:c.-386+5014del:p.(=); COMT:ENST00000407537.5:c.-270+5014del:p.(=)

Pathogenicity Data:: Best Score: 0.087779105; CADD: 0.088 (0.399)

Frequency Data:: No frequency data

PTK2B

Exomiser Score: 0.044

Phenotype Score: 0.507

Variant Score: 0.539

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.044

Phenotype Score: 0.507

Variant Score: 0.539

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.27378601C>CTGTG [-/1] rs58485965 (variation viewer)

Variant score: 0.539 CONTRIBUTING VARIANT

Transcripts:: PTK2B:ENST00000346049.10:c.-37-18947_-37-18946insTGTG:p.(=); PTK2B:ENST00000397501.5:c.-37-18947_-37-18946insTGTG:p.(=); PTK2B:ENST00000420218.3:c.-37-18947_-37-18946insTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.53889483; CADD: 0.539 (3.362)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.507

Variant Score: 0.395

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.27378601C>CTGTG [-/1] rs58485965 (variation viewer)

Variant score: 0.539 CONTRIBUTING VARIANT

Transcripts:: PTK2B:ENST00000346049.10:c.-37-18947_-37-18946insTGTG:p.(=); PTK2B:ENST00000397501.5:c.-37-18947_-37-18946insTGTG:p.(=); PTK2B:ENST00000420218.3:c.-37-18947_-37-18946insTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.53889483; CADD: 0.539 (3.362)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.27345070G>A [0/1] rs979275633 (variation viewer)

Variant score: 0.250 CONTRIBUTING VARIANT

Transcripts:: PTK2B:ENST00000346049.10:c.-38+19389G>A:p.(=); PTK2B:ENST00000397501.5:c.-38+19389G>A:p.(=); PTK2B:ENST00000420218.3:c.-38+19389G>A:p.(=)

Pathogenicity Data:: Best Score: 0.25062364; CADD: 0.251 (1.253)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.27350990A>AAAAAATATATATATATAT [0/1]

Variant score: 0.224

Transcripts:: PTK2B:ENST00000346049.10:c.-38+25309_-38+25310insAAAAATATATATATATAT:p.(=); PTK2B:ENST00000397501.5:c.-38+25309_-38+25310insAAAAATATATATATATAT:p.(=); PTK2B:ENST00000420218.3:c.-38+25309_-38+25310insAAAAATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.22446752; CADD: 0.224 (1.104)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.27438918G>A [0/1] rs184233417 (variation viewer)

Variant score: 0.008

Transcripts:: PTK2B:ENST00000346049.10:c.1644-113G>A:p.(=); PTK2B:ENST00000397501.5:c.1644-113G>A:p.(=); PTK2B:ENST00000420218.3:c.1644-113G>A:p.(=); PTK2B:ENST00000517339.5:c.1644-113G>A:p.(=)

Pathogenicity Data:: Best Score: 0.009624243; CADD: 0.010 (0.042)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1864%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.3580%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.6297%; gnomAD_G_NFE: 0.4602%; gnomAD_G_OTH: 0.3055%

MAPK8

Exomiser Score: 0.043

Phenotype Score: 0.502

Variant Score: 0.541

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.200

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48413815T>TTATATATA [-/1] rs59042608 (variation viewer)

Variant score: 0.200 CONTRIBUTING VARIANT

Transcripts:: MAPK8:ENST00000360332.7:c.450+3647_450+3648insTATATATA:p.(=); MAPK8:ENST00000374176.8:c.450+3647_450+3648insTATATATA:p.(=); MAPK8:ENST00000374179.8:c.450+3647_450+3648insTATATATA:p.(=); MAPK8:ENST00000374182.7:c.450+3647_450+3648insTATATATA:p.(=); MAPK8:ENST00000374189.5:c.450+3647_450+3648insTATATATA:p.(=); MAPK8:ENST00000395611.7:c.450+3647_450+3648insTATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.19979733; CADD: 0.200 (0.968)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.043

Phenotype Score: 0.502

Variant Score: 0.541

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333830A>G [0|1] rs1190535662 (variation viewer)

Variant score: 0.549 CONTRIBUTING VARIANT

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7865A>G:p.(=); MAPK8:ENST00000374189.5:c.-50+27009A>G:p.(=); MAPK8:ENST00000395611.7:c.-50+27009A>G:p.(=); MAPK8:ENST00000476134.1:c.-50+25542A>G:p.(=)

Pathogenicity Data:: Best Score: 0.63017184; CADD: 0.630 (4.320)

Frequency Data:: gnomAD_G_AFR: 0.6706%; gnomAD_G_AMR: 0.5515%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.6387%; gnomAD_G_FIN: 0.6232%; gnomAD_G_NFE: 0.3336%; gnomAD_G_OTH: 0.5464%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333832A>G [0|1] rs1046257467 (variation viewer)

Variant score: 0.534 CONTRIBUTING VARIANT

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7867A>G:p.(=); MAPK8:ENST00000374189.5:c.-50+27011A>G:p.(=); MAPK8:ENST00000395611.7:c.-50+27011A>G:p.(=); MAPK8:ENST00000476134.1:c.-50+25544A>G:p.(=)

Pathogenicity Data:: Best Score: 0.61523104; CADD: 0.615 (4.148)

Frequency Data:: gnomAD_G_AFR: 0.6803%; gnomAD_G_AMR: 0.5415%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.5435%; gnomAD_G_FIN: 0.5655%; gnomAD_G_NFE: 0.3153%; gnomAD_G_OTH: 0.5405%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333818T>A [0|1] rs1323368245 (variation viewer)

Variant score: 0.469

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7853T>A:p.(=); MAPK8:ENST00000374189.5:c.-50+26997T>A:p.(=); MAPK8:ENST00000395611.7:c.-50+26997T>A:p.(=); MAPK8:ENST00000476134.1:c.-50+25530T>A:p.(=)

Pathogenicity Data:: Best Score: 0.5211494; CADD: 0.521 (3.198)

Frequency Data:: gnomAD_G_AFR: 0.5527%; gnomAD_G_AMR: 0.3690%; gnomAD_G_FIN: 0.4464%; gnomAD_G_NFE: 0.3482%; gnomAD_G_OTH: 0.2801%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333842G>A [0|1] rs1426590772 (variation viewer)

Variant score: 0.399

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7877G>A:p.(=); MAPK8:ENST00000374189.5:c.-50+27021G>A:p.(=); MAPK8:ENST00000395611.7:c.-50+27021G>A:p.(=); MAPK8:ENST00000476134.1:c.-50+25554G>A:p.(=)

Pathogenicity Data:: Best Score: 0.46592778; CADD: 0.466 (2.724)

Frequency Data:: gnomAD_G_AFR: 0.5397%; gnomAD_G_AMR: 0.7246%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.2679%; gnomAD_G_FIN: 0.5126%; gnomAD_G_NFE: 0.2717%; gnomAD_G_OTH: 0.1393%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333827C>T [0|1] rs1445702645 (variation viewer)

Variant score: 0.390

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7862C>T:p.(=); MAPK8:ENST00000374189.5:c.-50+27006C>T:p.(=); MAPK8:ENST00000395611.7:c.-50+27006C>T:p.(=); MAPK8:ENST00000476134.1:c.-50+25539C>T:p.(=)

Pathogenicity Data:: Best Score: 0.45699978; CADD: 0.457 (2.652)

Frequency Data:: gnomAD_G_AFR: 0.7194%; gnomAD_G_AMR: 0.7246%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.7339%; gnomAD_G_FIN: 0.6268%; gnomAD_G_NFE: 0.3499%; gnomAD_G_OTH: 0.4121%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333833G>A [0/1] rs1480570385 (variation viewer)

Variant score: 0.389

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7868G>A:p.(=); MAPK8:ENST00000374189.5:c.-50+27012G>A:p.(=); MAPK8:ENST00000395611.7:c.-50+27012G>A:p.(=); MAPK8:ENST00000476134.1:c.-50+25545G>A:p.(=)

Pathogenicity Data:: Best Score: 0.45007938; CADD: 0.450 (2.597)

Frequency Data:: gnomAD_G_AFR: 0.6962%; gnomAD_G_AMR: 0.5455%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.5445%; gnomAD_G_FIN: 0.5203%; gnomAD_G_NFE: 0.3151%; gnomAD_G_OTH: 0.5420%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333841G>C [0|1] rs1177914803 (variation viewer)

Variant score: 0.361

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7876G>C:p.(=); MAPK8:ENST00000374189.5:c.-50+27020G>C:p.(=); MAPK8:ENST00000395611.7:c.-50+27020G>C:p.(=); MAPK8:ENST00000476134.1:c.-50+25553G>C:p.(=)

Pathogenicity Data:: Best Score: 0.4017262; CADD: 0.402 (2.231)

Frequency Data:: gnomAD_G_AFR: 0.4934%; gnomAD_G_AMR: 0.5455%; gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.2712%; gnomAD_G_FIN: 0.5581%; gnomAD_G_NFE: 0.2151%

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333822A>G [0|1] rs1209921839 (variation viewer)

Variant score: 0.316

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7857A>G:p.(=); MAPK8:ENST00000374189.5:c.-50+27001A>G:p.(=); MAPK8:ENST00000395611.7:c.-50+27001A>G:p.(=); MAPK8:ENST00000476134.1:c.-50+25534A>G:p.(=)

Pathogenicity Data:: Best Score: 0.39060342; CADD: 0.391 (2.151)

Frequency Data:: gnomAD_G_AFR: 0.8322%; gnomAD_G_AMR: 0.5495%; gnomAD_G_ASJ: 0.3425%; gnomAD_G_EAS: 0.7246%; gnomAD_G_FIN: 0.8815%; gnomAD_G_NFE: 0.4578%; gnomAD_G_OTH: 0.2755%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48413815TTA>T [-/1] rs59042608 (variation viewer)

Variant score: 0.180

Transcripts:: MAPK8:ENST00000360332.7:c.450+3648_450+3649del:p.(=); MAPK8:ENST00000374176.8:c.450+3648_450+3649del:p.(=); MAPK8:ENST00000374179.8:c.450+3648_450+3649del:p.(=); MAPK8:ENST00000374182.7:c.450+3648_450+3649del:p.(=); MAPK8:ENST00000374189.5:c.450+3648_450+3649del:p.(=); MAPK8:ENST00000395611.7:c.450+3648_450+3649del:p.(=)

Pathogenicity Data:: Best Score: 0.17964846; CADD: 0.180 (0.860)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333783C>G [0|1] rs899881479 (variation viewer)

Variant score: 0.163

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7818C>G:p.(=); MAPK8:ENST00000374189.5:c.-50+26962C>G:p.(=); MAPK8:ENST00000395611.7:c.-50+26962C>G:p.(=); MAPK8:ENST00000476134.1:c.-50+25495C>G:p.(=)

Pathogenicity Data:: Best Score: 0.16266352; CADD: 0.163 (0.771)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr10:g.48333817A>C [0|1] rs1261376431 (variation viewer)

Variant score: 0.147

Transcripts:: MAPK8:ENST00000374179.8:c.-95+7852A>C:p.(=); MAPK8:ENST00000374189.5:c.-50+26996A>C:p.(=); MAPK8:ENST00000395611.7:c.-50+26996A>C:p.(=); MAPK8:ENST00000476134.1:c.-50+25529A>C:p.(=)

Pathogenicity Data:: Best Score: 0.16420454; CADD: 0.164 (0.779)

Frequency Data:: gnomAD_G_AFR: 0.5837%; gnomAD_G_AMR: 0.5556%; gnomAD_G_FIN: 0.5000%; gnomAD_G_NFE: 0.3401%; gnomAD_G_OTH: 0.4261%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48405106G>GATATATAT [-/1] rs10657070 (variation viewer)

Variant score: 0.087

Transcripts:: MAPK8:ENST00000360332.7:c.252+125_252+126insATATATAT:p.(=); MAPK8:ENST00000374176.8:c.252+125_252+126insATATATAT:p.(=); MAPK8:ENST00000374179.8:c.252+125_252+126insATATATAT:p.(=); MAPK8:ENST00000374182.7:c.252+125_252+126insATATATAT:p.(=); MAPK8:ENST00000374189.5:c.252+125_252+126insATATATAT:p.(=); MAPK8:ENST00000395611.7:c.252+125_252+126insATATATAT:p.(=); MAPK8:ENST00000476134.1:c.252+125_252+126insATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.60987836; CADD: 0.610 (4.088)

Frequency Data:: gnomAD_G_AFR: 1.7795%; gnomAD_G_AMR: 1.0870%; gnomAD_G_ASJ: 1.5267%; gnomAD_G_FIN: 1.0025%; gnomAD_G_NFE: 1.9928%; gnomAD_G_OTH: 1.0256%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48402346GCTTCA>G [0/1] rs1194213813 (variation viewer)

Variant score: 0.000

Transcripts:: MAPK8:ENST00000360332.7:c.122+565_122+569del:p.(=); MAPK8:ENST00000374176.8:c.122+565_122+569del:p.(=); MAPK8:ENST00000374179.8:c.122+565_122+569del:p.(=); MAPK8:ENST00000374182.7:c.122+565_122+569del:p.(=); MAPK8:ENST00000374189.5:c.122+565_122+569del:p.(=); MAPK8:ENST00000395611.7:c.122+565_122+569del:p.(=); MAPK8:ENST00000476134.1:c.122+565_122+569del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: TOPMed: 0.0016%

CHMP6

Exomiser Score: 0.042

Phenotype Score: 0.505

Variant Score: 0.534

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.164

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.80980625G>T [0/1]

Variant score: 0.164 CONTRIBUTING VARIANT

Transcripts:: CHMP6:ENST00000325167.9::

Pathogenicity Data:: Best Score: 0.16439694; CADD: 0.164 (0.780)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.042

Phenotype Score: 0.505

Variant Score: 0.534

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.81005821G>A [1/1]

Variant score: 0.534 CONTRIBUTING VARIANT

Transcripts:: CHMP6:ENST00000325167.9::

Pathogenicity Data:: Best Score: 0.5340922; CADD: 0.534 (3.317)

Frequency Data:: No frequency data

Other passed variants:

DTNA

Exomiser Score: 0.041

Phenotype Score: 0.504

Variant Score: 0.534

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:604169 Left ventricular noncompaction 1, with or without congenital heart defects - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.041

Phenotype Score: 0.504

Variant Score: 0.534

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34753366ATTTTTTTTTTTTTTTTATT>A [0/1] rs1482939161 (variation viewer)

Variant score: 0.534 CONTRIBUTING VARIANT

Transcripts:: DTNA:ENST00000283365.13:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000315456.10:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000348997.9:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000399121.9:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000554864.7:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000595022.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000596745.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000597599.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000598142.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000598334.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000598774.5:c.-1-2609_-1-2591del:p.(=)

Pathogenicity Data:: Best Score: 0.5335555; CADD: 0.534 (3.312)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.252

Variant Score: 0.482

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34753366ATTTTTTTTTTTTTTTTATT>A [0/1] rs1482939161 (variation viewer)

Variant score: 0.534 CONTRIBUTING VARIANT

Transcripts:: DTNA:ENST00000283365.13:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000315456.10:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000348997.9:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000399121.9:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000554864.7:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000595022.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000596745.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000597599.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000598142.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000598334.5:c.-1-2609_-1-2591del:p.(=); DTNA:ENST00000598774.5:c.-1-2609_-1-2591del:p.(=)

Pathogenicity Data:: Best Score: 0.5335555; CADD: 0.534 (3.312)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34598546G>A [0/1] rs1425071993 (variation viewer)

Variant score: 0.430 CONTRIBUTING VARIANT

Transcripts:: DTNA:ENST00000283365.13:c.-126-80922G>A:p.(=); DTNA:ENST00000315456.10:c.-126-80922G>A:p.(=); DTNA:ENST00000399121.9:c.-127+5008G>A:p.(=); DTNA:ENST00000554864.7:c.-127+5008G>A:p.(=); DTNA:ENST00000595022.5:c.-127+5008G>A:p.(=); DTNA:ENST00000596745.5:c.-126-80922G>A:p.(=); DTNA:ENST00000598334.5:c.-127+5008G>A:p.(=)

Pathogenicity Data:: Best Score: 0.43036062; CADD: 0.430 (2.444)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.34886925T>C [0/1] rs117028834 (variation viewer)

Variant score: 0.299

Transcripts:: DTNA:ENST00000598334.5:c.2035-3375T>C:p.(=); DTNA:ENST00000269192.11:c.*32-841T>C:p.(=); DTNA:ENST00000283365.13:c.*32-841T>C:p.(=); DTNA:ENST00000399121.9:c.*32-841T>C:p.(=); DTNA:ENST00000444659.5:c.*32-841T>C:p.(=); DTNA:ENST00000556414.7:c.*32-841T>C:p.(=); DTNA:ENST00000590831.2:c.*31+2149T>C:p.(=); DTNA:ENST00000591182.5:c.*32-841T>C:p.(=); DTNA:ENST00000595022.5:c.*32-841T>C:p.(=); DTNA:ENST00000598142.5:c.*32-841T>C:p.(=); DTNA:ENST00000601125.5:c.*32-841T>C:p.(=)

Pathogenicity Data:: Best Score: 0.52302015; CADD: 0.523 (3.215)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.5312%; UK10K: 0.9257%; gnomAD_G_AFR: 0.1946%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4868%; gnomAD_G_NFE: 1.1787%; gnomAD_G_OTH: 1.4257%

INTERGENIC_VARIANT chr18:g.34908494C>CT [0/1] rs140962815 (variation viewer)

Variant score: 0.237

Transcripts:: DTNA:ENST00000444659.5::; DTNA:ENST00000413393.5::

Pathogenicity Data:: Best Score: 0.23704308; CADD: 0.237 (1.175)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.34860220GTTT>G [1/1] rs55673388 (variation viewer)

Variant score: 0.203

Transcripts:: DTNA:ENST00000269192.11:c.692+1823_692+1825del:p.(=); DTNA:ENST00000283365.13:c.1394+1823_1394+1825del:p.(=); DTNA:ENST00000348997.9:c.1556+1823_1556+1825del:p.(=); DTNA:ENST00000399113.7:c.1565+1823_1565+1825del:p.(=); DTNA:ENST00000399121.9:c.1385+1823_1385+1825del:p.(=); DTNA:ENST00000444659.5:c.1565+1823_1565+1825del:p.(=); DTNA:ENST00000556414.7:c.521+1823_521+1825del:p.(=); DTNA:ENST00000591182.5:c.509+1823_509+1825del:p.(=); DTNA:ENST00000595022.5:c.1385+1823_1385+1825del:p.(=); DTNA:ENST00000596745.5:c.815+1823_815+1825del:p.(=); DTNA:ENST00000597599.5:c.1385+1823_1385+1825del:p.(=); DTNA:ENST00000597674.5:c.431+1823_431+1825del:p.(=); DTNA:ENST00000598142.5:c.1394+1823_1394+1825del:p.(=); DTNA:ENST00000598334.5:c.1385+1823_1385+1825del:p.(=); DTNA:ENST00000598774.5:c.1394+1823_1394+1825del:p.(=); DTNA:ENST00000599844.5:c.431+1823_431+1825del:p.(=); DTNA:ENST00000601125.5:c.431+1823_431+1825del:p.(=)

Pathogenicity Data:: Best Score: 0.20347393; CADD: 0.203 (0.988)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.34881437C>CT [0/1] rs752828928 (variation viewer)

Variant score: 0.194

Transcripts:: DTNA:ENST00000269192.11:c.1209-632_1209-631insT:p.(=); DTNA:ENST00000283365.13:c.1911-632_1911-631insT:p.(=); DTNA:ENST00000399113.7:c.2082-632_2082-631insT:p.(=); DTNA:ENST00000399121.9:c.1923-632_1923-631insT:p.(=); DTNA:ENST00000444659.5:c.2082-632_2082-631insT:p.(=); DTNA:ENST00000556414.7:c.1038-632_1038-631insT:p.(=); DTNA:ENST00000590831.2:c.360-632_360-631insT:p.(=); DTNA:ENST00000591182.5:c.1026-632_1026-631insT:p.(=); DTNA:ENST00000595022.5:c.1902-632_1902-631insT:p.(=); DTNA:ENST00000598142.5:c.1911-632_1911-631insT:p.(=); DTNA:ENST00000598334.5:c.1902-632_1902-631insT:p.(=); DTNA:ENST00000601125.5:c.948-632_948-631insT:p.(=)

Pathogenicity Data:: Best Score: 0.19387943; CADD: 0.194 (0.936)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.34859339C>T [0/1] rs181944756 (variation viewer)

Variant score: 0.181

Transcripts:: DTNA:ENST00000269192.11:c.692+941C>T:p.(=); DTNA:ENST00000283365.13:c.1394+941C>T:p.(=); DTNA:ENST00000348997.9:c.1556+941C>T:p.(=); DTNA:ENST00000399113.7:c.1565+941C>T:p.(=); DTNA:ENST00000399121.9:c.1385+941C>T:p.(=); DTNA:ENST00000444659.5:c.1565+941C>T:p.(=); DTNA:ENST00000556414.7:c.521+941C>T:p.(=); DTNA:ENST00000591182.5:c.509+941C>T:p.(=); DTNA:ENST00000595022.5:c.1385+941C>T:p.(=); DTNA:ENST00000596745.5:c.815+941C>T:p.(=); DTNA:ENST00000597599.5:c.1385+941C>T:p.(=); DTNA:ENST00000597674.5:c.431+941C>T:p.(=); DTNA:ENST00000598142.5:c.1394+941C>T:p.(=); DTNA:ENST00000598334.5:c.1385+941C>T:p.(=); DTNA:ENST00000598774.5:c.1394+941C>T:p.(=); DTNA:ENST00000599844.5:c.431+941C>T:p.(=); DTNA:ENST00000601125.5:c.431+941C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2670067; CADD: 0.267 (1.349)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.5527%; UK10K: 0.9654%; gnomAD_G_AFR: 0.1833%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 1.1797%; gnomAD_G_OTH: 1.2220%

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34747086C>T [0/1] rs117786051 (variation viewer)

Variant score: 0.154

Transcripts:: DTNA:ENST00000283365.13:c.-1-8890C>T:p.(=); DTNA:ENST00000315456.10:c.-1-8890C>T:p.(=); DTNA:ENST00000348997.9:c.-1-8890C>T:p.(=); DTNA:ENST00000399121.9:c.-1-8890C>T:p.(=); DTNA:ENST00000554864.7:c.-1-8890C>T:p.(=); DTNA:ENST00000595022.5:c.-1-8890C>T:p.(=); DTNA:ENST00000596745.5:c.-1-8890C>T:p.(=); DTNA:ENST00000597599.5:c.-1-8890C>T:p.(=); DTNA:ENST00000598142.5:c.-1-8890C>T:p.(=); DTNA:ENST00000598334.5:c.-1-8890C>T:p.(=); DTNA:ENST00000598774.5:c.-1-8890C>T:p.(=)

Pathogenicity Data:: Best Score: 0.21168464; CADD: 0.212 (1.033)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3703%; UK10K: 0.4364%; gnomAD_G_AFR: 0.1804%; gnomAD_G_FIN: 0.7179%; gnomAD_G_NFE: 1.1062%; gnomAD_G_OTH: 1.0753%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.34805359C>CT [0/1] rs201445148 (variation viewer)

Variant score: 0.130

Transcripts:: DTNA:ENST00000283365.13:c.363-860_363-859insT:p.(=); DTNA:ENST00000315456.10:c.363-860_363-859insT:p.(=); DTNA:ENST00000348997.9:c.363-860_363-859insT:p.(=); DTNA:ENST00000399113.7:c.363-860_363-859insT:p.(=); DTNA:ENST00000399121.9:c.363-860_363-859insT:p.(=); DTNA:ENST00000444659.5:c.363-860_363-859insT:p.(=); DTNA:ENST00000554864.7:c.363-860_363-859insT:p.(=); DTNA:ENST00000595022.5:c.363-860_363-859insT:p.(=); DTNA:ENST00000596745.5:c.363-860_363-859insT:p.(=); DTNA:ENST00000597599.5:c.363-860_363-859insT:p.(=); DTNA:ENST00000598142.5:c.363-860_363-859insT:p.(=); DTNA:ENST00000598334.5:c.363-860_363-859insT:p.(=); DTNA:ENST00000598774.5:c.363-860_363-859insT:p.(=)

Pathogenicity Data:: Best Score: 0.19202113; CADD: 0.192 (0.926)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.5567%; UK10K: 0.8992%; gnomAD_G_AFR: 0.1950%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4868%; gnomAD_G_NFE: 1.1938%; gnomAD_G_OTH: 1.2220%

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34517460C>CATGTGTGTGTGTGT [0/1] rs57616989 (variation viewer)

Variant score: 0.095

Transcripts:: DTNA:ENST00000283365.13:c.-127+23946_-127+23947insATGTGTGTGTGTGT:p.(=); DTNA:ENST00000315456.10:c.-127+23946_-127+23947insATGTGTGTGTGTGT:p.(=); DTNA:ENST00000596745.5:c.-127+23946_-127+23947insATGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.095309556; CADD: 0.095 (0.435)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr18:g.34475046G>A [0/1] rs191941723 (variation viewer)

Variant score: 0.074

Transcripts:: DTNA:ENST00000283365.13::

Pathogenicity Data:: Best Score: 0.09405881; CADD: 0.094 (0.429)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2963%; UK10K: 0.5686%; gnomAD_G_AFR: 0.1146%; gnomAD_G_FIN: 0.3440%; gnomAD_G_NFE: 0.9368%; gnomAD_G_OTH: 0.8197%

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34747438G>A [0/1] rs192927143 (variation viewer)

Variant score: 0.036

Transcripts:: DTNA:ENST00000283365.13:c.-1-8538G>A:p.(=); DTNA:ENST00000315456.10:c.-1-8538G>A:p.(=); DTNA:ENST00000348997.9:c.-1-8538G>A:p.(=); DTNA:ENST00000399121.9:c.-1-8538G>A:p.(=); DTNA:ENST00000554864.7:c.-1-8538G>A:p.(=); DTNA:ENST00000595022.5:c.-1-8538G>A:p.(=); DTNA:ENST00000596745.5:c.-1-8538G>A:p.(=); DTNA:ENST00000597599.5:c.-1-8538G>A:p.(=); DTNA:ENST00000598142.5:c.-1-8538G>A:p.(=); DTNA:ENST00000598334.5:c.-1-8538G>A:p.(=); DTNA:ENST00000598774.5:c.-1-8538G>A:p.(=)

Pathogenicity Data:: Best Score: 0.079974234; CADD: 0.080 (0.362)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.8792%; UK10K: 0.9918%; gnomAD_G_AFR: 0.2298%; gnomAD_G_AMR: 0.9592%; gnomAD_G_FIN: 0.4882%; gnomAD_G_NFE: 1.5186%; gnomAD_G_OTH: 1.6293%

FIVE_PRIME_UTR_INTRON_VARIANT chr18:g.34742629T>TTCTATTATCTATCTAGATAGATAGATAA [1/1] rs6146258 (variation viewer)

Variant score: 0.032

Transcripts:: DTNA:ENST00000283365.13:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000315456.10:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000348997.9:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000399121.9:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000554864.7:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000595022.5:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000596745.5:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000597599.5:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000598142.5:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000598334.5:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=); DTNA:ENST00000598774.5:c.-1-13347_-1-13346insTCTATTATCTATCTAGATAGATAGATAA:p.(=)

Pathogenicity Data:: Best Score: 0.03216797; CADD: 0.032 (0.142)

Frequency Data:: No frequency data

CTNNA1

Exomiser Score: 0.040

Phenotype Score: 0.508

Variant Score: 0.527

Phenotype matches:

Proximity score 0.508 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:608970 Macular dystrophy, patterned, 2 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.040

Phenotype Score: 0.508

Variant Score: 0.527

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138825482G>GTTTTTTTTTTTTTTT [0/1] rs756586452 (variation viewer)

Variant score: 0.527 CONTRIBUTING VARIANT

Transcripts:: CTNNA1:ENST00000302763.12:c.858+683_858+684insTTTTTTTTTTTTTTT:p.(=); CTNNA1:ENST00000518825.5:c.858+683_858+684insTTTTTTTTTTTTTTT:p.(=); CTNNA1:ENST00000627109.2:c.858+683_858+684insTTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.5267398; CADD: 0.527 (3.249)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.254

Variant Score: 0.571

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.138777029C>G [0/1] rs1234457764 (variation viewer)

Variant score: 0.615 CONTRIBUTING VARIANT

Transcripts:: CTNNA1:ENST00000302763.12:c.-2-4894C>G:p.(=); CTNNA1:ENST00000627109.2:c.-2-4894C>G:p.(=)

Pathogenicity Data:: Best Score: 0.6276083; CADD: 0.628 (4.290)

Frequency Data:: gnomAD_G_AFR: 0.0623%; gnomAD_G_AMR: 0.1276%; gnomAD_G_EAS: 0.1364%; gnomAD_G_FIN: 0.0602%; gnomAD_G_NFE: 0.0716%; gnomAD_G_OTH: 0.1087%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138825482G>GTTTTTTTTTTTTTTT [0/1] rs756586452 (variation viewer)

Variant score: 0.527 CONTRIBUTING VARIANT

Transcripts:: CTNNA1:ENST00000302763.12:c.858+683_858+684insTTTTTTTTTTTTTTT:p.(=); CTNNA1:ENST00000518825.5:c.858+683_858+684insTTTTTTTTTTTTTTT:p.(=); CTNNA1:ENST00000627109.2:c.858+683_858+684insTTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.5267398; CADD: 0.527 (3.249)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.138755845CTTTTTTTTTTT>C [1/1] rs60260246 (variation viewer)

Variant score: 0.367

Transcripts:: CTNNA1:ENST00000302763.12:c.-3+2336_-3+2346del:p.(=); CTNNA1:ENST00000627109.2:c.-3+2336_-3+2346del:p.(=)

Pathogenicity Data:: Best Score: 0.36671382; CADD: 0.367 (1.984)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138915930T>A [0/1] rs188290793 (variation viewer)

Variant score: 0.274

Transcripts:: CTNNA1:ENST00000302763.12:c.1390-1812T>A:p.(=); CTNNA1:ENST00000518825.5:c.1390-1812T>A:p.(=); CTNNA1:ENST00000540387.5:c.280-1812T>A:p.(=); CTNNA1:ENST00000627109.2:c.1390-1812T>A:p.(=)

Pathogenicity Data:: Best Score: 0.27589756; CADD: 0.276 (1.402)

Frequency Data:: TOPMed: 0.0223%; UK10K: 0.0397%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138885562C>T [0/1]

Variant score: 0.263

Transcripts:: CTNNA1:ENST00000302763.12:c.1063-650C>T:p.(=); CTNNA1:ENST00000518825.5:c.1063-650C>T:p.(=); CTNNA1:ENST00000627109.2:c.1063-650C>T:p.(=); CTNNA1:ENST00000540387.5:c.-48-650C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2626053; CADD: 0.263 (1.323)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr5:g.138739191T>TGAGGCAGAGGGTGAGGCAGAGGGGAG [1|1] rs139679559 (variation viewer)

Variant score: 0.194

Transcripts:: CTNNA1:ENST00000627109.2::; CTNNA1:ENST00000475257.1::

Pathogenicity Data:: Best Score: 0.19406503; CADD: 0.194 (0.937)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138879171T>TA [0/1] rs35271091 (variation viewer)

Variant score: 0.128

Transcripts:: CTNNA1:ENST00000302763.12:c.1063-7041_1063-7040insA:p.(=); CTNNA1:ENST00000518825.5:c.1063-7041_1063-7040insA:p.(=); CTNNA1:ENST00000627109.2:c.1063-7041_1063-7040insA:p.(=); CTNNA1:ENST00000540387.5:c.-49+3433_-49+3434insA:p.(=)

Pathogenicity Data:: Best Score: 0.12763143; CADD: 0.128 (0.593)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.138768558GT>G [1/1] rs36038829 (variation viewer)

Variant score: 0.069

Transcripts:: CTNNA1:ENST00000302763.12:c.-2-13364del:p.(=); CTNNA1:ENST00000627109.2:c.-2-13364del:p.(=)

Pathogenicity Data:: Best Score: 0.06910652; CADD: 0.069 (0.311)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138852871G>GCGCACACACACACGCGCGCGCGCA [1|1] rs869240008 (variation viewer)

Variant score: 0.049

Transcripts:: CTNNA1:ENST00000302763.12:c.1062+25153_1062+25154insCGCACACACACACGCGCGCGCGCA:p.(=); CTNNA1:ENST00000518825.5:c.1062+25153_1062+25154insCGCACACACACACGCGCGCGCGCA:p.(=); CTNNA1:ENST00000627109.2:c.1062+25153_1062+25154insCGCACACACACACGCGCGCGCGCA:p.(=)

Pathogenicity Data:: Best Score: 0.048957348; CADD: 0.049 (0.218)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138810914A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA1:ENST00000302763.12:c.468+710A>*:p.(=); CTNNA1:ENST00000518825.5:c.468+710A>*:p.(=); CTNNA1:ENST00000627109.2:c.468+710A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138810963A>* [-/1]

Variant score: 0.000

Transcripts:: CTNNA1:ENST00000302763.12:c.468+759A>*:p.(=); CTNNA1:ENST00000518825.5:c.468+759A>*:p.(=); CTNNA1:ENST00000627109.2:c.468+759A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ITPR1

Exomiser Score: 0.040

Phenotype Score: 0.507

Variant Score: 0.527

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:117360 Spinocerebellar ataxia 29, congenital nonprogressive - autosomal dominant; OMIM:206700 Gillespie syndrome - autosomal dominant/recessive; OMIM:606658 Spinocerebellar ataxia 15 - autosomal dominant; ORPHA:1065 Aniridia-cerebellar ataxia-intellectual disability syndrome; ORPHA:208513 Spinocerebellar ataxia type 29; ORPHA:98769 Spinocerebellar ataxia type 15/16

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.507

Variant Score: 0.279

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4707407G>A [0/1] rs948704838 (variation viewer)

Variant score: 0.279 CONTRIBUTING VARIANT

Transcripts:: ITPR1:ENST00000302640.12:c.4797+1056G>A:p.(=); ITPR1:ENST00000354582.11:c.4815+1056G>A:p.(=); ITPR1:ENST00000357086.10:c.4815+1056G>A:p.(=); ITPR1:ENST00000443694.4:c.4797+1056G>A:p.(=); ITPR1:ENST00000456211.8:c.4770+1056G>A:p.(=); ITPR1:ENST00000544951.6:c.996+53521G>A:p.(=); ITPR1:ENST00000648266.1:c.4815+1056G>A:p.(=); ITPR1:ENST00000648309.1:c.4770+1056G>A:p.(=); ITPR1:ENST00000649015.1:c.4842+1056G>A:p.(=); ITPR1:ENST00000650294.1:c.4797+1056G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2798881; CADD: 0.280 (1.426)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_AFR: 0.0229%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.040

Phenotype Score: 0.507

Variant Score: 0.527

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4807110GCTTACAAAGAGAGGGGGGCTTACAAAGAGAGGGGGGA>G [1/1] rs534474592 (variation viewer)

Variant score: 0.527 CONTRIBUTING VARIANT

Transcripts:: ITPR1:ENST00000302640.12:c.7227+844_7227+880del:p.(=); ITPR1:ENST00000354582.11:c.7248+844_7248+880del:p.(=); ITPR1:ENST00000357086.10:c.7128+844_7128+880del:p.(=); ITPR1:ENST00000443694.4:c.7227+844_7227+880del:p.(=); ITPR1:ENST00000456211.8:c.7083+844_7083+880del:p.(=); ITPR1:ENST00000544951.6:c.1161+844_1161+880del:p.(=); ITPR1:ENST00000648266.1:c.7245+844_7245+880del:p.(=); ITPR1:ENST00000648309.1:c.7200+844_7200+880del:p.(=); ITPR1:ENST00000649015.1:c.7272+844_7272+880del:p.(=); ITPR1:ENST00000650294.1:c.7230+844_7230+880del:p.(=)

Pathogenicity Data:: Best Score: 0.52684873; CADD: 0.527 (3.250)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4564462T>C [0/1] rs147568102 (variation viewer)

Variant score: 0.501

Transcripts:: ITPR1:ENST00000302640.12:c.163+43368T>C:p.(=); ITPR1:ENST00000354582.11:c.163+43368T>C:p.(=); ITPR1:ENST00000357086.10:c.163+43368T>C:p.(=); ITPR1:ENST00000443694.4:c.163+43368T>C:p.(=); ITPR1:ENST00000456211.8:c.163+43368T>C:p.(=); ITPR1:ENST00000467056.6:c.163+43368T>C:p.(=); ITPR1:ENST00000544951.6:c.163+43368T>C:p.(=); ITPR1:ENST00000648266.1:c.163+43368T>C:p.(=); ITPR1:ENST00000648309.1:c.163+43368T>C:p.(=); ITPR1:ENST00000649015.1:c.163+43368T>C:p.(=); ITPR1:ENST00000650294.1:c.163+43368T>C:p.(=)

Pathogenicity Data:: Best Score: 0.51649606; CADD: 0.516 (3.156)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1234%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.0999%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4641096G>A [0/1] rs141635457 (variation viewer)

Variant score: 0.443

Transcripts:: ITPR1:ENST00000302640.12:c.367-997G>A:p.(=); ITPR1:ENST00000354582.11:c.367-997G>A:p.(=); ITPR1:ENST00000357086.10:c.367-997G>A:p.(=); ITPR1:ENST00000443694.4:c.367-997G>A:p.(=); ITPR1:ENST00000456211.8:c.367-997G>A:p.(=); ITPR1:ENST00000467056.6:c.367-997G>A:p.(=); ITPR1:ENST00000544951.6:c.367-997G>A:p.(=); ITPR1:ENST00000648266.1:c.367-997G>A:p.(=); ITPR1:ENST00000648309.1:c.367-997G>A:p.(=); ITPR1:ENST00000649015.1:c.367-997G>A:p.(=); ITPR1:ENST00000650294.1:c.367-997G>A:p.(=)

Pathogenicity Data:: Best Score: 0.706573; CADD: 0.707 (5.325)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 0.6498%; UK10K: 0.6348%; gnomAD_G_AFR: 0.1261%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.9731%; gnomAD_G_NFE: 0.7136%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4602373A>C [0|1] rs11714782 (variation viewer)

Variant score: 0.272

Transcripts:: ITPR1:ENST00000302640.12:c.164-25390A>C:p.(=); ITPR1:ENST00000354582.11:c.164-25390A>C:p.(=); ITPR1:ENST00000357086.10:c.164-25390A>C:p.(=); ITPR1:ENST00000443694.4:c.164-25390A>C:p.(=); ITPR1:ENST00000456211.8:c.164-25390A>C:p.(=); ITPR1:ENST00000467056.6:c.164-25390A>C:p.(=); ITPR1:ENST00000544951.6:c.164-25390A>C:p.(=); ITPR1:ENST00000648266.1:c.164-25390A>C:p.(=); ITPR1:ENST00000648309.1:c.164-25390A>C:p.(=); ITPR1:ENST00000649015.1:c.164-25390A>C:p.(=); ITPR1:ENST00000650294.1:c.164-25390A>C:p.(=)

Pathogenicity Data:: Best Score: 0.27706373; CADD: 0.277 (1.409)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0860%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1269%; gnomAD_G_OTH: 0.1022%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.4498040T>C [0/1] rs543410135 (variation viewer)

Variant score: 0.153

Transcripts:: ITPR1:ENST00000302640.12:c.-17+3534T>C:p.(=); ITPR1:ENST00000354582.11:c.-17+3534T>C:p.(=); ITPR1:ENST00000357086.10:c.-17+3534T>C:p.(=); ITPR1:ENST00000456211.8:c.-17+3534T>C:p.(=); ITPR1:ENST00000467056.6:c.-17+3534T>C:p.(=); ITPR1:ENST00000544951.6:c.-17+3534T>C:p.(=); ITPR1:ENST00000648266.1:c.-17+3534T>C:p.(=); ITPR1:ENST00000649015.1:c.-17+3534T>C:p.(=); ITPR1:ENST00000650294.1:c.-17+3534T>C:p.(=)

Pathogenicity Data:: Best Score: 0.15316266; CADD: 0.153 (0.722)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0008%; gnomAD_G_AFR: 0.0115%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4582646C>G [0/1] rs17040959 (variation viewer)

Variant score: 0.128

Transcripts:: ITPR1:ENST00000302640.12:c.164-45117C>G:p.(=); ITPR1:ENST00000354582.11:c.164-45117C>G:p.(=); ITPR1:ENST00000357086.10:c.164-45117C>G:p.(=); ITPR1:ENST00000443694.4:c.164-45117C>G:p.(=); ITPR1:ENST00000456211.8:c.164-45117C>G:p.(=); ITPR1:ENST00000467056.6:c.164-45117C>G:p.(=); ITPR1:ENST00000544951.6:c.164-45117C>G:p.(=); ITPR1:ENST00000648266.1:c.164-45117C>G:p.(=); ITPR1:ENST00000648309.1:c.164-45117C>G:p.(=); ITPR1:ENST00000649015.1:c.164-45117C>G:p.(=); ITPR1:ENST00000650294.1:c.164-45117C>G:p.(=)

Pathogenicity Data:: Best Score: 0.8620887; CADD: 0.862 (8.604)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.9493%; UK10K: 1.6398%; gnomAD_G_AFR: 0.2864%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.3148%; gnomAD_G_NFE: 1.4059%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4787337C>CA [1/1] rs71053443 (variation viewer)

Variant score: 0.125

Transcripts:: ITPR1:ENST00000302640.12:c.6571-610_6571-609insA:p.(=); ITPR1:ENST00000354582.11:c.6592-610_6592-609insA:p.(=); ITPR1:ENST00000357086.10:c.6472-610_6472-609insA:p.(=); ITPR1:ENST00000443694.4:c.6571-610_6571-609insA:p.(=); ITPR1:ENST00000456211.8:c.6427-610_6427-609insA:p.(=); ITPR1:ENST00000544951.6:c.997-18766_997-18765insA:p.(=); ITPR1:ENST00000648266.1:c.6589-610_6589-609insA:p.(=); ITPR1:ENST00000648309.1:c.6544-610_6544-609insA:p.(=); ITPR1:ENST00000649015.1:c.6616-610_6616-609insA:p.(=); ITPR1:ENST00000650294.1:c.6574-610_6574-609insA:p.(=)

Pathogenicity Data:: Best Score: 0.12501621; CADD: 0.125 (0.580)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4704281G>A [0/1] rs1225282988 (variation viewer)

Variant score: 0.123

Transcripts:: ITPR1:ENST00000302640.12:c.4612+1331G>A:p.(=); ITPR1:ENST00000354582.11:c.4630+1331G>A:p.(=); ITPR1:ENST00000357086.10:c.4630+1331G>A:p.(=); ITPR1:ENST00000443694.4:c.4612+1331G>A:p.(=); ITPR1:ENST00000456211.8:c.4585+1331G>A:p.(=); ITPR1:ENST00000544951.6:c.996+50395G>A:p.(=); ITPR1:ENST00000648266.1:c.4630+1331G>A:p.(=); ITPR1:ENST00000648309.1:c.4585+1331G>A:p.(=); ITPR1:ENST00000649015.1:c.4657+1331G>A:p.(=); ITPR1:ENST00000650294.1:c.4612+1331G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12541908; CADD: 0.125 (0.582)

Frequency Data:: TOPMed: 0.0104%; gnomAD_G_AMR: 0.1193%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4552976T>C [0/1] rs111915636 (variation viewer)

Variant score: 0.118

Transcripts:: ITPR1:ENST00000302640.12:c.163+31882T>C:p.(=); ITPR1:ENST00000354582.11:c.163+31882T>C:p.(=); ITPR1:ENST00000357086.10:c.163+31882T>C:p.(=); ITPR1:ENST00000443694.4:c.163+31882T>C:p.(=); ITPR1:ENST00000456211.8:c.163+31882T>C:p.(=); ITPR1:ENST00000467056.6:c.163+31882T>C:p.(=); ITPR1:ENST00000544951.6:c.163+31882T>C:p.(=); ITPR1:ENST00000648266.1:c.163+31882T>C:p.(=); ITPR1:ENST00000648309.1:c.163+31882T>C:p.(=); ITPR1:ENST00000649015.1:c.163+31882T>C:p.(=); ITPR1:ENST00000650294.1:c.163+31882T>C:p.(=)

Pathogenicity Data:: Best Score: 0.14670342; CADD: 0.147 (0.689)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.4794%; UK10K: 0.8860%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.6869%; gnomAD_G_NFE: 0.7662%; gnomAD_G_OTH: 0.8147%

INTERGENIC_VARIANT chr3:g.4482796CT>C [1/1] rs35930607 (variation viewer)

Variant score: 0.116

Transcripts:: ITPR1:ENST00000357086.10::

Pathogenicity Data:: Best Score: 0.11569923; CADD: 0.116 (0.534)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4602057T>C [0/1] rs2322736 (variation viewer)

Variant score: 0.101

Transcripts:: ITPR1:ENST00000302640.12:c.164-25706T>C:p.(=); ITPR1:ENST00000354582.11:c.164-25706T>C:p.(=); ITPR1:ENST00000357086.10:c.164-25706T>C:p.(=); ITPR1:ENST00000443694.4:c.164-25706T>C:p.(=); ITPR1:ENST00000456211.8:c.164-25706T>C:p.(=); ITPR1:ENST00000467056.6:c.164-25706T>C:p.(=); ITPR1:ENST00000544951.6:c.164-25706T>C:p.(=); ITPR1:ENST00000648266.1:c.164-25706T>C:p.(=); ITPR1:ENST00000648309.1:c.164-25706T>C:p.(=); ITPR1:ENST00000649015.1:c.164-25706T>C:p.(=); ITPR1:ENST00000650294.1:c.164-25706T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6809197; CADD: 0.681 (4.961)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.9557%; UK10K: 1.7059%; gnomAD_G_AFR: 0.2750%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.3148%; gnomAD_G_NFE: 1.4655%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4524301GT>G [0/1] rs56380229 (variation viewer)

Variant score: 0.094

Transcripts:: ITPR1:ENST00000302640.12:c.163+3208del:p.(=); ITPR1:ENST00000354582.11:c.163+3208del:p.(=); ITPR1:ENST00000357086.10:c.163+3208del:p.(=); ITPR1:ENST00000443694.4:c.163+3208del:p.(=); ITPR1:ENST00000456211.8:c.163+3208del:p.(=); ITPR1:ENST00000467056.6:c.163+3208del:p.(=); ITPR1:ENST00000544951.6:c.163+3208del:p.(=); ITPR1:ENST00000648266.1:c.163+3208del:p.(=); ITPR1:ENST00000648309.1:c.163+3208del:p.(=); ITPR1:ENST00000649015.1:c.163+3208del:p.(=); ITPR1:ENST00000650294.1:c.163+3208del:p.(=)

Pathogenicity Data:: Best Score: 0.09426743; CADD: 0.094 (0.430)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4600195C>T [0/1] rs112132919 (variation viewer)

Variant score: 0.080

Transcripts:: ITPR1:ENST00000302640.12:c.164-27568C>T:p.(=); ITPR1:ENST00000354582.11:c.164-27568C>T:p.(=); ITPR1:ENST00000357086.10:c.164-27568C>T:p.(=); ITPR1:ENST00000443694.4:c.164-27568C>T:p.(=); ITPR1:ENST00000456211.8:c.164-27568C>T:p.(=); ITPR1:ENST00000467056.6:c.164-27568C>T:p.(=); ITPR1:ENST00000544951.6:c.164-27568C>T:p.(=); ITPR1:ENST00000648266.1:c.164-27568C>T:p.(=); ITPR1:ENST00000648309.1:c.164-27568C>T:p.(=); ITPR1:ENST00000649015.1:c.164-27568C>T:p.(=); ITPR1:ENST00000650294.1:c.164-27568C>T:p.(=)

Pathogenicity Data:: Best Score: 0.53633964; CADD: 0.536 (3.338)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.8330%; UK10K: 1.4679%; gnomAD_G_AFR: 0.2635%; gnomAD_G_AMR: 0.8373%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.3148%; gnomAD_G_NFE: 1.3058%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4609021A>C [0/1] rs968132513 (variation viewer)

Variant score: 0.039

Transcripts:: ITPR1:ENST00000302640.12:c.164-18742A>C:p.(=); ITPR1:ENST00000354582.11:c.164-18742A>C:p.(=); ITPR1:ENST00000357086.10:c.164-18742A>C:p.(=); ITPR1:ENST00000443694.4:c.164-18742A>C:p.(=); ITPR1:ENST00000456211.8:c.164-18742A>C:p.(=); ITPR1:ENST00000467056.6:c.164-18742A>C:p.(=); ITPR1:ENST00000544951.6:c.164-18742A>C:p.(=); ITPR1:ENST00000648266.1:c.164-18742A>C:p.(=); ITPR1:ENST00000648309.1:c.164-18742A>C:p.(=); ITPR1:ENST00000649015.1:c.164-18742A>C:p.(=); ITPR1:ENST00000650294.1:c.164-18742A>C:p.(=)

Pathogenicity Data:: Best Score: 0.04720384; CADD: 0.047 (0.210)

Frequency Data:: gnomAD_G_AFR: 0.1229%; gnomAD_G_AMR: 0.5587%; gnomAD_G_ASJ: 0.8065%; gnomAD_G_NFE: 0.6760%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.4690014C>T [0/1] rs555132066 (variation viewer)

Variant score: 0.005

Transcripts:: ITPR1:ENST00000302640.12:c.3784-1130C>T:p.(=); ITPR1:ENST00000354582.11:c.3802-1130C>T:p.(=); ITPR1:ENST00000357086.10:c.3802-1130C>T:p.(=); ITPR1:ENST00000443694.4:c.3784-1130C>T:p.(=); ITPR1:ENST00000456211.8:c.3757-1130C>T:p.(=); ITPR1:ENST00000544951.6:c.996+36128C>T:p.(=); ITPR1:ENST00000648266.1:c.3802-1130C>T:p.(=); ITPR1:ENST00000648309.1:c.3757-1130C>T:p.(=); ITPR1:ENST00000649015.1:c.3829-1130C>T:p.(=); ITPR1:ENST00000650294.1:c.3784-1130C>T:p.(=)

Pathogenicity Data:: Best Score: 0.033726633; CADD: 0.034 (0.149)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.2684%; UK10K: 0.4099%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.5861%; gnomAD_G_OTH: 0.3061%

KIF13B

Exomiser Score: 0.039

Phenotype Score: 0.501

Variant Score: 0.530

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.501

Variant Score: 0.193

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29106632C>CAA [-/1] rs71222590 (variation viewer)

Variant score: 0.193 CONTRIBUTING VARIANT

Transcripts:: KIF13B:ENST00000524189.6:c.4215+1506_4215+1507insTT:p.(=)

Pathogenicity Data:: Best Score: 0.19332242; CADD: 0.193 (0.933)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.039

Phenotype Score: 0.501

Variant Score: 0.530

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29119673A>G [0/1] rs138185140 (variation viewer)

Variant score: 0.556 CONTRIBUTING VARIANT

Transcripts:: KIF13B:ENST00000524189.6:c.3536-681T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6322946; CADD: 0.632 (4.345)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3074%; UK10K: 0.6348%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.2862%; gnomAD_G_NFE: 0.6264%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29220293G>A [0/1] rs62502858 (variation viewer)

Variant score: 0.503 CONTRIBUTING VARIANT

Transcripts:: KIF13B:ENST00000521515.1:c.150-24094C>T:p.(=); KIF13B:ENST00000524189.6:c.150-24094C>T:p.(=)

Pathogenicity Data:: Best Score: 0.57538044; CADD: 0.575 (3.720)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.4659%; UK10K: 0.5951%; gnomAD_G_AFR: 0.1146%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.1146%; gnomAD_G_NFE: 0.6598%; gnomAD_G_OTH: 0.2041%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29211962T>C [0/1] rs555133518 (variation viewer)

Variant score: 0.457

Transcripts:: KIF13B:ENST00000521515.1:c.150-15763A>G:p.(=); KIF13B:ENST00000524189.6:c.150-15763A>G:p.(=)

Pathogenicity Data:: Best Score: 0.48560113; CADD: 0.486 (2.887)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1051%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0343%; gnomAD_G_AMR: 0.3580%; gnomAD_G_NFE: 0.1732%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29242190C>T [0/1] rs62505665 (variation viewer)

Variant score: 0.348

Transcripts:: KIF13B:ENST00000521515.1:c.149+3156G>A:p.(=); KIF13B:ENST00000524189.6:c.149+3156G>A:p.(=)

Pathogenicity Data:: Best Score: 0.40351433; CADD: 0.404 (2.244)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.5487%; UK10K: 0.5819%; gnomAD_G_AFR: 0.1033%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.0575%; gnomAD_G_NFE: 0.7007%; gnomAD_G_OTH: 0.3067%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29222515CTTTTTTTTTTTTTTTTTTTTT>C [0/1] rs58488862 (variation viewer)

Variant score: 0.188

Transcripts:: KIF13B:ENST00000521515.1:c.149+22810_149+22830del:p.(=); KIF13B:ENST00000524189.6:c.149+22810_149+22830del:p.(=)

Pathogenicity Data:: Best Score: 0.18773079; CADD: 0.188 (0.903)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29105650G>GTT [1/1] rs869030059 (variation viewer)

Variant score: 0.176

Transcripts:: KIF13B:ENST00000524189.6:c.4215+2488_4215+2489insAA:p.(=)

Pathogenicity Data:: Best Score: 0.1758619; CADD: 0.176 (0.840)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29165904T>TTCGACTGTAGATCGAAGTACC [-/1] rs1554610894 (variation viewer)

Variant score: 0.155

Transcripts:: KIF13B:ENST00000521515.1:c.1159-133_1159-132insGGTACTTCGATCTACAGTCGA:p.(=); KIF13B:ENST00000524189.6:c.1159-133_1159-132insGGTACTTCGATCTACAGTCGA:p.(=)

Pathogenicity Data:: Best Score: 0.15491575; CADD: 0.155 (0.731)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29165904T>TTCGATTGTAGATCGAAGTACC [-/1] rs56100744 (variation viewer)

Variant score: 0.155

Transcripts:: KIF13B:ENST00000521515.1:c.1159-133_1159-132insGGTACTTCGATCTACAATCGA:p.(=); KIF13B:ENST00000524189.6:c.1159-133_1159-132insGGTACTTCGATCTACAATCGA:p.(=)

Pathogenicity Data:: Best Score: 0.15491575; CADD: 0.155 (0.731)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29096293CT>C [1/1] rs61008499 (variation viewer)

Variant score: 0.136

Transcripts:: KIF13B:ENST00000524189.6:c.4324+2839del:p.(=)

Pathogenicity Data:: Best Score: 0.13582838; CADD: 0.136 (0.634)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29228472A>AAAATATATATATAT [1/1] rs368036370 (variation viewer)

Variant score: 0.112

Transcripts:: KIF13B:ENST00000521515.1:c.149+16873_149+16874insATATATATATATTT:p.(=); KIF13B:ENST00000524189.6:c.149+16873_149+16874insATATATATATATTT:p.(=)

Pathogenicity Data:: Best Score: 0.11182201; CADD: 0.112 (0.515)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29183168G>GT [0/1] rs58034349 (variation viewer)

Variant score: 0.105

Transcripts:: KIF13B:ENST00000521515.1:c.498-1163_498-1162insA:p.(=); KIF13B:ENST00000524189.6:c.498-1163_498-1162insA:p.(=)

Pathogenicity Data:: Best Score: 0.10484135; CADD: 0.105 (0.481)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29106632CA>C [-/1] rs71222590 (variation viewer)

Variant score: 0.088

Transcripts:: KIF13B:ENST00000524189.6:c.4215+1506del:p.(=)

Pathogenicity Data:: Best Score: 0.08798915; CADD: 0.088 (0.400)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29078127C>CAAAAAAA [1/1] rs10530503 (variation viewer)

Variant score: 0.058

Transcripts:: KIF13B:ENST00000524189.6:c.4459-2785_4459-2784insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.057893515; CADD: 0.058 (0.259)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29098170CAA>C [0/1] rs147089450 (variation viewer)

Variant score: 0.050

Transcripts:: KIF13B:ENST00000524189.6:c.4324+961_4324+962del:p.(=)

Pathogenicity Data:: Best Score: 0.05027032; CADD: 0.050 (0.224)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.29080327C>CAA [1/1] rs5890439 (variation viewer)

Variant score: 0.025

Transcripts:: KIF13B:ENST00000524189.6:c.4459-4985_4459-4984insTT:p.(=)

Pathogenicity Data:: Best Score: 0.025234818; CADD: 0.025 (0.111)

Frequency Data:: No frequency data

LRP6

Exomiser Score: 0.038

Phenotype Score: 0.505

Variant Score: 0.524

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:610947 Coronary artery disease, autosomal dominant, 2 (susceptibility); OMIM:616724 Tooth agenesis, selective, 7 - autosomal dominant; ORPHA:99798 Oligodontia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.038

Phenotype Score: 0.505

Variant Score: 0.524

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12257459T>C [0/1] rs1353787738 (variation viewer)

Variant score: 0.524 CONTRIBUTING VARIANT

Transcripts:: LRP6:ENST00000261349.9:c.55+9222A>G:p.(=); LRP6:ENST00000543091.1:c.55+9222A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5240076; CADD: 0.524 (3.224)

Frequency Data:: TOPMed: 0.0008%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.253

Variant Score: 0.459

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12257459T>C [0/1] rs1353787738 (variation viewer)

Variant score: 0.524 CONTRIBUTING VARIANT

Transcripts:: LRP6:ENST00000261349.9:c.55+9222A>G:p.(=); LRP6:ENST00000543091.1:c.55+9222A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5240076; CADD: 0.524 (3.224)

Frequency Data:: TOPMed: 0.0008%

THREE_PRIME_UTR_EXON_VARIANT chr12:g.12119990A>AATATAT [-/1] rs550587604 (variation viewer)

Variant score: 0.393 CONTRIBUTING VARIANT

Transcripts:: LRP6:ENST00000261349.9:c.*1130_*1135dup:p.(=)

Pathogenicity Data:: Best Score: 0.3932637; CADD: 0.393 (2.170)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12171090T>A [0/1] rs528995056 (variation viewer)

Variant score: 0.284

Transcripts:: LRP6:ENST00000261349.9:c.1546-5795A>T:p.(=); LRP6:ENST00000543091.1:c.1546-5795A>T:p.(=)

Pathogenicity Data:: Best Score: 0.34506232; CADD: 0.345 (1.838)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2732%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0353%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2865%; gnomAD_G_NFE: 0.8396%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12254162A>AAG [0/1] rs567794631 (variation viewer)

Variant score: 0.266

Transcripts:: LRP6:ENST00000261349.9:c.56-9508_56-9507insCT:p.(=); LRP6:ENST00000543091.1:c.56-9508_56-9507insCT:p.(=)

Pathogenicity Data:: Best Score: 0.30960125; CADD: 0.310 (1.609)

Frequency Data:: gnomAD_G_AFR: 0.7152%; gnomAD_G_ASJ: 0.3876%; gnomAD_G_EAS: 0.1935%; gnomAD_G_FIN: 0.0514%; gnomAD_G_NFE: 0.4197%; gnomAD_G_OTH: 0.1404%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12264143TA>T [0/1] rs559250351 (variation viewer)

Variant score: 0.248

Transcripts:: LRP6:ENST00000261349.9:c.55+2537del:p.(=); LRP6:ENST00000543091.1:c.55+2537del:p.(=)

Pathogenicity Data:: Best Score: 0.24785775; CADD: 0.248 (1.237)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr12:g.12112372C>CAA [1/1] rs369889103 (variation viewer)

Variant score: 0.165

Transcripts:: LRP6:ENST00000261349.9::; LRP6:ENST00000539347.1::

Pathogenicity Data:: Best Score: 0.16458935; CADD: 0.165 (0.781)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12173421C>T [0/1] rs117176756 (variation viewer)

Variant score: 0.132

Transcripts:: LRP6:ENST00000261349.9:c.1545+6389G>A:p.(=); LRP6:ENST00000543091.1:c.1545+6389G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15782952; CADD: 0.158 (0.746)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2588%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2865%; gnomAD_G_NFE: 0.7926%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.12196289C>T [0/1] rs181344171 (variation viewer)

Variant score: 0.054

Transcripts:: LRP6:ENST00000261349.9:c.647+6914G>A:p.(=); LRP6:ENST00000543091.1:c.647+6914G>A:p.(=)

Pathogenicity Data:: Best Score: 0.066530764; CADD: 0.067 (0.299)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2644%; UK10K: 0.1984%; gnomAD_G_AFR: 0.0460%; gnomAD_G_AMR: 0.1199%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2926%; gnomAD_G_NFE: 0.8645%; gnomAD_G_OTH: 0.3080%

PTPN23

Exomiser Score: 0.036

Phenotype Score: 0.505

Variant Score: 0.518

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618890 Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.252

Variant Score: 0.530

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47398628C>T [0/1] rs544286363 (variation viewer)

Variant score: 0.530 CONTRIBUTING VARIANT

Transcripts:: PTPN23:ENST00000265562.5:c.159+2411C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5312945; CADD: 0.531 (3.291)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.036

Phenotype Score: 0.505

Variant Score: 0.518

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47398628C>T [0/1] rs544286363 (variation viewer)

Variant score: 0.530 CONTRIBUTING VARIANT

Transcripts:: PTPN23:ENST00000265562.5:c.159+2411C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5312945; CADD: 0.531 (3.291)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47387093G>C [0/1] rs997044954 (variation viewer)

Variant score: 0.507 CONTRIBUTING VARIANT

Transcripts:: PTPN23:ENST00000265562.5:c.84+5913G>C:p.(=)

Pathogenicity Data:: Best Score: 0.5077338; CADD: 0.508 (3.078)

Frequency Data:: gnomAD_G_NFE: 0.0133%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47391232C>T [0/1] rs560692942 (variation viewer)

Variant score: 0.407

Transcripts:: PTPN23:ENST00000265562.5:c.85-4911C>T:p.(=)

Pathogenicity Data:: Best Score: 0.40843838; CADD: 0.408 (2.280)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47399458G>C [0/1] rs544418825 (variation viewer)

Variant score: 0.294

Transcripts:: PTPN23:ENST00000265562.5:c.159+3241G>C:p.(=)

Pathogenicity Data:: Best Score: 0.29449517; CADD: 0.294 (1.515)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.47386412C>T [0/1] rs868212804 (variation viewer)

Variant score: 0.078

Transcripts:: PTPN23:ENST00000265562.5:c.84+5232C>T:p.(=)

Pathogenicity Data:: Best Score: 0.07785332; CADD: 0.078 (0.352)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

DOWNSTREAM_GENE_VARIANT chr3:g.47413487G>GAACTT [0/1] rs531518140 (variation viewer)

Variant score: 0.032

Transcripts:: PTPN23:ENST00000265562.5::; PTPN23:ENST00000265565.10::

Pathogenicity Data:: Best Score: 0.074023426; CADD: 0.074 (0.334)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0599%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.3083%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.0467%; gnomAD_G_OTH: 0.1018%

ASXL1

Exomiser Score: 0.036

Phenotype Score: 0.503

Variant Score: 0.519

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:605039 Bohring-Opitz syndrome - autosomal dominant; OMIM:614286 Myelodysplastic syndrome, somatic - somatic; ORPHA:97297 Bohring-Opitz syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.036

Phenotype Score: 0.503

Variant Score: 0.519

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.32369718CT>C [0/1] rs386393629 (variation viewer)

Variant score: 0.519 CONTRIBUTING VARIANT

Transcripts:: ASXL1:ENST00000306058.9:c.237+596del:p.(=); ASXL1:ENST00000375687.10:c.252+596del:p.(=); ASXL1:ENST00000375689.5:c.240+596del:p.(=); ASXL1:ENST00000497249.6:c.222+596del:p.(=); ASXL1:ENST00000542461.5:c.252+596del:p.(=); ASXL1:ENST00000613218.4:c.252+596del:p.(=); ASXL1:ENST00000620121.4:c.252+596del:p.(=); ASXL1:ENST00000646367.1:c.252+596del:p.(=); ASXL1:ENST00000646985.1:c.222+596del:p.(=); ASXL1:ENST00000651418.1:c.252+596del:p.(=)

Pathogenicity Data:: Best Score: 0.5192714; CADD: 0.519 (3.181)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.252

Variant Score: 0.433

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.32369718CT>C [0/1] rs386393629 (variation viewer)

Variant score: 0.519 CONTRIBUTING VARIANT

Transcripts:: ASXL1:ENST00000306058.9:c.237+596del:p.(=); ASXL1:ENST00000375687.10:c.252+596del:p.(=); ASXL1:ENST00000375689.5:c.240+596del:p.(=); ASXL1:ENST00000497249.6:c.222+596del:p.(=); ASXL1:ENST00000542461.5:c.252+596del:p.(=); ASXL1:ENST00000613218.4:c.252+596del:p.(=); ASXL1:ENST00000620121.4:c.252+596del:p.(=); ASXL1:ENST00000646367.1:c.252+596del:p.(=); ASXL1:ENST00000646985.1:c.222+596del:p.(=); ASXL1:ENST00000651418.1:c.252+596del:p.(=)

Pathogenicity Data:: Best Score: 0.5192714; CADD: 0.519 (3.181)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr20:g.32344601A>G [0/1] rs73108575 (variation viewer)

Variant score: 0.347 CONTRIBUTING VARIANT

Transcripts:: ASXL1:ENST00000651418.1::

Pathogenicity Data:: Best Score: 0.5552664; CADD: 0.555 (3.519)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5630%; UK10K: 0.6876%; gnomAD_G_AFR: 0.1605%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.6904%; gnomAD_G_NFE: 1.2537%; gnomAD_G_OTH: 1.3265%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.32418809CTTTTTTTTT>C [1/1] rs71338437 (variation viewer)

Variant score: 0.237

Transcripts:: ASXL1:ENST00000306058.9:c.238-9318_238-9310del:p.(=); ASXL1:ENST00000375687.10:c.253-9318_253-9310del:p.(=); ASXL1:ENST00000613218.4:c.253-9318_253-9310del:p.(=); ASXL1:ENST00000620121.4:c.253-9318_253-9310del:p.(=); ASXL1:ENST00000646985.1:c.223-9318_223-9310del:p.(=); ASXL1:ENST00000651418.1:c.253-9318_253-9310del:p.(=)

Pathogenicity Data:: Best Score: 0.23686743; CADD: 0.237 (1.174)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr20:g.32342905C>CTTTTT [0/1] rs3075352 (variation viewer)

Variant score: 0.111

Transcripts:: ASXL1:ENST00000651418.1::

Pathogenicity Data:: Best Score: 0.110798895; CADD: 0.111 (0.510)

Frequency Data:: No frequency data

ARCN1

Exomiser Score: 0.035

Phenotype Score: 0.504

Variant Score: 0.516

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617164 Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.035

Phenotype Score: 0.504

Variant Score: 0.516

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.118567742T>A [0/1]

Variant score: 0.516 CONTRIBUTING VARIANT

Transcripts:: ARCN1:ENST00000392859.7::; ARCN1:ENST00000264021.7::

Pathogenicity Data:: Best Score: 0.5160506; CADD: 0.516 (3.152)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.258

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.118567742T>A [0/1]

Variant score: 0.516 CONTRIBUTING VARIANT

Transcripts:: ARCN1:ENST00000392859.7::; ARCN1:ENST00000264021.7::

Pathogenicity Data:: Best Score: 0.5160506; CADD: 0.516 (3.152)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.118578874CTT>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: ARCN1:ENST00000264028.5:c.4-2372_4-2370delCTTins*:p.(=); ARCN1:ENST00000359415.8:c.127-2372_127-2370delCTTins*:p.(=); ARCN1:ENST00000392859.7:c.4-4305_4-4303delCTTins*:p.(=); ARCN1:ENST00000534182.2:c.4-2372_4-2370delCTTins*:p.(=); ARCN1:ENST00000614498.4:c.4-2372_4-2370delCTTins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

PKP4

Exomiser Score: 0.035

Phenotype Score: 0.502

Variant Score: 0.518

Phenotype matches:

Proximity score 0.502 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.502

Variant Score: 0.314

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158496416C>A [0/1]

Variant score: 0.314 CONTRIBUTING VARIANT

Transcripts:: PKP4:ENST00000389757.7:c.-5-36764C>A:p.(=); PKP4:ENST00000389759.7:c.-5-36764C>A:p.(=); PKP4:ENST00000628904.2:c.-5-36764C>A:p.(=)

Pathogenicity Data:: Best Score: 0.31388015; CADD: 0.314 (1.636)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.035

Phenotype Score: 0.502

Variant Score: 0.518

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158499691A>G [0/1] rs116732898 (variation viewer)

Variant score: 0.722 CONTRIBUTING VARIANT

Transcripts:: PKP4:ENST00000389757.7:c.-5-33489A>G:p.(=); PKP4:ENST00000389759.7:c.-5-33489A>G:p.(=); PKP4:ENST00000628904.2:c.-5-33489A>G:p.(=)

Pathogenicity Data:: Best Score: 0.8597832; CADD: 0.860 (8.532)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.4539%; UK10K: 0.7802%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.1718%; gnomAD_G_NFE: 0.7732%; gnomAD_G_OTH: 0.6110%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158496416C>A [0/1]

Variant score: 0.314 CONTRIBUTING VARIANT

Transcripts:: PKP4:ENST00000389757.7:c.-5-36764C>A:p.(=); PKP4:ENST00000389759.7:c.-5-36764C>A:p.(=); PKP4:ENST00000628904.2:c.-5-36764C>A:p.(=)

Pathogenicity Data:: Best Score: 0.31388015; CADD: 0.314 (1.636)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158500720A>C [0/1] rs762967139 (variation viewer)

Variant score: 0.313

Transcripts:: PKP4:ENST00000389757.7:c.-5-32460A>C:p.(=); PKP4:ENST00000389759.7:c.-5-32460A>C:p.(=); PKP4:ENST00000628904.2:c.-5-32460A>C:p.(=)

Pathogenicity Data:: Best Score: 0.3140381; CADD: 0.314 (1.637)

Frequency Data:: TOPMed: 0.0064%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.158545645A>G [0/1] rs1256093716 (variation viewer)

Variant score: 0.243

Transcripts:: PKP4:ENST00000389757.7:c.132+12329A>G:p.(=); PKP4:ENST00000389759.7:c.132+12329A>G:p.(=); PKP4:ENST00000628904.2:c.132+12329A>G:p.(=)

Pathogenicity Data:: Best Score: 0.24351555; CADD: 0.244 (1.212)

Frequency Data:: TOPMed: 0.0048%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158472612C>CA [0/1] rs67665979 (variation viewer)

Variant score: 0.226

Transcripts:: PKP4:ENST00000389757.7:c.-6+15394_-6+15395insA:p.(=); PKP4:ENST00000389759.7:c.-6+15394_-6+15395insA:p.(=); PKP4:ENST00000628904.2:c.-6+15394_-6+15395insA:p.(=)

Pathogenicity Data:: Best Score: 0.22607303; CADD: 0.226 (1.113)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.158554433T>TA [0/1] rs779655761 (variation viewer)

Variant score: 0.184

Transcripts:: PKP4:ENST00000389757.7:c.132+21117_132+21118insA:p.(=); PKP4:ENST00000389759.7:c.132+21117_132+21118insA:p.(=); PKP4:ENST00000628904.2:c.132+21117_132+21118insA:p.(=)

Pathogenicity Data:: Best Score: 0.21331656; CADD: 0.213 (1.042)

Frequency Data:: gnomAD_G_AFR: 0.1874%; gnomAD_G_AMR: 0.3846%; gnomAD_G_ASJ: 0.7042%; gnomAD_G_NFE: 0.2181%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158508366C>CA [0/1] rs747754927 (variation viewer)

Variant score: 0.175

Transcripts:: PKP4:ENST00000389757.7:c.-5-24814_-5-24813insA:p.(=); PKP4:ENST00000389759.7:c.-5-24814_-5-24813insA:p.(=); PKP4:ENST00000628904.2:c.-5-24814_-5-24813insA:p.(=)

Pathogenicity Data:: Best Score: 0.1747225; CADD: 0.175 (0.834)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.158538534CT>C [0/1] rs11346852 (variation viewer)

Variant score: 0.114

Transcripts:: PKP4:ENST00000389757.7:c.132+5219del:p.(=); PKP4:ENST00000389759.7:c.132+5219del:p.(=); PKP4:ENST00000628904.2:c.132+5219del:p.(=)

Pathogenicity Data:: Best Score: 0.114068806; CADD: 0.114 (0.526)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.158545073CTT>C [1/1] rs386391605 (variation viewer)

Variant score: 0.101

Transcripts:: PKP4:ENST00000389757.7:c.132+11758_132+11759del:p.(=); PKP4:ENST00000389759.7:c.132+11758_132+11759del:p.(=); PKP4:ENST00000628904.2:c.132+11758_132+11759del:p.(=)

Pathogenicity Data:: Best Score: 0.10050243; CADD: 0.101 (0.460)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.158608808C>CTT [0/1] rs66933766 (variation viewer)

Variant score: 0.028

Transcripts:: PKP4:ENST00000389757.7:c.280+5704_280+5705insTT:p.(=); PKP4:ENST00000389759.7:c.280+5704_280+5705insTT:p.(=); PKP4:ENST00000628904.2:c.280+5704_280+5705insTT:p.(=)

Pathogenicity Data:: Best Score: 0.02837205; CADD: 0.028 (0.125)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158470208C>* [-/1]

Variant score: 0.000

Transcripts:: PKP4:ENST00000389757.7:c.-6+12990C>*:p.(=); PKP4:ENST00000389759.7:c.-6+12990C>*:p.(=); PKP4:ENST00000628904.2:c.-6+12990C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.158508389G>* [-/1]

Variant score: 0.000

Transcripts:: PKP4:ENST00000389757.7:c.-5-24791G>*:p.(=); PKP4:ENST00000389759.7:c.-5-24791G>*:p.(=); PKP4:ENST00000628904.2:c.-5-24791G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.158550145G>GATCTCTCAGAATAAAACATTACTTTTCTGCCAAGAATCTATTAATTCTATTAATAGATTCTATTAAATTCTA [0|1]

Variant score: 0.000

Transcripts:: PKP4:ENST00000389757.7:c.132+16829_132+16830insATCTCTCAGAATAAAACATTACTTTTCTGCCAAGAATCTATTAATTCTATTAATAGATTCTATTAAATTCTA:p.(=); PKP4:ENST00000389759.7:c.132+16829_132+16830insATCTCTCAGAATAAAACATTACTTTTCTGCCAAGAATCTATTAATTCTATTAATAGATTCTATTAAATTCTA:p.(=); PKP4:ENST00000628904.2:c.132+16829_132+16830insATCTCTCAGAATAAAACATTACTTTTCTGCCAAGAATCTATTAATTCTATTAATAGATTCTATTAAATTCTA:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SREBF2

Exomiser Score: 0.035

Phenotype Score: 0.504

Variant Score: 0.515

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.264

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41859799C>CT [0/1] rs1174473976 (variation viewer)

Variant score: 0.264 CONTRIBUTING VARIANT

Transcripts:: SREBF2:ENST00000361204.9:c.89-7032_89-7031insT:p.(=); SREBF2:ENST00000612482.4:c.-2-7032_-2-7031insT:p.(=)

Pathogenicity Data:: Best Score: 0.26447064; CADD: 0.264 (1.334)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.035

Phenotype Score: 0.504

Variant Score: 0.515

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41848051G>T [0/1] rs191928165 (variation viewer)

Variant score: 0.586 CONTRIBUTING VARIANT

Transcripts:: SREBF2:ENST00000361204.9:c.88+14693G>T:p.(=); SREBF2:ENST00000612482.4:c.-3+14693G>T:p.(=)

Pathogenicity Data:: Best Score: 0.59700465; CADD: 0.597 (3.947)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0764%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1232%; gnomAD_G_NFE: 0.0944%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41848433G>A [0/1] rs181459649 (variation viewer)

Variant score: 0.444 CONTRIBUTING VARIANT

Transcripts:: SREBF2:ENST00000361204.9:c.88+15075G>A:p.(=); SREBF2:ENST00000612482.4:c.-3+15075G>A:p.(=)

Pathogenicity Data:: Best Score: 0.45549732; CADD: 0.455 (2.640)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0876%; UK10K: 0.1719%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.1200%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41864261TAC>T [-/1] rs1158750306 (variation viewer)

Variant score: 0.129

Transcripts:: SREBF2:ENST00000361204.9:c.89-2569_89-2568del:p.(=); SREBF2:ENST00000612482.4:c.-2-2569_-2-2568del:p.(=)

Pathogenicity Data:: Best Score: 0.12883586; CADD: 0.129 (0.599)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41847662C>CATT [0/1] rs756928142 (variation viewer)

Variant score: 0.104

Transcripts:: SREBF2:ENST00000361204.9:c.88+14304_88+14305insATT:p.(=); SREBF2:ENST00000612482.4:c.-3+14304_-3+14305insATT:p.(=)

Pathogenicity Data:: Best Score: 0.105047464; CADD: 0.105 (0.482)

Frequency Data:: TOPMed: 0.0271%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41867694C>A [0/1] rs111439400 (variation viewer)

Variant score: 0.068

Transcripts:: SREBF2:ENST00000361204.9:c.538+414C>A:p.(=); SREBF2:ENST00000612482.4:c.448+414C>A:p.(=)

Pathogenicity Data:: Best Score: 0.15860486; CADD: 0.159 (0.750)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.4738%; UK10K: 0.7538%; gnomAD_G_AFR: 0.1147%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.2301%; gnomAD_G_NFE: 0.5339%; gnomAD_G_OTH: 0.6160%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41835989T>C [0/1]

Variant score: 0.049

Transcripts:: SREBF2:ENST00000361204.9:c.88+2631T>C:p.(=); SREBF2:ENST00000612482.4:c.-3+2631T>C:p.(=)

Pathogenicity Data:: Best Score: 0.049176276; CADD: 0.049 (0.219)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr22:g.41830979G>A [0/1] rs374952571 (variation viewer)

Variant score: 0.047

Transcripts:: SREBF2:ENST00000612482.4::; SREBF2:ENST00000255784.5::

Pathogenicity Data:: Best Score: 0.12037003; CADD: 0.120 (0.557)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.2087%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0118%; gnomAD_G_AMR: 0.2433%; gnomAD_G_ASJ: 1.7007%; gnomAD_G_NFE: 0.1793%; gnomAD_G_OTH: 0.2160%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41856823C>G [0/1] rs113110907 (variation viewer)

Variant score: 0.023

Transcripts:: SREBF2:ENST00000361204.9:c.89-10008C>G:p.(=); SREBF2:ENST00000612482.4:c.-2-10008C>G:p.(=)

Pathogenicity Data:: Best Score: 0.15257746; CADD: 0.153 (0.719)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.6913%; UK10K: 1.0976%; gnomAD_G_AFR: 0.1263%; gnomAD_G_AMR: 0.5995%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.3450%; gnomAD_G_NFE: 0.7758%; gnomAD_G_OTH: 0.6122%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41864261TAC>* [-/1]

Variant score: 0.000

Transcripts:: SREBF2:ENST00000361204.9:c.89-2570_89-2568delTACins*:p.(=); SREBF2:ENST00000612482.4:c.-2-2570_-2-2568delTACins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41869502G>* [-/1]

Variant score: 0.000

Transcripts:: SREBF2:ENST00000361204.9:c.720+710G>*:p.(=); SREBF2:ENST00000612482.4:c.630+710G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PTGS2

Exomiser Score: 0.035

Phenotype Score: 0.503

Variant Score: 0.515

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.035

Phenotype Score: 0.503

Variant Score: 0.515

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.186664062ATTTTTTTT>A [0/1] rs71104883 (variation viewer)

Variant score: 0.515 CONTRIBUTING VARIANT

Transcripts:: PTGS2:ENST00000367468.10::; PTGS2:ENST00000450032.2::

Pathogenicity Data:: Best Score: 0.5152699; CADD: 0.515 (3.145)

Frequency Data:: No frequency data

Other passed variants:

SEC23B

Exomiser Score: 0.033

Phenotype Score: 0.505

Variant Score: 0.509

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:224100 Dyserythropoietic anemia, congenital, type II - autosomal recessive; OMIM:616858 ?Cowden syndrome 7 (unconfirmed); ORPHA:201 Cowden syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.033

Phenotype Score: 0.505

Variant Score: 0.509

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.18508716C>CT [1/1] rs398035473 (variation viewer)

Variant score: 0.509 CONTRIBUTING VARIANT

Transcripts:: SEC23B:ENST00000262544.6:c.-15+686_-15+687insT:p.(=); SEC23B:ENST00000336714.8:c.-15+726_-15+727insT:p.(=); SEC23B:ENST00000377465.6:c.-15+419_-15+420insT:p.(=); SEC23B:ENST00000643747.1:c.-15+726_-15+727insT:p.(=); SEC23B:ENST00000650089.1:c.-15+744_-15+745insT:p.(=)

Pathogenicity Data:: Best Score: 0.5089791; CADD: 0.509 (3.089)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.18544901A>G [0/1] rs111391364 (variation viewer)

Variant score: 0.178

Transcripts:: SEC23B:ENST00000262544.6:c.1666-1055A>G:p.(=); SEC23B:ENST00000336714.8:c.1666-1055A>G:p.(=); SEC23B:ENST00000377465.6:c.1666-1055A>G:p.(=); SEC23B:ENST00000643747.1:c.1612-1055A>G:p.(=); SEC23B:ENST00000650089.1:c.1666-1055A>G:p.(=)

Pathogenicity Data:: Best Score: 0.23897308; CADD: 0.239 (1.186)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.6952%; UK10K: 0.8728%; gnomAD_G_AFR: 0.2444%; gnomAD_G_AMR: 0.8454%; gnomAD_G_FIN: 0.0906%; gnomAD_G_NFE: 1.0638%; gnomAD_G_OTH: 0.3205%

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.18518582G>GTTTTTT [1/1] rs57231166 (variation viewer)

Variant score: 0.083

Transcripts:: SEC23B:ENST00000262544.6:c.366+2846_366+2847insTTTTTT:p.(=); SEC23B:ENST00000336714.8:c.366+2846_366+2847insTTTTTT:p.(=); SEC23B:ENST00000377465.6:c.366+2846_366+2847insTTTTTT:p.(=); SEC23B:ENST00000643747.1:c.366+2846_366+2847insTTTTTT:p.(=); SEC23B:ENST00000650089.1:c.366+2846_366+2847insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.082512856; CADD: 0.083 (0.374)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.18540692C>T [0|1] rs112882700 (variation viewer)

Variant score: 0.070

Transcripts:: SEC23B:ENST00000262544.6:c.1405-1604C>T:p.(=); SEC23B:ENST00000336714.8:c.1405-1604C>T:p.(=); SEC23B:ENST00000377465.6:c.1405-1604C>T:p.(=); SEC23B:ENST00000643747.1:c.1351-1604C>T:p.(=); SEC23B:ENST00000650089.1:c.1405-1604C>T:p.(=)

Pathogenicity Data:: Best Score: 0.38595527; CADD: 0.386 (2.118)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 1.1670%; UK10K: 1.7456%; gnomAD_G_AFR: 0.3321%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.5441%; gnomAD_G_NFE: 1.9533%; gnomAD_G_OTH: 1.2220%

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.18557745CT>C [1/1] rs11477198 (variation viewer)

Variant score: 0.048

Transcripts:: SEC23B:ENST00000262544.6:c.2214+2573del:p.(=); SEC23B:ENST00000336714.8:c.2214+2573del:p.(=); SEC23B:ENST00000377465.6:c.2214+2573del:p.(=); SEC23B:ENST00000643747.1:c.2160+2573del:p.(=); SEC23B:ENST00000650089.1:c.2214+2573del:p.(=)

Pathogenicity Data:: Best Score: 0.04764253; CADD: 0.048 (0.212)

Frequency Data:: No frequency data

OGT

Exomiser Score: 0.033

Phenotype Score: 0.507

Variant Score: 0.506

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300997 Mental retardation, X-linked 106 - X-linked recessive

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.033

Phenotype Score: 0.507

Variant Score: 0.506

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.71544126G>C [1/1] rs189119237 (variation viewer)

Variant score: 0.506 CONTRIBUTING VARIANT

Transcripts:: OGT:ENST00000373701.7:c.433-441G>C:p.(=); OGT:ENST00000373719.8:c.463-441G>C:p.(=)

Pathogenicity Data:: Best Score: 0.57985425; CADD: 0.580 (3.766)

Frequency Data:: 1000Genomes: 0.2649%; TOPMed: 0.2517%; UK10K: 0.0606%; gnomAD_G_AFR: 0.3770%; gnomAD_G_AMR: 0.6612%; gnomAD_G_FIN: 0.0390%; gnomAD_G_NFE: 0.0765%

Other passed variants:

YWHAZ

Exomiser Score: 0.033

Phenotype Score: 0.509

Variant Score: 0.504

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving YWHAZ.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.509 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.033

Phenotype Score: 0.509

Variant Score: 0.504

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.100928763C>T [0/1] rs528970309 (variation viewer)

Variant score: 0.504 CONTRIBUTING VARIANT

Transcripts:: YWHAZ:ENST00000353245.7:c.295-3724G>A:p.(=); YWHAZ:ENST00000395948.6:c.64-3724G>A:p.(=); YWHAZ:ENST00000395951.7:c.295-3724G>A:p.(=); YWHAZ:ENST00000395953.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000395956.7:c.295-3724G>A:p.(=); YWHAZ:ENST00000395957.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000395958.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000419477.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000457309.2:c.295-3724G>A:p.(=); YWHAZ:ENST00000522542.5:c.70-3724G>A:p.(=); YWHAZ:ENST00000521309.5:c.-66-3724G>A:p.(=); YWHAZ:ENST00000522819.5:c.-67+3266G>A:p.(=)

Pathogenicity Data:: Best Score: 0.50682616; CADD: 0.507 (3.070)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0048%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.006

Phenotype Score: 0.509

Variant Score: 0.308

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.100928763C>T [0/1] rs528970309 (variation viewer)

Variant score: 0.504 CONTRIBUTING VARIANT

Transcripts:: YWHAZ:ENST00000353245.7:c.295-3724G>A:p.(=); YWHAZ:ENST00000395948.6:c.64-3724G>A:p.(=); YWHAZ:ENST00000395951.7:c.295-3724G>A:p.(=); YWHAZ:ENST00000395953.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000395956.7:c.295-3724G>A:p.(=); YWHAZ:ENST00000395957.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000395958.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000419477.6:c.295-3724G>A:p.(=); YWHAZ:ENST00000457309.2:c.295-3724G>A:p.(=); YWHAZ:ENST00000522542.5:c.70-3724G>A:p.(=); YWHAZ:ENST00000521309.5:c.-66-3724G>A:p.(=); YWHAZ:ENST00000522819.5:c.-67+3266G>A:p.(=)

Pathogenicity Data:: Best Score: 0.50682616; CADD: 0.507 (3.070)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0048%

THREE_PRIME_UTR_EXON_VARIANT chr8:g.100918408T>TTATATATATATATA [-/1] rs71572094 (variation viewer)

Variant score: 0.113 CONTRIBUTING VARIANT

Transcripts:: YWHAZ:ENST00000395957.6:c.*2271_*2284dup:p.(=); YWHAZ:ENST00000395958.6:c.*2271_*2284dup:p.(=)

Pathogenicity Data:: Best Score: 0.11284399; CADD: 0.113 (0.520)

Frequency Data:: No frequency data

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr8:g.100918408T>TTATATATATATATATA [-/1] rs71572094 (variation viewer)

Variant score: 0.109

Transcripts:: YWHAZ:ENST00000395957.6:c.*2269_*2284dup:p.(=); YWHAZ:ENST00000395958.6:c.*2269_*2284dup:p.(=)

Pathogenicity Data:: Best Score: 0.10854381; CADD: 0.109 (0.499)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.100930824C>T [0/1] rs187620099 (variation viewer)

Variant score: 0.107

Transcripts:: YWHAZ:ENST00000353245.7:c.295-5785G>A:p.(=); YWHAZ:ENST00000395948.6:c.64-5785G>A:p.(=); YWHAZ:ENST00000395951.7:c.295-5785G>A:p.(=); YWHAZ:ENST00000395953.6:c.295-5785G>A:p.(=); YWHAZ:ENST00000395956.7:c.295-5785G>A:p.(=); YWHAZ:ENST00000395957.6:c.295-5785G>A:p.(=); YWHAZ:ENST00000395958.6:c.295-5785G>A:p.(=); YWHAZ:ENST00000419477.6:c.295-5785G>A:p.(=); YWHAZ:ENST00000457309.2:c.295-5785G>A:p.(=); YWHAZ:ENST00000522542.5:c.70-5785G>A:p.(=); YWHAZ:ENST00000521309.5:c.-66-5785G>A:p.(=); YWHAZ:ENST00000522819.5:c.-67+1205G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12299919; CADD: 0.123 (0.570)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.3432%; UK10K: 0.6744%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.3723%; gnomAD_G_NFE: 0.5264%; gnomAD_G_OTH: 0.2041%

MAP2

Exomiser Score: 0.032

Phenotype Score: 0.501

Variant Score: 0.508

Phenotype matches:

Phenotypic similarity 0.445 to mouse mutant involving MAP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003460, decreased fear-related response

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.032

Phenotype Score: 0.501

Variant Score: 0.508

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209652446A>C [0/1]

Variant score: 0.508 CONTRIBUTING VARIANT

Transcripts:: MAP2:ENST00000199940.10:c.-29-696A>C:p.(=); MAP2:ENST00000360351.8:c.-29-696A>C:p.(=); MAP2:ENST00000361559.8:c.-29-696A>C:p.(=); MAP2:ENST00000392194.5:c.-29-696A>C:p.(=)

Pathogenicity Data:: Best Score: 0.5083002; CADD: 0.508 (3.083)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.501

Variant Score: 0.405

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209652446A>C [0/1]

Variant score: 0.508 CONTRIBUTING VARIANT

Transcripts:: MAP2:ENST00000199940.10:c.-29-696A>C:p.(=); MAP2:ENST00000360351.8:c.-29-696A>C:p.(=); MAP2:ENST00000361559.8:c.-29-696A>C:p.(=); MAP2:ENST00000392194.5:c.-29-696A>C:p.(=)

Pathogenicity Data:: Best Score: 0.5083002; CADD: 0.508 (3.083)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209598620C>T [0/1]

Variant score: 0.302 CONTRIBUTING VARIANT

Transcripts:: MAP2:ENST00000199940.10:c.-107+18520C>T:p.(=); MAP2:ENST00000360351.8:c.-107+18520C>T:p.(=); MAP2:ENST00000361559.8:c.-107+18520C>T:p.(=); MAP2:ENST00000392194.5:c.-107+18520C>T:p.(=)

Pathogenicity Data:: Best Score: 0.30224973; CADD: 0.302 (1.563)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209487646A>G [0/1] rs113676400 (variation viewer)

Variant score: 0.298

Transcripts:: MAP2:ENST00000199940.10:c.-221-19946A>G:p.(=)

Pathogenicity Data:: Best Score: 0.46445; CADD: 0.464 (2.712)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.6371%; UK10K: 1.2960%; gnomAD_G_AFR: 0.1947%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.2003%; gnomAD_G_NFE: 0.8527%; gnomAD_G_OTH: 1.0183%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209648585G>A [0/1] rs139377054 (variation viewer)

Variant score: 0.296

Transcripts:: MAP2:ENST00000199940.10:c.-29-4557G>A:p.(=); MAP2:ENST00000360351.8:c.-29-4557G>A:p.(=); MAP2:ENST00000361559.8:c.-29-4557G>A:p.(=); MAP2:ENST00000392194.5:c.-29-4557G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3359512; CADD: 0.336 (1.778)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4420%; gnomAD_G_AFR: 0.1210%; gnomAD_G_AMR: 0.2591%; gnomAD_G_FIN: 0.4071%; gnomAD_G_NFE: 0.6319%; gnomAD_G_OTH: 0.1166%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209652476C>T [0/1] rs956152148 (variation viewer)

Variant score: 0.225

Transcripts:: MAP2:ENST00000199940.10:c.-29-666C>T:p.(=); MAP2:ENST00000360351.8:c.-29-666C>T:p.(=); MAP2:ENST00000361559.8:c.-29-666C>T:p.(=); MAP2:ENST00000392194.5:c.-29-666C>T:p.(=)

Pathogenicity Data:: Best Score: 0.22535986; CADD: 0.225 (1.109)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr2:g.209418047T>C [0/1] rs138284617 (variation viewer)

Variant score: 0.160

Transcripts:: MAP2:ENST00000199940.10::; MAP2:ENST00000416092.1::

Pathogenicity Data:: Best Score: 0.19573349; CADD: 0.196 (0.946)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.3910%; UK10K: 0.8463%; gnomAD_G_AFR: 0.1145%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.2016%; gnomAD_G_NFE: 0.5740%; gnomAD_G_OTH: 0.4090%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209593634A>AAAAATATAT [1/1] rs1286103137 (variation viewer)

Variant score: 0.118

Transcripts:: MAP2:ENST00000199940.10:c.-107+13534_-107+13535insAAAATATAT:p.(=); MAP2:ENST00000360351.8:c.-107+13534_-107+13535insAAAATATAT:p.(=); MAP2:ENST00000361559.8:c.-107+13534_-107+13535insAAAATATAT:p.(=); MAP2:ENST00000392194.5:c.-107+13534_-107+13535insAAAATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.11813927; CADD: 0.118 (0.546)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209513206G>A [0/1] rs113985770 (variation viewer)

Variant score: 0.091

Transcripts:: MAP2:ENST00000199940.10:c.-172+5565G>A:p.(=)

Pathogenicity Data:: Best Score: 0.42535448; CADD: 0.425 (2.406)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 1.0170%; UK10K: 1.9175%; gnomAD_G_AFR: 0.2636%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.9164%; gnomAD_G_NFE: 1.4006%; gnomAD_G_OTH: 1.8367%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209578929GT>G [0/1] rs112409137 (variation viewer)

Variant score: 0.072

Transcripts:: MAP2:ENST00000199940.10:c.-171-1106del:p.(=)

Pathogenicity Data:: Best Score: 0.1352312; CADD: 0.135 (0.631)

Frequency Data:: gnomAD_G_AFR: 1.1469%; gnomAD_G_AMR: 1.4957%; gnomAD_G_ASJ: 1.1278%; gnomAD_G_EAS: 0.4575%; gnomAD_G_FIN: 0.8760%; gnomAD_G_NFE: 0.8797%; gnomAD_G_OTH: 0.5510%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.209674621A>G [0/1] rs755093029 (variation viewer)

Variant score: 0.065

Transcripts:: MAP2:ENST00000199940.10:c.263-3951A>G:p.(=); MAP2:ENST00000360351.8:c.263-3951A>G:p.(=); MAP2:ENST00000361559.8:c.263-3951A>G:p.(=); MAP2:ENST00000392194.5:c.263-3951A>G:p.(=); MAP2:ENST00000447185.5:c.263-3951A>G:p.(=)

Pathogenicity Data:: Best Score: 0.06480968; CADD: 0.065 (0.291)

Frequency Data:: UK10K: 0.0264%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209559479CA>C [0/1] rs59788211 (variation viewer)

Variant score: 0.049

Transcripts:: MAP2:ENST00000199940.10:c.-171-20556del:p.(=)

Pathogenicity Data:: Best Score: 0.049176276; CADD: 0.049 (0.219)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209523093C>T [0/1] rs181613510 (variation viewer)

Variant score: 0.030

Transcripts:: MAP2:ENST00000199940.10:c.-172+15452C>T:p.(=)

Pathogenicity Data:: Best Score: 0.036392868; CADD: 0.036 (0.161)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.4460%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.4007%; gnomAD_G_NFE: 0.6398%; gnomAD_G_OTH: 0.4073%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.209651758G>T [0/1] rs145006403 (variation viewer)

Variant score: 0.027

Transcripts:: MAP2:ENST00000199940.10:c.-29-1384G>T:p.(=); MAP2:ENST00000360351.8:c.-29-1384G>T:p.(=); MAP2:ENST00000361559.8:c.-29-1384G>T:p.(=); MAP2:ENST00000392194.5:c.-29-1384G>T:p.(=)

Pathogenicity Data:: Best Score: 0.033281565; CADD: 0.033 (0.147)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.4380%; UK10K: 0.8992%; gnomAD_G_AFR: 0.1374%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.4009%; gnomAD_G_NFE: 0.6133%; gnomAD_G_OTH: 0.5102%

STAM2

Exomiser Score: 0.032

Phenotype Score: 0.506

Variant Score: 0.503

Phenotype matches:

Proximity score 0.506 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.032

Phenotype Score: 0.506

Variant Score: 0.503

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.152170023A>T [0|1] rs763172182 (variation viewer)

Variant score: 0.503 CONTRIBUTING VARIANT

Transcripts:: STAM2:ENST00000263904.5:c.40+5580T>A:p.(=)

Pathogenicity Data:: Best Score: 0.5036363; CADD: 0.504 (3.042)

Frequency Data:: TOPMed: 0.0032%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.006

Phenotype Score: 0.506

Variant Score: 0.319

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.152170023A>T [0|1] rs763172182 (variation viewer)

Variant score: 0.503 CONTRIBUTING VARIANT

Transcripts:: STAM2:ENST00000263904.5:c.40+5580T>A:p.(=)

Pathogenicity Data:: Best Score: 0.5036363; CADD: 0.504 (3.042)

Frequency Data:: TOPMed: 0.0032%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

DOWNSTREAM_GENE_VARIANT chr2:g.152115016CAAAAAAAA>C [0/1] rs61615704 (variation viewer)

Variant score: 0.135 CONTRIBUTING VARIANT

Transcripts:: STAM2:ENST00000263904.5::; STAM2:ENST00000539935.6::

Pathogenicity Data:: Best Score: 0.1352312; CADD: 0.135 (0.631)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.152159110T>TATATATATATATATATATATACAC [0/1] rs575009275 (variation viewer)

Variant score: 0.085

Transcripts:: STAM2:ENST00000263904.5:c.41-8882_41-8881insGTGTATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.08525509; CADD: 0.085 (0.387)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.152136262G>A [0/1] rs141035087 (variation viewer)

Variant score: 0.023

Transcripts:: STAM2:ENST00000263904.5:c.705-659C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14059079; CADD: 0.141 (0.658)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.9214%; UK10K: 1.6530%; gnomAD_G_AFR: 0.1837%; gnomAD_G_AMR: 0.5981%; gnomAD_G_FIN: 1.9687%; gnomAD_G_NFE: 1.5612%; gnomAD_G_OTH: 0.9202%

COPA

Exomiser Score: 0.032

Phenotype Score: 0.252

Variant Score: 0.788

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:616414 Autoimmune interstitial lung, joint, and kidney disease (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.032

Phenotype Score: 0.252

Variant Score: 0.788

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.160318468T>TA [1/1] rs71090307 (variation viewer)

Variant score: 0.788 CONTRIBUTING VARIANT

Transcripts:: COPA:ENST00000241704.8:c.707-4344_707-4343insT:p.(=); COPA:ENST00000368069.7:c.707-4344_707-4343insT:p.(=); COPA:ENST00000647683.1:c.707-4344_707-4343insT:p.(=); COPA:ENST00000649787.1:c.707-4344_707-4343insT:p.(=)

Pathogenicity Data:: Best Score: 0.7884563; CADD: 0.788 (6.746)

Frequency Data:: No frequency data

Other passed variants:

GRAP2

Exomiser Score: 0.030

Phenotype Score: 0.505

Variant Score: 0.498

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.163

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr22:g.39899475A>G [0/1] rs762315985 (variation viewer)

Variant score: 0.163 CONTRIBUTING VARIANT

Transcripts:: GRAP2:ENST00000344138.9::; GRAP2:ENST00000325157.7::

Pathogenicity Data:: Best Score: 0.16458935; CADD: 0.165 (0.781)

Frequency Data:: TOPMed: 0.0199%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.030

Phenotype Score: 0.505

Variant Score: 0.498

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.39922516C>A [0/1] rs543426108 (variation viewer)

Variant score: 0.756 CONTRIBUTING VARIANT

Transcripts:: GRAP2:ENST00000344138.9:c.-15+21186C>A:p.(=)

Pathogenicity Data:: Best Score: 0.8532764; CADD: 0.853 (8.335)

Frequency Data:: TOPMed: 0.1832%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0458%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.2867%; gnomAD_G_OTH: 0.6122%

INTERGENIC_VARIANT chr22:g.39986958C>T [0/1] rs147689559 (variation viewer)

Variant score: 0.239 CONTRIBUTING VARIANT

Transcripts:: GRAP2:ENST00000344138.9::; GRAP2:ENST00000333407.11::

Pathogenicity Data:: Best Score: 0.30513567; CADD: 0.305 (1.581)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.6172%; UK10K: 0.9521%; gnomAD_G_AFR: 0.1951%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1146%; gnomAD_G_NFE: 0.6480%; gnomAD_G_OTH: 0.6122%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.39931796C>T [0/1] rs185592828 (variation viewer)

Variant score: 0.143

Transcripts:: GRAP2:ENST00000344138.9:c.-14-15297C>T:p.(=)

Pathogenicity Data:: Best Score: 0.27972227; CADD: 0.280 (1.425)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.4197%; UK10K: 0.5951%; gnomAD_G_AFR: 0.1719%; gnomAD_G_AMR: 0.2404%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.6881%; gnomAD_G_NFE: 0.5860%; gnomAD_G_OTH: 1.5275%

DOWNSTREAM_GENE_VARIANT chr22:g.39978050AG>A [0|1] rs372735823 (variation viewer)

Variant score: 0.086

Transcripts:: GRAP2:ENST00000344138.9::; GRAP2:ENST00000333407.11::

Pathogenicity Data:: Best Score: 0.106077254; CADD: 0.106 (0.487)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_AFR: 0.3735%; gnomAD_G_AMR: 0.8357%; gnomAD_G_ASJ: 0.3650%; gnomAD_G_EAS: 0.6250%; gnomAD_G_FIN: 0.8807%; gnomAD_G_NFE: 0.1406%; gnomAD_G_OTH: 0.3432%

DOWNSTREAM_GENE_VARIANT chr22:g.39978052AAAG>A [0|1] rs1170923392 (variation viewer)

Variant score: 0.048

Transcripts:: GRAP2:ENST00000344138.9::; GRAP2:ENST00000333407.11::

Pathogenicity Data:: Best Score: 0.05441624; CADD: 0.054 (0.243)

Frequency Data:: gnomAD_G_AFR: 0.3159%; gnomAD_G_AMR: 0.2695%; gnomAD_G_ASJ: 0.3546%; gnomAD_G_EAS: 0.6196%; gnomAD_G_FIN: 0.0784%; gnomAD_G_NFE: 0.0894%

PRKAR2B

Exomiser Score: 0.028

Phenotype Score: 0.507

Variant Score: 0.488

Phenotype matches:

Phenotypic similarity 0.389 to mouse mutant involving PRKAR2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001433, polyphagia

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.012

Phenotype Score: 0.507

Variant Score: 0.396

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.107065322ATGTG>A [0/1] rs71134248 (variation viewer)

Variant score: 0.396 CONTRIBUTING VARIANT

Transcripts:: PRKAR2B:ENST00000265717.5:c.308-4958_308-4955del:p.(=)

Pathogenicity Data:: Best Score: 0.39563406; CADD: 0.396 (2.187)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.028

Phenotype Score: 0.507

Variant Score: 0.488

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.107136945G>C [0/1] rs540142308 (variation viewer)

Variant score: 0.580 CONTRIBUTING VARIANT

Transcripts:: PRKAR2B:ENST00000265717.5:c.481-3902G>C:p.(=)

Pathogenicity Data:: Best Score: 0.6084385; CADD: 0.608 (4.072)

Frequency Data:: TOPMed: 0.1019%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0572%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.2932%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.107065322ATGTG>A [0/1] rs71134248 (variation viewer)

Variant score: 0.396 CONTRIBUTING VARIANT

Transcripts:: PRKAR2B:ENST00000265717.5:c.308-4958_308-4955del:p.(=)

Pathogenicity Data:: Best Score: 0.39563406; CADD: 0.396 (2.187)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.107050333C>CT [0/1] rs57752789 (variation viewer)

Variant score: 0.157

Transcripts:: PRKAR2B:ENST00000265717.5:c.307+5119_307+5120insT:p.(=)

Pathogenicity Data:: Best Score: 0.15705353; CADD: 0.157 (0.742)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.107114324C>CTG [-/1] rs58110858 (variation viewer)

Variant score: 0.147

Transcripts:: PRKAR2B:ENST00000265717.5:c.344-7628_344-7627insTG:p.(=)

Pathogenicity Data:: Best Score: 0.14709628; CADD: 0.147 (0.691)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr7:g.107167146TA>T [1/1] rs565158354 (variation viewer)

Variant score: 0.074

Transcripts:: PRKAR2B:ENST00000265717.5::

Pathogenicity Data:: Best Score: 0.082512856; CADD: 0.083 (0.374)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.5591%

DOWNSTREAM_GENE_VARIANT chr7:g.107161979G>GGTGTGTGTGTGT [-/1] rs143373585 (variation viewer)

Variant score: 0.057

Transcripts:: PRKAR2B:ENST00000265717.5::; PRKAR2B:ENST00000468410.5::

Pathogenicity Data:: Best Score: 0.057025373; CADD: 0.057 (0.255)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.107148492A>G [0/1] rs138809646 (variation viewer)

Variant score: 0.016

Transcripts:: PRKAR2B:ENST00000265717.5:c.741+2031A>G:p.(=)

Pathogenicity Data:: Best Score: 0.04082024; CADD: 0.041 (0.181)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 1.1100%; UK10K: 1.7191%; gnomAD_G_AFR: 0.2978%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.6304%; gnomAD_G_NFE: 1.3530%; gnomAD_G_OTH: 0.8163%

CDH15

Exomiser Score: 0.028

Phenotype Score: 0.509

Variant Score: 0.484

Phenotype matches:

Proximity score 0.509 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612580 Mental retardation, autosomal dominant 3 - autosomal dominant; ORPHA:178469 Autosomal dominant non-syndromic intellectual disability

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.028

Phenotype Score: 0.509

Variant Score: 0.484

Variants contributing to score:

INTERGENIC_VARIANT chr16:g.89157568A>C [0/1]

Variant score: 0.484 CONTRIBUTING VARIANT

Transcripts:: CDH15:ENST00000289746.3::

Pathogenicity Data:: Best Score: 0.48417783; CADD: 0.484 (2.875)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.254

Variant Score: 0.291

Variants contributing to score:

INTERGENIC_VARIANT chr16:g.89157568A>C [0/1]

Variant score: 0.484 CONTRIBUTING VARIANT

Transcripts:: CDH15:ENST00000289746.3::

Pathogenicity Data:: Best Score: 0.48417783; CADD: 0.484 (2.875)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.89179323C>T [0/1] rs577868281 (variation viewer)

Variant score: 0.097 CONTRIBUTING VARIANT

Transcripts:: CDH15:ENST00000289746.3:c.43-93C>T:p.(=)

Pathogenicity Data:: Best Score: 0.10277784; CADD: 0.103 (0.471)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1139%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1470%; gnomAD_G_OTH: 0.2041%

Other passed variants:

JAK1

Exomiser Score: 0.028

Phenotype Score: 0.252

Variant Score: 0.774

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618999 Autoinflammation, immune dysregulation, and eosinophilia - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.188

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.64928778C>CAAAAAAAAA [0/1] rs1183218798 (variation viewer)

Variant score: 0.188 CONTRIBUTING VARIANT

Transcripts:: JAK1:ENST00000342505.5:c.-78+37554_-78+37555insTTTTTTTTT:p.(=); JAK1:ENST00000671929.1:c.-78+28155_-78+28156insTTTTTTTTT:p.(=); JAK1:ENST00000671954.1:c.-77-42438_-77-42437insTTTTTTTTT:p.(=); JAK1:ENST00000672179.1:c.-78+38102_-78+38103insTTTTTTTTT:p.(=); JAK1:ENST00000672247.1:c.-78+28155_-78+28156insTTTTTTTTT:p.(=); JAK1:ENST00000672434.1:c.-78+28155_-78+28156insTTTTTTTTT:p.(=); JAK1:ENST00000673046.1:c.-78+37554_-78+37555insTTTTTTTTT:p.(=); JAK1:ENST00000673254.1:c.-78+37554_-78+37555insTTTTTTTTT:p.(=); JAK1:ENST00000673502.1:c.-77-42438_-77-42437insTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.18773079; CADD: 0.188 (0.903)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.028

Phenotype Score: 0.252

Variant Score: 0.774

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.64907493T>C [0/1] rs372526013 (variation viewer)

Variant score: 0.777 CONTRIBUTING VARIANT

Transcripts:: JAK1:ENST00000342505.5:c.-77-21152A>G:p.(=); JAK1:ENST00000671929.1:c.-77-21152A>G:p.(=); JAK1:ENST00000671954.1:c.-77-21152A>G:p.(=); JAK1:ENST00000672179.1:c.-77-21152A>G:p.(=); JAK1:ENST00000672247.1:c.-77-21152A>G:p.(=); JAK1:ENST00000672434.1:c.-77-21152A>G:p.(=); JAK1:ENST00000673046.1:c.-77-21152A>G:p.(=); JAK1:ENST00000673254.1:c.-77-21152A>G:p.(=); JAK1:ENST00000673502.1:c.-77-21152A>G:p.(=)

Pathogenicity Data:: Best Score: 0.860331; CADD: 0.860 (8.549)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.0581%; UK10K: 0.0661%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0600%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.64963630T>C [0/1] rs372831404 (variation viewer)

Variant score: 0.770 CONTRIBUTING VARIANT

Transcripts:: JAK1:ENST00000342505.5:c.-78+2703A>G:p.(=); JAK1:ENST00000671929.1:c.-162+2419A>G:p.(=); JAK1:ENST00000671954.1:c.-77-77289A>G:p.(=); JAK1:ENST00000672179.1:c.-78+3251A>G:p.(=); JAK1:ENST00000672247.1:c.-162+2703A>G:p.(=); JAK1:ENST00000672434.1:c.-161-6613A>G:p.(=); JAK1:ENST00000673046.1:c.-78+2703A>G:p.(=); JAK1:ENST00000673254.1:c.-78+2703A>G:p.(=); JAK1:ENST00000673502.1:c.-77-77289A>G:p.(=)

Pathogenicity Data:: Best Score: 0.83582765; CADD: 0.836 (7.847)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.0215%; UK10K: 0.0397%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0133%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.64861593A>G [0/1] rs375464564 (variation viewer)

Variant score: 0.440

Transcripts:: JAK1:ENST00000342505.5:c.1177-1331T>C:p.(=); JAK1:ENST00000671929.1:c.1177-1331T>C:p.(=); JAK1:ENST00000671954.1:c.1177-1331T>C:p.(=); JAK1:ENST00000672179.1:c.1177-1331T>C:p.(=); JAK1:ENST00000672247.1:c.1177-1331T>C:p.(=); JAK1:ENST00000672434.1:c.1177-1331T>C:p.(=); JAK1:ENST00000673046.1:c.1177-1331T>C:p.(=); JAK1:ENST00000673254.1:c.1045-1331T>C:p.(=); JAK1:ENST00000673502.1:c.1177-1331T>C:p.(=)

Pathogenicity Data:: Best Score: 0.47976446; CADD: 0.480 (2.838)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.0191%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.64878573A>G [0|1] rs199963297 (variation viewer)

Variant score: 0.407

Transcripts:: JAK1:ENST00000342505.5:c.329+452T>C:p.(=); JAK1:ENST00000671929.1:c.329+452T>C:p.(=); JAK1:ENST00000671954.1:c.329+452T>C:p.(=); JAK1:ENST00000672179.1:c.329+452T>C:p.(=); JAK1:ENST00000672247.1:c.329+452T>C:p.(=); JAK1:ENST00000672434.1:c.329+452T>C:p.(=); JAK1:ENST00000673046.1:c.329+452T>C:p.(=); JAK1:ENST00000673254.1:c.329+452T>C:p.(=); JAK1:ENST00000673502.1:c.329+452T>C:p.(=)

Pathogenicity Data:: Best Score: 0.53548473; CADD: 0.535 (3.330)

Frequency Data:: gnomAD_G_AFR: 0.3709%; gnomAD_G_AMR: 0.2463%; gnomAD_G_ASJ: 1.0204%; gnomAD_G_EAS: 0.8841%; gnomAD_G_FIN: 0.1524%; gnomAD_G_NFE: 0.3725%; gnomAD_G_OTH: 0.1894%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.64902583A>AGAGAGAGTGTGT [1/1] rs775479498 (variation viewer)

Variant score: 0.224

Transcripts:: JAK1:ENST00000342505.5:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000671929.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000671954.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000672179.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000672247.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000672434.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000673046.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000673254.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=); JAK1:ENST00000673502.1:c.-77-16243_-77-16242insACACACTCTCTC:p.(=)

Pathogenicity Data:: Best Score: 0.22428894; CADD: 0.224 (1.103)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.64913705A>AAGGG [1/1] rs369849593 (variation viewer)

Variant score: 0.219

Transcripts:: JAK1:ENST00000342505.5:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000671929.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000671954.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000672179.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000672247.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000672434.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000673046.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000673254.1:c.-77-27365_-77-27364insCCCT:p.(=); JAK1:ENST00000673502.1:c.-77-27365_-77-27364insCCCT:p.(=)

Pathogenicity Data:: Best Score: 0.21909177; CADD: 0.219 (1.074)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.65052584C>T [0/1] rs560195532 (variation viewer)

Variant score: 0.113

Transcripts:: JAK1:ENST00000671954.1:c.-180-8002G>A:p.(=); JAK1:ENST00000672434.1:c.-162+14044G>A:p.(=); JAK1:ENST00000673502.1:c.-78+13537G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13343728; CADD: 0.133 (0.622)

Frequency Data:: 1000Genomes: 0.7588%; TOPMed: 0.7588%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0536%; gnomAD_G_OTH: 0.2053%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.65052109C>T [0/1] rs540365860 (variation viewer)

Variant score: 0.094

Transcripts:: JAK1:ENST00000671954.1:c.-180-7527G>A:p.(=); JAK1:ENST00000672434.1:c.-162+14519G>A:p.(=); JAK1:ENST00000673502.1:c.-78+14012G>A:p.(=)

Pathogenicity Data:: Best Score: 0.093850195; CADD: 0.094 (0.428)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_NFE: 0.0069%

FIVE_PRIME_UTR_INTRON_VARIANT chr1:g.64913641G>GAGAAAGGAAGGAAAGAAGGA [1/1] rs1357274757 (variation viewer)

Variant score: 0.036

Transcripts:: JAK1:ENST00000342505.5:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000671929.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000671954.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000672179.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000672247.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000672434.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000673046.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000673254.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=); JAK1:ENST00000673502.1:c.-77-27301_-77-27300insTCCTTCTTTCCTTCCTTTCT:p.(=)

Pathogenicity Data:: Best Score: 0.03594899; CADD: 0.036 (0.159)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.64878563A>* [-/1]

Variant score: 0.000

Transcripts:: JAK1:ENST00000342505.5:c.329+462T>:p.(=); JAK1:ENST00000671929.1:c.329+462T>:p.(=); JAK1:ENST00000671954.1:c.329+462T>:p.(=); JAK1:ENST00000672179.1:c.329+462T>:p.(=); JAK1:ENST00000672247.1:c.329+462T>:p.(=); JAK1:ENST00000672434.1:c.329+462T>:p.(=); JAK1:ENST00000673046.1:c.329+462T>:p.(=); JAK1:ENST00000673254.1:c.329+462T>:p.(=); JAK1:ENST00000673502.1:c.329+462T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.64878567A>* [-/1]

Variant score: 0.000

Transcripts:: JAK1:ENST00000342505.5:c.329+458T>:p.(=); JAK1:ENST00000671929.1:c.329+458T>:p.(=); JAK1:ENST00000671954.1:c.329+458T>:p.(=); JAK1:ENST00000672179.1:c.329+458T>:p.(=); JAK1:ENST00000672247.1:c.329+458T>:p.(=); JAK1:ENST00000672434.1:c.329+458T>:p.(=); JAK1:ENST00000673046.1:c.329+458T>:p.(=); JAK1:ENST00000673254.1:c.329+458T>:p.(=); JAK1:ENST00000673502.1:c.329+458T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

PLA2G6

Exomiser Score: 0.027

Phenotype Score: 0.531

Variant Score: 0.455

Phenotype matches:

Phenotypic similarity 0.479 to Adult-onset dystonia-parkinsonism associated with PLA2G6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.531 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:256600 Infantile neuroaxonal dystrophy 1 - autosomal recessive; OMIM:610217 Neurodegeneration with brain iron accumulation 2B - autosomal recessive; OMIM:612953 Parkinson disease 14, autosomal recessive - autosomal recessive; ORPHA:199351 Adult-onset dystonia-parkinsonism; ORPHA:35069 Infantile neuroaxonal dystrophy; ORPHA:35069 Infantile neuroaxonal dystrophy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.266

Variant Score: 0.283

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.38210623A>AGTGTGTGTGTGT [-/1] rs71195095 (variation viewer)

Variant score: 0.283 CONTRIBUTING VARIANT

Transcripts:: PLA2G6:ENST00000660610.1:c.-42+3829_-42+3830insACACACACACAC:p.(=); PLA2G6:ENST00000338483.7:c.-31-3200_-31-3199insGTGTGTGTGTGT:p.(=); PLA2G6:ENST00000426621.6:c.-31-3200_-31-3199insGTGTGTGTGTGT:p.(=); PLA2G6:ENST00000538320.5:c.-31-3200_-31-3199insGTGTGTGTGTGT:p.(=); PLA2G6:ENST00000538999.1:c.-51-3797_-51-3796insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.2825362; CADD: 0.283 (1.442)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.027

Phenotype Score: 0.531

Variant Score: 0.455

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.38198123A>AAAAAAAAAAATAAAT [1/1] rs373867543 (variation viewer)

Variant score: 0.455 CONTRIBUTING VARIANT

Transcripts:: PLA2G6:ENST00000660610.1:c.-42+16329_-42+16330insATTTATTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.4552465; CADD: 0.455 (2.638)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.38210623A>AGTGTGTGTGTGTGT [-/1] rs71195095 (variation viewer)

Variant score: 0.273

Transcripts:: PLA2G6:ENST00000660610.1:c.-42+3829_-42+3830insACACACACACACAC:p.(=); PLA2G6:ENST00000338483.7:c.-31-3200_-31-3199insGTGTGTGTGTGTGT:p.(=); PLA2G6:ENST00000426621.6:c.-31-3200_-31-3199insGTGTGTGTGTGTGT:p.(=); PLA2G6:ENST00000538320.5:c.-31-3200_-31-3199insGTGTGTGTGTGTGT:p.(=); PLA2G6:ENST00000538999.1:c.-51-3797_-51-3796insGTGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.27322495; CADD: 0.273 (1.386)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.38145784A>AACACAC [0/1] rs132936 (variation viewer)

Variant score: 0.180

Transcripts:: PLA2G6:ENST00000332509.8:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000335539.7:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000402064.5:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000660610.1:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000663895.1:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000664587.1:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000667521.1:c.210-132_210-131insGTGTGT:p.(=); PLA2G6:ENST00000668949.1:c.210-132_210-131insGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.17964846; CADD: 0.180 (0.860)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.38199261C>T [0|1] rs147973693 (variation viewer)

Variant score: 0.075

Transcripts:: PLA2G6:ENST00000660610.1:c.-42+15192G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12037003; CADD: 0.120 (0.557)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.5710%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1259%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 1.0394%; gnomAD_G_OTH: 0.8163%

CDKL5

Exomiser Score: 0.026

Phenotype Score: 0.514

Variant Score: 0.472

Phenotype matches:

Phenotypic similarity 0.462 to Atypical Rett syndrome associated with CDKL5.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0030215, Inappropriate crying

Phenotypic similarity 0.436 to mouse mutant involving CDKL5.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.514 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.514 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Known diseases:: OMIM:300672 Developmental and epileptic encephalopathy 2 - X-linked dominant; ORPHA:1934 Early infantile epileptic encephalopathy; ORPHA:3095 Atypical Rett syndrome; ORPHA:3451 West syndrome; ORPHA:505652 CDKL5-related epileptic encephalopathy

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.257

Variant Score: 0.513

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.18523035A>G [1/1] rs568330527 (variation viewer)

Variant score: 0.513 CONTRIBUTING VARIANT

Transcripts:: CDKL5:ENST00000379989.6:c.99+12181A>G:p.(=); CDKL5:ENST00000379996.7:c.99+12181A>G:p.(=); CDKL5:ENST00000623535.2:c.99+12181A>G:p.(=); CDKL5:ENST00000635828.1:c.99+12181A>G:p.(=); CDKL5:ENST00000674046.1:c.99+12181A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5242268; CADD: 0.524 (3.226)

Frequency Data:: 1000Genomes: 0.0265%; TOPMed: 0.0948%; UK10K: 0.1061%; gnomAD_G_NFE: 0.1259%; gnomAD_G_OTH: 0.1414%

X_DOMINANT

Exomiser Score: 0.026

Phenotype Score: 0.514

Variant Score: 0.472

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr23:g.18450377A>G [1/1]

Variant score: 0.472 CONTRIBUTING VARIANT

Transcripts:: CDKL5:ENST00000379989.6:c.-163+7954A>G:p.(=); CDKL5:ENST00000379996.7:c.-163+24682A>G:p.(=); CDKL5:ENST00000623535.2:c.-163+24682A>G:p.(=); CDKL5:ENST00000635828.1:c.-163+23976A>G:p.(=); CDKL5:ENST00000674046.1:c.-163+24682A>G:p.(=)

Pathogenicity Data:: Best Score: 0.47191966; CADD: 0.472 (2.773)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.18568133T>G [1/1] rs556497648 (variation viewer)

Variant score: 0.453

Transcripts:: CDKL5:ENST00000379989.6:c.145+3611T>G:p.(=); CDKL5:ENST00000379996.7:c.145+3611T>G:p.(=); CDKL5:ENST00000623535.2:c.145+3611T>G:p.(=); CDKL5:ENST00000635828.1:c.145+3611T>G:p.(=); CDKL5:ENST00000674046.1:c.145+3611T>G:p.(=)

Pathogenicity Data:: Best Score: 0.46259707; CADD: 0.463 (2.697)

Frequency Data:: 1000Genomes: 0.0265%; TOPMed: 0.0956%; UK10K: 0.1213%; gnomAD_G_AFR: 0.0167%; gnomAD_G_NFE: 0.1125%; gnomAD_G_OTH: 0.1377%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.18651264TGA>T [1/1] rs1191836877 (variation viewer)

Variant score: 0.150

Transcripts:: CDKL5:ENST00000379989.6:c.2980+673_2980+674del:p.(=); CDKL5:ENST00000379996.7:c.2980+673_2980+674del:p.(=); CDKL5:ENST00000379984.4:c.185-3934_185-3933del:p.(=)

Pathogenicity Data:: Best Score: 0.14984131; CADD: 0.150 (0.705)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr23:g.18427726A>T [1/1] rs546520006 (variation viewer)

Variant score: 0.142

Transcripts:: CDKL5:ENST00000379996.7:c.-163+2031A>T:p.(=); CDKL5:ENST00000623535.2:c.-163+2031A>T:p.(=); CDKL5:ENST00000635828.1:c.-163+1325A>T:p.(=); CDKL5:ENST00000674046.1:c.-163+2031A>T:p.(=)

Pathogenicity Data:: Best Score: 0.14453942; CADD: 0.145 (0.678)

Frequency Data:: TOPMed: 0.0964%; gnomAD_G_FIN: 0.0392%; gnomAD_G_NFE: 0.1232%; gnomAD_G_OTH: 0.1389%

COX18

Exomiser Score: 0.026

Phenotype Score: 0.503

Variant Score: 0.483

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.008

Phenotype Score: 0.503

Variant Score: 0.349

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.73067864A>AAAAAAATATATATATAT [0/1] rs59043145 (variation viewer)

Variant score: 0.349 CONTRIBUTING VARIANT

Transcripts:: COX18:ENST00000295890.8:c.434+164_434+165insATATATATATATTTTTT:p.(=); COX18:ENST00000507544.2:c.434+164_434+165insATATATATATATTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.34867162; CADD: 0.349 (1.862)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.026

Phenotype Score: 0.503

Variant Score: 0.483

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr4:g.73051309CTTT>C [1/1] rs71215478 (variation viewer)

Variant score: 0.483 CONTRIBUTING VARIANT

Transcripts:: COX18:ENST00000295890.8::; COX18:ENST00000604027.1::

Pathogenicity Data:: Best Score: 0.48263144; CADD: 0.483 (2.862)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr4:g.73070669TTTAC>T [0/1] rs546426395 (variation viewer)

Variant score: 0.261

Transcripts:: COX18:ENST00000295890.8::; COX18:ENST00000358602.9::

Pathogenicity Data:: Best Score: 0.2946576; CADD: 0.295 (1.516)

Frequency Data:: UK10K: 0.6083%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.1196%; gnomAD_G_FIN: 0.2292%; gnomAD_G_NFE: 0.5596%; gnomAD_G_OTH: 0.5092%

UBE4A

Exomiser Score: 0.025

Phenotype Score: 0.505

Variant Score: 0.478

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.025

Phenotype Score: 0.505

Variant Score: 0.478

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.118355830C>CGTGTGTATATACGTATATACACAA [0/1] rs200701373 (variation viewer)

Variant score: 0.478 CONTRIBUTING VARIANT

Transcripts:: UBE4A:ENST00000252108.7::; UBE4A:ENST00000532917.2::

Pathogenicity Data:: Best Score: 0.4776038; CADD: 0.478 (2.820)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.019

Phenotype Score: 0.505

Variant Score: 0.445

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.118355830C>CGTGTGTATATACGTATATACACAA [0/1] rs200701373 (variation viewer)

Variant score: 0.478 CONTRIBUTING VARIANT

Transcripts:: UBE4A:ENST00000252108.7::; UBE4A:ENST00000532917.2::

Pathogenicity Data:: Best Score: 0.4776038; CADD: 0.478 (2.820)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.118363324T>C [0/1] rs574403536 (variation viewer)

Variant score: 0.412 CONTRIBUTING VARIANT

Transcripts:: UBE4A:ENST00000252108.7:c.-41-1716T>C:p.(=); UBE4A:ENST00000431736.6:c.-41-1716T>C:p.(=)

Pathogenicity Data:: Best Score: 0.50226295; CADD: 0.502 (3.030)

Frequency Data:: UK10K: 0.5554%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.8430%; gnomAD_G_NFE: 0.4369%; gnomAD_G_OTH: 0.3061%

Other passed variants:

UPSTREAM_GENE_VARIANT chr11:g.118355518CATAT>C [0|1] rs201141134 (variation viewer)

Variant score: 0.352

Transcripts:: UBE4A:ENST00000252108.7::; UBE4A:ENST00000532917.2::

Pathogenicity Data:: Best Score: 0.37309754; CADD: 0.373 (2.028)

Frequency Data:: gnomAD_G_AFR: 0.0912%; gnomAD_G_NFE: 0.3555%; gnomAD_G_OTH: 0.1754%

UPSTREAM_GENE_VARIANT chr11:g.118355524CACATGTATATATACACAT>C [0|1] rs1229561712 (variation viewer)

Variant score: 0.287

Transcripts:: UBE4A:ENST00000252108.7::; UBE4A:ENST00000532917.2::

Pathogenicity Data:: Best Score: 0.31166476; CADD: 0.312 (1.622)

Frequency Data:: gnomAD_G_AFR: 0.1387%; gnomAD_G_NFE: 0.4615%; gnomAD_G_OTH: 0.4651%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.118380134CGTGTGTGTGT>C [0/1] rs55892936 (variation viewer)

Variant score: 0.248

Transcripts:: UBE4A:ENST00000252108.7:c.1876+385_1876+394del:p.(=); UBE4A:ENST00000431736.6:c.1897+385_1897+394del:p.(=); UBE4A:ENST00000545354.1:c.292+385_292+394del:p.(=)

Pathogenicity Data:: Best Score: 0.24768448; CADD: 0.248 (1.236)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr11:g.118355614CATATACATATATGTATATATACACATATGTAT>C [0|1] rs201588951 (variation viewer)

Variant score: 0.211

Transcripts:: UBE4A:ENST00000252108.7::; UBE4A:ENST00000532917.2::

Pathogenicity Data:: Best Score: 0.23263848; CADD: 0.233 (1.150)

Frequency Data:: gnomAD_G_AFR: 0.1147%; gnomAD_G_NFE: 0.4505%; gnomAD_G_OTH: 0.5208%

SLC6A11

Exomiser Score: 0.025

Phenotype Score: 0.510

Variant Score: 0.471

Phenotype matches:

Proximity score 0.510 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.510

Variant Score: 0.029

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.10882327G>A [0/1] rs1471061443 (variation viewer)

Variant score: 0.029 CONTRIBUTING VARIANT

Transcripts:: SLC6A11:ENST00000254488.7:c.891+7232G>A:p.(=)

Pathogenicity Data:: Best Score: 0.029266536; CADD: 0.029 (0.129)

Frequency Data:: TOPMed: 0.0040%; gnomAD_G_AFR: 0.0229%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.025

Phenotype Score: 0.510

Variant Score: 0.471

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.10960240G>C [0/1] rs139302870 (variation viewer)

Variant score: 0.606 CONTRIBUTING VARIANT

Transcripts:: SLC6A11:ENST00000254488.7::; SLC6A11:ENST00000646702.1::

Pathogenicity Data:: Best Score: 0.6937331; CADD: 0.694 (5.139)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.2196%; UK10K: 0.1322%; gnomAD_G_AFR: 0.3328%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.2068%; gnomAD_G_OTH: 0.2041%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.10915216C>G [0/1] rs1012845437 (variation viewer)

Variant score: 0.336 CONTRIBUTING VARIANT

Transcripts:: SLC6A11:ENST00000254488.7:c.995+3023C>G:p.(=)

Pathogenicity Data:: Best Score: 0.3544944; CADD: 0.354 (1.901)

Frequency Data:: TOPMed: 0.0159%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0133%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.10876766CAG>C [0/1] rs71055842 (variation viewer)

Variant score: 0.019

Transcripts:: SLC6A11:ENST00000254488.7:c.891+1672_891+1673del:p.(=)

Pathogenicity Data:: Best Score: 0.019381702; CADD: 0.019 (0.085)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.10948413A>ATCATCCCCTGGAC [0/1]

Variant score: 0.000

Transcripts:: SLC6A11:ENST00000254488.7::; SLC6A11:ENST00000646702.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CHRNB2

Exomiser Score: 0.025

Phenotype Score: 0.523

Variant Score: 0.455

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving CHRNB2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.523 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.523 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:605375 Epilepsy, nocturnal frontal lobe, 3 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.025

Phenotype Score: 0.523

Variant Score: 0.455

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr1:g.154579528G>A [0/1] rs200059610 (variation viewer)

Variant score: 0.455 CONTRIBUTING VARIANT

Transcripts:: CHRNB2:ENST00000368476.4:c.*3596G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4604894; CADD: 0.460 (2.680)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0143%; gnomAD_G_NFE: 0.0133%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.261

Variant Score: 0.286

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr1:g.154579528G>A [0/1] rs200059610 (variation viewer)

Variant score: 0.455 CONTRIBUTING VARIANT

Transcripts:: CHRNB2:ENST00000368476.4:c.*3596G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4604894; CADD: 0.460 (2.680)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.0143%; gnomAD_G_NFE: 0.0133%

UPSTREAM_GENE_VARIANT chr1:g.154563459AAAAC>A [0/1] rs1009937104 (variation viewer)

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: CHRNB2:ENST00000368476.4::

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.3589%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.1067%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr1:g.154580056T>C [0/1] rs72698184 (variation viewer)

Variant score: 0.008

Transcripts:: CHRNB2:ENST00000368476.4::

Pathogenicity Data:: Best Score: 0.015988886; CADD: 0.016 (0.070)

Frequency Data:: 1000Genomes: 1.1380%; TOPMed: 0.9851%; UK10K: 1.5472%; gnomAD_G_AFR: 0.2865%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.4579%; gnomAD_G_NFE: 1.5069%; gnomAD_G_OTH: 0.7128%

AP1S1

Exomiser Score: 0.024

Phenotype Score: 0.252

Variant Score: 0.760

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:609313 MEDNIK syndrome - autosomal recessive; ORPHA:171851 MEDNIK syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.024

Phenotype Score: 0.252

Variant Score: 0.760

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.101160006A>ACATGCCCTGGCACACACACC [0/1] rs1554366328 (variation viewer)

Variant score: 0.760 CONTRIBUTING VARIANT

Transcripts:: AP1S1:ENST00000337619.11:c.430-513_430-512insCATGCCCTGGCACACACACC:p.(=); AP1S1:ENST00000646560.1:c.427-513_427-512insCATGCCCTGGCACACACACC:p.(=)

Pathogenicity Data:: Best Score: 0.7600062; CADD: 0.760 (6.198)

Frequency Data:: No frequency data

Other passed variants:

SEC24B

Exomiser Score: 0.024

Phenotype Score: 0.505

Variant Score: 0.470

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.183

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109530895CA>C [0/1] rs35997146 (variation viewer)

Variant score: 0.183 CONTRIBUTING VARIANT

Transcripts:: SEC24B:ENST00000265175.5:c.3252+432del:p.(=); SEC24B:ENST00000399100.6:c.3147+432del:p.(=); SEC24B:ENST00000504968.6:c.3342+432del:p.(=)

Pathogenicity Data:: Best Score: 0.18322957; CADD: 0.183 (0.879)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.024

Phenotype Score: 0.505

Variant Score: 0.470

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.109550265G>A [0/1] rs139583530 (variation viewer)

Variant score: 0.492 CONTRIBUTING VARIANT

Transcripts:: SEC24B:ENST00000265175.5::

Pathogenicity Data:: Best Score: 0.5610652; CADD: 0.561 (3.576)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.3926%; UK10K: 0.6480%; gnomAD_G_AFR: 0.1035%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.6325%; gnomAD_G_NFE: 0.4607%; gnomAD_G_OTH: 0.1025%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109439223A>G [0/1] rs144635151 (variation viewer)

Variant score: 0.448 CONTRIBUTING VARIANT

Transcripts:: SEC24B:ENST00000265175.5:c.133+5221A>G:p.(=); SEC24B:ENST00000399100.6:c.133+5221A>G:p.(=); SEC24B:ENST00000504968.6:c.133+5221A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5086398; CADD: 0.509 (3.086)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.4006%; UK10K: 0.6215%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.6304%; gnomAD_G_NFE: 0.4598%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109439474ATTTTTTTTTTT>A [1/1] rs70949077 (variation viewer)

Variant score: 0.336

Transcripts:: SEC24B:ENST00000265175.5:c.133+5473_133+5483del:p.(=); SEC24B:ENST00000399100.6:c.133+5473_133+5483del:p.(=); SEC24B:ENST00000504968.6:c.133+5473_133+5483del:p.(=)

Pathogenicity Data:: Best Score: 0.33640975; CADD: 0.336 (1.781)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109515064A>G [0/1] rs547329791 (variation viewer)

Variant score: 0.336

Transcripts:: SEC24B:ENST00000265175.5:c.2013+1208A>G:p.(=); SEC24B:ENST00000399100.6:c.1908+1208A>G:p.(=); SEC24B:ENST00000504968.6:c.2103+1208A>G:p.(=)

Pathogenicity Data:: Best Score: 0.35790396; CADD: 0.358 (1.924)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1919%; UK10K: 0.3703%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.2067%

INTERGENIC_VARIANT chr4:g.109416182G>T [0/1] rs137867867 (variation viewer)

Variant score: 0.294

Transcripts:: SEC24B:ENST00000504968.6::; SEC24B:ENST00000507797.1::

Pathogenicity Data:: Best Score: 0.31451178; CADD: 0.315 (1.640)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1752%; UK10K: 0.3967%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.1933%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109452369A>C [0/1] rs189020346 (variation viewer)

Variant score: 0.155

Transcripts:: SEC24B:ENST00000265175.5:c.134-10532A>C:p.(=); SEC24B:ENST00000399100.6:c.134-10532A>C:p.(=); SEC24B:ENST00000504968.6:c.226+2860A>C:p.(=)

Pathogenicity Data:: Best Score: 0.831267; CADD: 0.831 (7.728)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.8728%; UK10K: 1.8381%; gnomAD_G_AFR: 0.1946%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.9473%; gnomAD_G_NFE: 1.3661%; gnomAD_G_OTH: 1.4286%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109507667C>T [0/1] rs141069324 (variation viewer)

Variant score: 0.057

Transcripts:: SEC24B:ENST00000265175.5:c.1673+1155C>T:p.(=); SEC24B:ENST00000399100.6:c.1568+1155C>T:p.(=); SEC24B:ENST00000504968.6:c.1763+1155C>T:p.(=)

Pathogenicity Data:: Best Score: 0.06480968; CADD: 0.065 (0.291)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3958%; UK10K: 0.6612%; gnomAD_G_AFR: 0.0926%; gnomAD_G_AMR: 0.3606%; gnomAD_G_FIN: 0.6517%; gnomAD_G_NFE: 0.4651%; gnomAD_G_OTH: 0.1055%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109483003C>CAT [0|1] rs1554001151 (variation viewer)

Variant score: 0.047

Transcripts:: SEC24B:ENST00000265175.5:c.1165+1222_1165+1223insAT:p.(=); SEC24B:ENST00000399100.6:c.1061-8324_1061-8323insAT:p.(=); SEC24B:ENST00000504968.6:c.1258+1222_1258+1223insAT:p.(=)

Pathogenicity Data:: Best Score: 0.046545446; CADD: 0.047 (0.207)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109453440GCC>G [1/1] rs867089639 (variation viewer)

Variant score: 0.017

Transcripts:: SEC24B:ENST00000265175.5:c.134-9460_134-9459del:p.(=); SEC24B:ENST00000399100.6:c.134-9460_134-9459del:p.(=); SEC24B:ENST00000504968.6:c.226+3932_226+3933del:p.(=)

Pathogenicity Data:: Best Score: 0.051799893; CADD: 0.052 (0.231)

Frequency Data:: gnomAD_G_AFR: 0.8675%; gnomAD_G_EAS: 1.4388%; gnomAD_G_FIN: 0.3563%; gnomAD_G_NFE: 1.7921%; gnomAD_G_OTH: 1.4286%

EPS15

Exomiser Score: 0.023

Phenotype Score: 0.505

Variant Score: 0.468

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.023

Phenotype Score: 0.505

Variant Score: 0.468

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51385288T>C [0/1] rs548201369 (variation viewer)

Variant score: 0.468 CONTRIBUTING VARIANT

Transcripts:: EPS15:ENST00000371730.6:c.1717+9093A>G:p.(=); EPS15:ENST00000371733.8:c.2119+9093A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4689933; CADD: 0.469 (2.749)

Frequency Data:: TOPMed: 0.0127%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.021

Phenotype Score: 0.505

Variant Score: 0.455

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51385288T>C [0/1] rs548201369 (variation viewer)

Variant score: 0.468 CONTRIBUTING VARIANT

Transcripts:: EPS15:ENST00000371730.6:c.1717+9093A>G:p.(=); EPS15:ENST00000371733.8:c.2119+9093A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4689933; CADD: 0.469 (2.749)

Frequency Data:: TOPMed: 0.0127%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51357426A>T [0/1] rs11805065 (variation viewer)

Variant score: 0.441 CONTRIBUTING VARIANT

Transcripts:: EPS15:ENST00000371730.6:c.2143-580T>A:p.(=); EPS15:ENST00000371733.8:c.2545-580T>A:p.(=)

Pathogenicity Data:: Best Score: 0.44127256; CADD: 0.441 (2.528)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51483398AGTGTGTGTGT>A [-/1] rs58892404 (variation viewer)

Variant score: 0.283

Transcripts:: EPS15:ENST00000371730.6:c.34-2094_34-2085del:p.(=); EPS15:ENST00000371733.8:c.34-2094_34-2085del:p.(=)

Pathogenicity Data:: Best Score: 0.28286654; CADD: 0.283 (1.444)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51384298C>CT [1/1] rs67265512 (variation viewer)

Variant score: 0.126

Transcripts:: EPS15:ENST00000371730.6:c.1717+10082_1717+10083insA:p.(=); EPS15:ENST00000371733.8:c.2119+10082_2119+10083insA:p.(=)

Pathogenicity Data:: Best Score: 0.12622422; CADD: 0.126 (0.586)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51476566C>T [0/1] rs143254280 (variation viewer)

Variant score: 0.082

Transcripts:: EPS15:ENST00000371730.6:c.76-3618G>A:p.(=); EPS15:ENST00000371733.8:c.76-3618G>A:p.(=)

Pathogenicity Data:: Best Score: 0.13443434; CADD: 0.134 (0.627)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.3839%; gnomAD_G_AFR: 1.3541%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51507148T>C [0/1] rs566952809 (variation viewer)

Variant score: 0.008

Transcripts:: EPS15:ENST00000371730.6:c.33+12051A>G:p.(=); EPS15:ENST00000371733.8:c.33+12051A>G:p.(=)

Pathogenicity Data:: Best Score: 0.0077982545; CADD: 0.008 (0.034)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0104%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51357393T>* [-/1]

Variant score: 0.000

Transcripts:: EPS15:ENST00000371730.6:c.2143-547A>:p.(=); EPS15:ENST00000371733.8:c.2545-547A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.51357395T>* [-/1]

Variant score: 0.000

Transcripts:: EPS15:ENST00000371730.6:c.2143-549A>:p.(=); EPS15:ENST00000371733.8:c.2545-549A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SAR1B

Exomiser Score: 0.022

Phenotype Score: 0.505

Variant Score: 0.464

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:246700 Chylomicron retention disease - autosomal recessive; ORPHA:71 Chylomicron retention disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.014

Phenotype Score: 0.252

Variant Score: 0.696

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134612641TAAAAAAAAAAAAAAA>T [0/1] rs34365859 (variation viewer)

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: SAR1B:ENST00000402673.7:c.244+35_244+49del:p.(=); SAR1B:ENST00000439578.5:c.244+35_244+49del:p.(=); SAR1B:ENST00000502539.5:c.40+35_40+49del:p.(=); SAR1B:ENST00000507419.5:c.40+35_40+49del:p.(=); SAR1B:ENST00000509937.5:c.40+35_40+49del:p.(=)

Pathogenicity Data:: Best Score: 0.6959115; CADD: 0.696 (5.170)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.022

Phenotype Score: 0.505

Variant Score: 0.464

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.134612641TAAAAAAAAAAAAAAA>T [0/1] rs34365859 (variation viewer)

Variant score: 0.696 CONTRIBUTING VARIANT

Transcripts:: SAR1B:ENST00000402673.7:c.244+35_244+49del:p.(=); SAR1B:ENST00000439578.5:c.244+35_244+49del:p.(=); SAR1B:ENST00000502539.5:c.40+35_40+49del:p.(=); SAR1B:ENST00000507419.5:c.40+35_40+49del:p.(=); SAR1B:ENST00000509937.5:c.40+35_40+49del:p.(=)

Pathogenicity Data:: Best Score: 0.6959115; CADD: 0.696 (5.170)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr5:g.134605659CA>C [0/1] rs1026047463 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: SAR1B:ENST00000402673.7:c.*1290del:p.(=)

Pathogenicity Data:: Best Score: 0.23193145; CADD: 0.232 (1.146)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.134643794C>T [0/1] rs932083336 (variation viewer)

Variant score: 0.118

Transcripts:: SAR1B:ENST00000507419.5:c.-218+4322G>A:p.(=)

Pathogenicity Data:: Best Score: 0.11773306; CADD: 0.118 (0.544)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr5:g.134598224C>CT [0/1] rs757743094 (variation viewer)

Variant score: 0.106

Transcripts:: SAR1B:ENST00000402673.7::; SAR1B:ENST00000395003.5::

Pathogenicity Data:: Best Score: 0.106488824; CADD: 0.106 (0.489)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr5:g.134626298CA>C [1/1] rs35668627 (variation viewer)

Variant score: 0.095

Transcripts:: SAR1B:ENST00000402673.7:c.-18-2262del:p.(=); SAR1B:ENST00000439578.5:c.-18-2262del:p.(=); SAR1B:ENST00000507419.5:c.-217-5298del:p.(=)

Pathogenicity Data:: Best Score: 0.09468442; CADD: 0.095 (0.432)

Frequency Data:: No frequency data

HSPA8

Exomiser Score: 0.022

Phenotype Score: 0.503

Variant Score: 0.466

Phenotype matches:

Proximity score 0.503 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.022

Phenotype Score: 0.503

Variant Score: 0.466

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr11:g.123062899G>C [0/1] rs987849272 (variation viewer)

Variant score: 0.466 CONTRIBUTING VARIANT

Transcripts:: HSPA8:ENST00000453788.6::; HSPA8:ENST00000448775.4::

Pathogenicity Data:: Best Score: 0.46580476; CADD: 0.466 (2.723)

Frequency Data:: TOPMed: 0.0032%

Other passed variants:

TGFBR2

Exomiser Score: 0.022

Phenotype Score: 0.255

Variant Score: 0.745

Phenotype matches:

Phenotypic similarity 0.471 to Lynch syndrome associated with TGFBR2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.511 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:133239 Esophageal cancer, somatic - somatic; OMIM:610168 Loeys-Dietz syndrome 2 - autosomal dominant; OMIM:614331 Colorectal cancer, hereditary nonpolyposis, type 6 - autosomal dominant; ORPHA:144 Lynch syndrome; ORPHA:60030 Loeys-Dietz syndrome; ORPHA:91387 Familial thoracic aortic aneurysm and aortic dissection; ORPHA:99977 Squamous cell carcinoma of the esophagus

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.511

Variant Score: 0.193

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.30636155ATGTGTGTG>A [-/1] rs61296907 (variation viewer)

Variant score: 0.193 CONTRIBUTING VARIANT

Transcripts:: TGFBR2:ENST00000295754.10:c.95-8591_95-8584del:p.(=); TGFBR2:ENST00000359013.4:c.170-8591_170-8584del:p.(=)

Pathogenicity Data:: Best Score: 0.19257909; CADD: 0.193 (0.929)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.022

Phenotype Score: 0.255

Variant Score: 0.745

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr3:g.30696871C>T [0/1] rs185256180 (variation viewer)

Variant score: 0.861 CONTRIBUTING VARIANT

Transcripts:: TGFBR2:ENST00000359013.4::; TGFBR2:ENST00000282538.9::

Pathogenicity Data:: Best Score: 0.87407845; CADD: 0.874 (8.999)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0717%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0458%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.1066%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.30631214G>A [0/1] rs148152916 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: TGFBR2:ENST00000295754.10:c.95-13533G>A:p.(=); TGFBR2:ENST00000359013.4:c.169+7941G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6419036; CADD: 0.642 (4.460)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1386%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0460%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0290%; gnomAD_G_NFE: 0.1273%; gnomAD_G_OTH: 0.1025%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr3:g.30697471T>C [0/1] rs565872858 (variation viewer)

Variant score: 0.544

Transcripts:: TGFBR2:ENST00000359013.4::; TGFBR2:ENST00000282538.9::

Pathogenicity Data:: Best Score: 0.7188747; CADD: 0.719 (5.511)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.2118%; UK10K: 0.1719%; gnomAD_G_AMR: 0.1196%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.0303%; gnomAD_G_NFE: 0.2931%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.30628528G>GTTT [0/1] rs569832149 (variation viewer)

Variant score: 0.185

Transcripts:: TGFBR2:ENST00000295754.10:c.95-16219_95-16218insTTT:p.(=); TGFBR2:ENST00000359013.4:c.169+5255_169+5256insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.18454498; CADD: 0.185 (0.886)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.30704876C>T [0/1] rs182980663 (variation viewer)

Variant score: 0.121

Transcripts:: TGFBR2:ENST00000359013.4::

Pathogenicity Data:: Best Score: 0.19239312; CADD: 0.192 (0.928)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.2947%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.9450%; gnomAD_G_NFE: 0.3731%; gnomAD_G_OTH: 0.9165%

INTERGENIC_VARIANT chr3:g.30600301C>CT [1/1] rs71093913 (variation viewer)

Variant score: 0.115

Transcripts:: TGFBR2:ENST00000295754.10::

Pathogenicity Data:: Best Score: 0.11468053; CADD: 0.115 (0.529)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.30704205C>A [0/1] rs182914715 (variation viewer)

Variant score: 0.039

Transcripts:: TGFBR2:ENST00000359013.4::

Pathogenicity Data:: Best Score: 0.042365015; CADD: 0.042 (0.188)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.2636%; UK10K: 0.2777%; gnomAD_G_AFR: 0.1074%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.2536%; gnomAD_G_OTH: 0.1025%

INTERGENIC_VARIANT chr3:g.30713520G>A [0/1] rs7631867 (variation viewer)

Variant score: 0.032

Transcripts:: TGFBR2:ENST00000359013.4::

Pathogenicity Data:: Best Score: 0.15374744; CADD: 0.154 (0.725)

Frequency Data:: 1000Genomes: 0.8786%; TOPMed: 0.8179%; UK10K: 0.2645%; gnomAD_G_AFR: 1.9244%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0868%; gnomAD_G_NFE: 0.2531%; gnomAD_G_OTH: 0.3061%

BAIAP2

Exomiser Score: 0.022

Phenotype Score: 0.501

Variant Score: 0.466

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81038898GGT>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: BAIAP2:ENST00000321280.11:c.54+3590_54+3592delGGTins*:p.(=); BAIAP2:ENST00000321300.10:c.54+3590_54+3592delGGTins*:p.(=); BAIAP2:ENST00000428708.6:c.54+3590_54+3592delGGTins*:p.(=); BAIAP2:ENST00000435091.7:c.54+3590_54+3592delGGTins*:p.(=); BAIAP2:ENST00000575245.5:c.153+1937_153+1939delGGTins*:p.(=); BAIAP2:ENST00000575712.5:c.54+3590_54+3592delGGTins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.022

Phenotype Score: 0.501

Variant Score: 0.466

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81074322ATGCACGGATACGTGTGAGTGTGCG>A [0/1] rs759301701 (variation viewer)

Variant score: 0.478 CONTRIBUTING VARIANT

Transcripts:: BAIAP2:ENST00000321280.11:c.218-10509_218-10486del:p.(=); BAIAP2:ENST00000321300.10:c.218-10509_218-10486del:p.(=); BAIAP2:ENST00000428708.6:c.218-10509_218-10486del:p.(=); BAIAP2:ENST00000435091.7:c.218-10509_218-10486del:p.(=); BAIAP2:ENST00000575245.5:c.317-10509_317-10486del:p.(=); BAIAP2:ENST00000575712.5:c.218-10509_218-10486del:p.(=)

Pathogenicity Data:: Best Score: 0.4860747; CADD: 0.486 (2.891)

Frequency Data:: UK10K: 0.1190%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0869%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81037861C>T [0/1] rs149792465 (variation viewer)

Variant score: 0.453 CONTRIBUTING VARIANT

Transcripts:: BAIAP2:ENST00000321280.11:c.54+2553C>T:p.(=); BAIAP2:ENST00000321300.10:c.54+2553C>T:p.(=); BAIAP2:ENST00000428708.6:c.54+2553C>T:p.(=); BAIAP2:ENST00000435091.7:c.54+2553C>T:p.(=); BAIAP2:ENST00000575245.5:c.153+900C>T:p.(=); BAIAP2:ENST00000575712.5:c.54+2553C>T:p.(=)

Pathogenicity Data:: Best Score: 0.49742603; CADD: 0.497 (2.988)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.3799%; UK10K: 0.5025%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.4773%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.3931%; gnomAD_G_OTH: 0.3055%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81061039G>A [0/1] rs778509649 (variation viewer)

Variant score: 0.390

Transcripts:: BAIAP2:ENST00000321280.11:c.217+3072G>A:p.(=); BAIAP2:ENST00000321300.10:c.217+3072G>A:p.(=); BAIAP2:ENST00000428708.6:c.217+3072G>A:p.(=); BAIAP2:ENST00000435091.7:c.217+3072G>A:p.(=); BAIAP2:ENST00000575245.5:c.316+3072G>A:p.(=); BAIAP2:ENST00000575712.5:c.217+3072G>A:p.(=)

Pathogenicity Data:: Best Score: 0.39813375; CADD: 0.398 (2.205)

Frequency Data:: TOPMed: 0.0860%; UK10K: 0.1455%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0600%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81113391G>A [0/1] rs994413671 (variation viewer)

Variant score: 0.068

Transcripts:: BAIAP2:ENST00000321300.10:c.1536-2379G>A:p.(=); BAIAP2:ENST00000428708.6:c.1536-2379G>A:p.(=); BAIAP2:ENST00000417379.6:c.*5011C>T:p.(=); BAIAP2:ENST00000435091.7:c.*19-2379G>A:p.(=); BAIAP2:ENST00000575245.5:c.*15-2379G>A:p.(=)

Pathogenicity Data:: Best Score: 0.06910652; CADD: 0.069 (0.311)

Frequency Data:: TOPMed: 0.0167%; gnomAD_G_AMR: 0.1193%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81055574G>GTTTTTTGTTTTTTTTTGTTTTT [1/1] rs370775327 (variation viewer)

Variant score: 0.033

Transcripts:: BAIAP2:ENST00000321280.11:c.130+1831_130+1832insTTTTTTGTTTTTTTTTGTTTTT:p.(=); BAIAP2:ENST00000321300.10:c.130+1831_130+1832insTTTTTTGTTTTTTTTTGTTTTT:p.(=); BAIAP2:ENST00000428708.6:c.130+1831_130+1832insTTTTTTGTTTTTTTTTGTTTTT:p.(=); BAIAP2:ENST00000435091.7:c.130+1831_130+1832insTTTTTTGTTTTTTTTTGTTTTT:p.(=); BAIAP2:ENST00000575245.5:c.229+1831_229+1832insTTTTTTGTTTTTTTTTGTTTTT:p.(=); BAIAP2:ENST00000575712.5:c.130+1831_130+1832insTTTTTTGTTTTTTTTTGTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.033281565; CADD: 0.033 (0.147)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81080062C>T [0/1] rs117188434 (variation viewer)

Variant score: 0.012

Transcripts:: BAIAP2:ENST00000321280.11:c.218-4770C>T:p.(=); BAIAP2:ENST00000321300.10:c.218-4770C>T:p.(=); BAIAP2:ENST00000428708.6:c.218-4770C>T:p.(=); BAIAP2:ENST00000435091.7:c.218-4770C>T:p.(=); BAIAP2:ENST00000575245.5:c.317-4770C>T:p.(=); BAIAP2:ENST00000575712.5:c.218-4770C>T:p.(=)

Pathogenicity Data:: Best Score: 0.053980708; CADD: 0.054 (0.241)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.6789%; UK10K: 1.7985%; gnomAD_G_AFR: 0.2979%; gnomAD_G_AMR: 1.9093%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.1741%; gnomAD_G_NFE: 1.8477%; gnomAD_G_OTH: 1.1202%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81048900C>T [0/1] rs750399656 (variation viewer)

Variant score: 0.009

Transcripts:: BAIAP2:ENST00000321280.11:c.55-4768C>T:p.(=); BAIAP2:ENST00000321300.10:c.55-4768C>T:p.(=); BAIAP2:ENST00000428708.6:c.55-4768C>T:p.(=); BAIAP2:ENST00000435091.7:c.55-4768C>T:p.(=); BAIAP2:ENST00000575245.5:c.154-4768C>T:p.(=); BAIAP2:ENST00000575712.5:c.55-4768C>T:p.(=)

Pathogenicity Data:: Best Score: 0.00985229; CADD: 0.010 (0.043)

Frequency Data:: TOPMed: 0.0334%; UK10K: 0.0264%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0200%

FAF2

Exomiser Score: 0.021

Phenotype Score: 0.506

Variant Score: 0.458

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.021

Phenotype Score: 0.506

Variant Score: 0.458

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.176526273T>C [0/1] rs906714388 (variation viewer)

Variant score: 0.458 CONTRIBUTING VARIANT

Transcripts:: FAF2:ENST00000261942.7::

Pathogenicity Data:: Best Score: 0.45849812; CADD: 0.458 (2.664)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.506

Variant Score: 0.341

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.176526273T>C [0/1] rs906714388 (variation viewer)

Variant score: 0.458 CONTRIBUTING VARIANT

Transcripts:: FAF2:ENST00000261942.7::

Pathogenicity Data:: Best Score: 0.45849812; CADD: 0.458 (2.664)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.176460513CGTGTGTGT>C [0/1] rs747582699 (variation viewer)

Variant score: 0.224 CONTRIBUTING VARIANT

Transcripts:: FAF2:ENST00000261942.7:c.63+12044_63+12051del:p.(=)

Pathogenicity Data:: Best Score: 0.22375286; CADD: 0.224 (1.100)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr5:g.176433013TC>T [1|1] rs1249089107 (variation viewer)

Variant score: 0.294

Transcripts:: FAF2:ENST00000261942.7::; FAF2:ENST00000310418.8::

Pathogenicity Data:: Best Score: 0.2941702; CADD: 0.294 (1.513)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr5:g.176433019TC>T [1|1] rs1333806893 (variation viewer)

Variant score: 0.269

Transcripts:: FAF2:ENST00000261942.7::; FAF2:ENST00000310418.8::

Pathogenicity Data:: Best Score: 0.26919752; CADD: 0.269 (1.362)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr5:g.176515595A>AGT [-/1] rs35697337 (variation viewer)

Variant score: 0.208

Transcripts:: FAF2:ENST00000261942.7::; FAF2:ENST00000274811.9::

Pathogenicity Data:: Best Score: 0.20841056; CADD: 0.208 (1.015)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr5:g.176429117C>CTT [0/1] rs66665565 (variation viewer)

Variant score: 0.203

Transcripts:: FAF2:ENST00000261942.7::; FAF2:ENST00000310418.8::

Pathogenicity Data:: Best Score: 0.4952225; CADD: 0.495 (2.969)

Frequency Data:: gnomAD_G_AFR: 1.6783%; gnomAD_G_ASJ: 1.2821%; gnomAD_G_EAS: 1.5244%; gnomAD_G_FIN: 1.3699%; gnomAD_G_NFE: 0.8612%; gnomAD_G_OTH: 0.5780%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.176471375CTTT>C [-/1] rs138149987 (variation viewer)

Variant score: 0.154

Transcripts:: FAF2:ENST00000261942.7:c.64-7812_64-7810del:p.(=)

Pathogenicity Data:: Best Score: 0.15355253; CADD: 0.154 (0.724)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr5:g.176513201CT>C [0/1] rs4868642 (variation viewer)

Variant score: 0.135

Transcripts:: FAF2:ENST00000261942.7::; FAF2:ENST00000274811.9::

Pathogenicity Data:: Best Score: 0.161699; CADD: 0.162 (0.766)

Frequency Data:: gnomAD_G_AFR: 0.0360%; gnomAD_G_AMR: 0.6116%; gnomAD_G_ASJ: 0.3676%; gnomAD_G_FIN: 0.5716%; gnomAD_G_NFE: 0.0285%; gnomAD_G_OTH: 0.8009%

INTERGENIC_VARIANT chr5:g.176523483CCCT>C [1/1] rs1260546138 (variation viewer)

Variant score: 0.050

Transcripts:: FAF2:ENST00000261942.7::

Pathogenicity Data:: Best Score: 0.08441222; CADD: 0.084 (0.383)

Frequency Data:: gnomAD_G_AFR: 0.0526%; gnomAD_G_AMR: 0.1389%; gnomAD_G_ASJ: 0.4237%; gnomAD_G_FIN: 1.3981%; gnomAD_G_NFE: 1.1853%; gnomAD_G_OTH: 0.3788%

CHRNA3

Exomiser Score: 0.021

Phenotype Score: 0.523

Variant Score: 0.439

Phenotype matches:

Proximity score 0.523 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.523 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:191800 Bladder dysfunction, autonomic, with impaired pupillary reflex and secondary CAKUT - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.021

Phenotype Score: 0.523

Variant Score: 0.439

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.78612586TA>T [1/1] rs200288582 (variation viewer)

Variant score: 0.439 CONTRIBUTING VARIANT

Transcripts:: CHRNA3:ENST00000326828.6:c.377+4437del:p.(=); CHRNA3:ENST00000348639.7:c.377+4437del:p.(=)

Pathogenicity Data:: Best Score: 0.4677692; CADD: 0.468 (2.739)

Frequency Data:: gnomAD_G_AFR: 0.3695%; gnomAD_G_AMR: 0.1302%; gnomAD_G_FIN: 0.0366%; gnomAD_G_OTH: 0.2740%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.78612618C>A [1/1] rs113450627 (variation viewer)

Variant score: 0.192

Transcripts:: CHRNA3:ENST00000326828.6:c.377+4406G>T:p.(=); CHRNA3:ENST00000348639.7:c.377+4406G>T:p.(=)

Pathogenicity Data:: Best Score: 0.38652056; CADD: 0.387 (2.122)

Frequency Data:: gnomAD_G_AFR: 1.4042%; gnomAD_G_AMR: 0.2933%; gnomAD_G_ASJ: 0.5319%; gnomAD_G_EAS: 0.5172%; gnomAD_G_FIN: 0.8000%; gnomAD_G_NFE: 0.8315%; gnomAD_G_OTH: 1.5517%

NDUFAF1

Exomiser Score: 0.021

Phenotype Score: 0.504

Variant Score: 0.460

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND5 and phenotypic similarity 0.864 to MELAS associated with MT-ND5.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618234 Mitochondrial complex I deficiency, nuclear type 11 - autosomal recessive; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.021

Phenotype Score: 0.504

Variant Score: 0.460

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr15:g.41383444C>T [0/1] rs1278069778 (variation viewer)

Variant score: 0.629 CONTRIBUTING VARIANT

Transcripts:: NDUFAF1:ENST00000260361.9::

Pathogenicity Data:: Best Score: 0.7090623; CADD: 0.709 (5.362)

Frequency Data:: gnomAD_G_AFR: 0.0771%; gnomAD_G_EAS: 0.0994%; gnomAD_G_FIN: 0.6068%; gnomAD_G_NFE: 0.2235%; gnomAD_G_OTH: 0.2660%

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.41391007C>T [0/1] rs189191636 (variation viewer)

Variant score: 0.291 CONTRIBUTING VARIANT

Transcripts:: NDUFAF1:ENST00000260361.9:c.760-2485G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3204835; CADD: 0.320 (1.678)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1760%; gnomAD_G_AFR: 0.1147%; gnomAD_G_FIN: 0.5233%; gnomAD_G_NFE: 0.2601%; gnomAD_G_OTH: 0.4098%

Other passed variants:

CCL8

Exomiser Score: 0.021

Phenotype Score: 0.502

Variant Score: 0.461

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.021

Phenotype Score: 0.502

Variant Score: 0.461

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr17:g.34325010G>A [0/1] rs1182371725 (variation viewer)

Variant score: 0.461 CONTRIBUTING VARIANT

Transcripts:: CCL8:ENST00000394620.2::; CCL8:ENST00000582638.1::

Pathogenicity Data:: Best Score: 0.46123427; CADD: 0.461 (2.686)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

SEPTIN5

Exomiser Score: 0.021

Phenotype Score: 0.507

Variant Score: 0.454

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving SEPTIN5.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.127

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.19699985T>TATATATATATATATATATA [0/1]

Variant score: 0.127 CONTRIBUTING VARIANT

Transcripts:: SEPTIN5:ENST00000455784.7::; SEPTIN5:ENST00000420012.1::

Pathogenicity Data:: Best Score: 0.12702864; CADD: 0.127 (0.590)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.021

Phenotype Score: 0.507

Variant Score: 0.454

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.19708443G>C [0/1] rs567698163 (variation viewer)

Variant score: 0.781 CONTRIBUTING VARIANT

Transcripts:: SEPTIN5:ENST00000455784.7::; SEPTIN5:ENST00000420012.1::

Pathogenicity Data:: Best Score: 0.8244099; CADD: 0.824 (7.555)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1720%; UK10K: 0.3306%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.1801%

INTERGENIC_VARIANT chr22:g.19699985T>TATATATATATATATATATA [0/1]

Variant score: 0.127 CONTRIBUTING VARIANT

Transcripts:: SEPTIN5:ENST00000455784.7::; SEPTIN5:ENST00000420012.1::

Pathogenicity Data:: Best Score: 0.12702864; CADD: 0.127 (0.590)

Frequency Data:: No frequency data

Other passed variants:

NDUFB11

Exomiser Score: 0.021

Phenotype Score: 0.504

Variant Score: 0.456

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300952 Linear skin defects with multiple congenital anomalies 3 - X-linked dominant; OMIM:301021 ?Mitochondrial complex I deficiency, nuclear type 30 (unconfirmed); ORPHA:2556 Microphthalmia with linear skin defects syndrome; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.021

Phenotype Score: 0.504

Variant Score: 0.456

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.47144446ACCC>A [1/1] rs374822796 (variation viewer)

Variant score: 0.456 CONTRIBUTING VARIANT

Transcripts:: NDUFB11:ENST00000276062.8:c.207+24_207+26del:p.(=); NDUFB11:ENST00000377811.3:c.207+24_207+26del:p.(=)

Pathogenicity Data:: Best Score: 0.45612383; CADD: 0.456 (2.645)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.021

Phenotype Score: 0.504

Variant Score: 0.456

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.47144446ACCC>A [1/1] rs374822796 (variation viewer)

Variant score: 0.456 CONTRIBUTING VARIANT

Transcripts:: NDUFB11:ENST00000276062.8:c.207+24_207+26del:p.(=); NDUFB11:ENST00000377811.3:c.207+24_207+26del:p.(=)

Pathogenicity Data:: Best Score: 0.45612383; CADD: 0.456 (2.645)

Frequency Data:: No frequency data

Other passed variants:

MBTPS1

Exomiser Score: 0.020

Phenotype Score: 0.504

Variant Score: 0.455

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618392 ?Spondyloepiphyseal dysplasia, Kondo-Fu type (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.252

Variant Score: 0.620

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.84058678A>T [0/1]

Variant score: 0.620 CONTRIBUTING VARIANT

Transcripts:: MBTPS1:ENST00000343411.8:c.2831+624T>A:p.(=)

Pathogenicity Data:: Best Score: 0.6198982; CADD: 0.620 (4.201)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.020

Phenotype Score: 0.504

Variant Score: 0.455

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.84058678A>T [0/1]

Variant score: 0.620 CONTRIBUTING VARIANT

Transcripts:: MBTPS1:ENST00000343411.8:c.2831+624T>A:p.(=)

Pathogenicity Data:: Best Score: 0.6198982; CADD: 0.620 (4.201)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.84097837C>CGTGTGT [0/1] rs71382894 (variation viewer)

Variant score: 0.289 CONTRIBUTING VARIANT

Transcripts:: MBTPS1:ENST00000343411.8:c.421+1215_421+1216insACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.28911394; CADD: 0.289 (1.482)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.84090999C>CA [0/1] rs868337179 (variation viewer)

Variant score: 0.210

Transcripts:: MBTPS1:ENST00000343411.8:c.964-58_964-57insT:p.(=)

Pathogenicity Data:: Best Score: 0.50637174; CADD: 0.506 (3.066)

Frequency Data:: gnomAD_G_AFR: 0.2239%; gnomAD_G_AMR: 0.3717%; gnomAD_G_ASJ: 0.4032%; gnomAD_G_EAS: 1.6734%; gnomAD_G_FIN: 0.4355%; gnomAD_G_NFE: 0.2552%; gnomAD_G_OTH: 0.9524%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.84080806C>T [0/1]

Variant score: 0.025

Transcripts:: MBTPS1:ENST00000343411.8:c.1448+941G>A:p.(=)

Pathogenicity Data:: Best Score: 0.024785817; CADD: 0.025 (0.109)

Frequency Data:: No frequency data

SLC6A3

Exomiser Score: 0.019

Phenotype Score: 0.504

Variant Score: 0.447

Phenotype matches:

Phenotypic similarity 0.383 to mouse mutant involving SLC6A3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:613135 Parkinsonism-dystonia, infantile, 1 - autosomal recessive; ORPHA:238455 Infantile dystonia-parkinsonism

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.019

Phenotype Score: 0.504

Variant Score: 0.447

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1422535C>A [0/1] rs758727750 (variation viewer)

Variant score: 0.681 CONTRIBUTING VARIANT

Transcripts:: SLC6A3:ENST00000270349.12:c.654-521G>T:p.(=)

Pathogenicity Data:: Best Score: 0.75294137; CADD: 0.753 (6.072)

Frequency Data:: gnomAD_G_AFR: 0.0498%; gnomAD_G_AMR: 0.1289%; gnomAD_G_ASJ: 0.5319%; gnomAD_G_FIN: 0.1848%; gnomAD_G_NFE: 0.1385%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1423668G>A [0/1] rs72763599 (variation viewer)

Variant score: 0.213 CONTRIBUTING VARIANT

Transcripts:: SLC6A3:ENST00000270349.12:c.654-1654C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4999655; CADD: 0.500 (3.010)

Frequency Data:: 1000Genomes: 0.8986%; TOPMed: 0.5607%; UK10K: 0.6876%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.1433%; gnomAD_G_NFE: 0.7338%; gnomAD_G_OTH: 0.6148%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1414424A>AGAAGGCACTGGGTGGGGGGCCGGGAGGGGCAGGGCGGG [1/1]

Variant score: 0.432

Transcripts:: SLC6A3:ENST00000270349.12:c.1156+266_1156+267insCCCGCCCTGCCCCTCCCGGCCCCCCACCCAGTGCCTTC:p.(=)

Pathogenicity Data:: Best Score: 0.43219393; CADD: 0.432 (2.458)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1414368C>T [0/1] rs540532680 (variation viewer)

Variant score: 0.177

Transcripts:: SLC6A3:ENST00000270349.12:c.1156+323G>A:p.(=)

Pathogenicity Data:: Best Score: 0.18454498; CADD: 0.185 (0.886)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0599%; UK10K: 0.1851%; gnomAD_G_AFR: 0.0739%; gnomAD_G_AMR: 0.2525%; gnomAD_G_EAS: 0.0639%; gnomAD_G_FIN: 0.0331%; gnomAD_G_NFE: 0.2723%; gnomAD_G_OTH: 0.1166%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1419323TCATCCATCCATCCATC>T [0/1] rs140944860 (variation viewer)

Variant score: 0.161

Transcripts:: SLC6A3:ENST00000270349.12:c.927+1230_927+1245del:p.(=)

Pathogenicity Data:: Best Score: 0.47724283; CADD: 0.477 (2.817)

Frequency Data:: gnomAD_G_AFR: 0.0911%; gnomAD_G_AMR: 0.2532%; gnomAD_G_ASJ: 1.7730%; gnomAD_G_EAS: 0.0703%; gnomAD_G_FIN: 0.1770%; gnomAD_G_NFE: 0.7684%; gnomAD_G_OTH: 0.6726%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1422351A>ATGCTGGGTGCCCACCGCTGCCCAGTGCTGCCCAAGG [0/1] rs1231305016 (variation viewer)

Variant score: 0.122

Transcripts:: SLC6A3:ENST00000270349.12:c.654-338_654-337insCCTTGGGCAGCACTGGGCAGCGGTGGGCACCCAGCA:p.(=)

Pathogenicity Data:: Best Score: 0.12541908; CADD: 0.125 (0.582)

Frequency Data:: gnomAD_G_AFR: 0.0115%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.1608%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.1415077G>A [0/1] rs28363068 (variation viewer)

Variant score: 0.058

Transcripts:: SLC6A3:ENST00000270349.12:c.1032-262C>T:p.(=)

Pathogenicity Data:: Best Score: 0.06459433; CADD: 0.065 (0.290)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.4842%; UK10K: 0.5554%; gnomAD_G_AFR: 0.4140%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.4211%; gnomAD_G_OTH: 0.3067%

NDUFS2

Exomiser Score: 0.019

Phenotype Score: 0.252

Variant Score: 0.732

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFS2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618228 Mitochondrial complex I deficiency, nuclear type 6 - autosomal recessive; ORPHA:104 Leber hereditary optic neuropathy; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:2609 Isolated complex I deficiency; ORPHA:70474 Leigh syndrome with cardiomyopathy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.019

Phenotype Score: 0.252

Variant Score: 0.732

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr1:g.161214269CTGTGTGTGTG>C [-/1] rs10629771 (variation viewer)

Variant score: 0.732 CONTRIBUTING VARIANT

Transcripts:: NDUFS2:ENST00000367993.7:c.*98_*107del:p.(=); NDUFS2:ENST00000392179.4:c.*350_*359del:p.(=)

Pathogenicity Data:: Best Score: 0.73202145; CADD: 0.732 (5.719)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.080

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.161207976AT>A [1/1] rs965466967 (variation viewer)

Variant score: 0.080 CONTRIBUTING VARIANT

Transcripts:: NDUFS2:ENST00000367993.7:c.394-1216del:p.(=); NDUFS2:ENST00000392179.4:c.394-1216del:p.(=)

Pathogenicity Data:: Best Score: 0.079974234; CADD: 0.080 (0.362)

Frequency Data:: No frequency data

Other passed variants:

NDUFA6

Exomiser Score: 0.019

Phenotype Score: 0.504

Variant Score: 0.445

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND5 and phenotypic similarity 0.864 to MELAS associated with MT-ND5.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618253 Mitochondrial complex I deficiency, nuclear type 33 - autosomal recessive; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.252

Variant Score: 0.506

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr22:g.42085142A>G [0/1] rs375377684 (variation viewer)

Variant score: 0.506 CONTRIBUTING VARIANT

Transcripts:: NDUFA6:ENST00000498737.8::

Pathogenicity Data:: Best Score: 0.5060307; CADD: 0.506 (3.063)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.019

Phenotype Score: 0.504

Variant Score: 0.445

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr22:g.42085142A>G [0/1] rs375377684 (variation viewer)

Variant score: 0.506 CONTRIBUTING VARIANT

Transcripts:: NDUFA6:ENST00000498737.8::

Pathogenicity Data:: Best Score: 0.5060307; CADD: 0.506 (3.063)

Frequency Data:: TOPMed: 0.0016%

INTERGENIC_VARIANT chr22:g.42104977G>A [0/1] rs182885215 (variation viewer)

Variant score: 0.384 CONTRIBUTING VARIANT

Transcripts:: NDUFA6:ENST00000617763.1::

Pathogenicity Data:: Best Score: 0.90045947; CADD: 0.900 (10.020)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1824%; UK10K: 0.0661%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1800%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.42088447C>T [0/1] rs187271622 (variation viewer)

Variant score: 0.110

Transcripts:: NDUFA6:ENST00000498737.8:c.140-1272G>A:p.(=); NDUFA6:ENST00000617763.1:c.218-1272G>A:p.(=)

Pathogenicity Data:: Best Score: 0.25698084; CADD: 0.257 (1.290)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2087%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0231%; gnomAD_G_AMR: 0.2415%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.0293%; gnomAD_G_NFE: 0.2024%; gnomAD_G_OTH: 0.1040%

PSMD7

Exomiser Score: 0.019

Phenotype Score: 0.504

Variant Score: 0.444

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.019

Phenotype Score: 0.504

Variant Score: 0.444

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr16:g.74310755T>A [0/1] rs1356010061 (variation viewer)

Variant score: 0.444 CONTRIBUTING VARIANT

Transcripts:: PSMD7:ENST00000219313.9::; PSMD7:ENST00000493458.2::

Pathogenicity Data:: Best Score: 0.44435167; CADD: 0.444 (2.552)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

CAB39

Exomiser Score: 0.018

Phenotype Score: 0.501

Variant Score: 0.445

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.501

Variant Score: 0.253

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr2:g.230825154C>CAAAAAA [0/1] rs56715904 (variation viewer)

Variant score: 0.253 CONTRIBUTING VARIANT

Transcripts:: CAB39:ENST00000258418.10::; CAB39:ENST00000603556.1::

Pathogenicity Data:: Best Score: 0.2525193; CADD: 0.253 (1.264)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.018

Phenotype Score: 0.501

Variant Score: 0.445

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.230832394C>T [0/1] rs114060951 (variation viewer)

Variant score: 0.547 CONTRIBUTING VARIANT

Transcripts:: CAB39:ENST00000258418.10::

Pathogenicity Data:: Best Score: 0.9451723; CADD: 0.945 (12.610)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.7781%; UK10K: 1.4150%; gnomAD_G_AFR: 0.1946%; gnomAD_G_AMR: 0.3580%; gnomAD_G_EAS: 0.0618%; gnomAD_G_FIN: 0.4296%; gnomAD_G_NFE: 1.0528%; gnomAD_G_OTH: 0.3055%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.230774167C>T [0/1] rs114407550 (variation viewer)

Variant score: 0.344 CONTRIBUTING VARIANT

Transcripts:: CAB39:ENST00000258418.10:c.114+14052C>T:p.(=); CAB39:ENST00000409788.7:c.114+14052C>T:p.(=); CAB39:ENST00000410084.7:c.114+14052C>T:p.(=); CAB39:ENST00000614925.1:c.114+14052C>T:p.(=)

Pathogenicity Data:: Best Score: 0.5366598; CADD: 0.537 (3.341)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.7757%; UK10K: 1.2960%; gnomAD_G_AFR: 0.2063%; gnomAD_G_AMR: 0.3580%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.4868%; gnomAD_G_NFE: 1.0526%; gnomAD_G_OTH: 0.4082%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.230770832A>T [0/1] rs537951690 (variation viewer)

Variant score: 0.276

Transcripts:: CAB39:ENST00000258418.10:c.114+10717A>T:p.(=); CAB39:ENST00000409788.7:c.114+10717A>T:p.(=); CAB39:ENST00000410084.7:c.114+10717A>T:p.(=); CAB39:ENST00000614925.1:c.114+10717A>T:p.(=)

Pathogenicity Data:: Best Score: 0.29042226; CADD: 0.290 (1.490)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1338%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0687%; gnomAD_G_NFE: 0.2534%

INTERGENIC_VARIANT chr2:g.230704505C>CT [1/1] rs71052543 (variation viewer)

Variant score: 0.143

Transcripts:: CAB39:ENST00000258418.10::; CAB39:ENST00000637608.1::

Pathogenicity Data:: Best Score: 0.14335674; CADD: 0.143 (0.672)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.230748831A>ATAT [0/1] rs1553669220 (variation viewer)

Variant score: 0.111

Transcripts:: CAB39:ENST00000258418.10:c.-43-11128_-43-11127insTAT:p.(=); CAB39:ENST00000409788.7:c.-43-11128_-43-11127insTAT:p.(=); CAB39:ENST00000410084.7:c.-43-11128_-43-11127insTAT:p.(=)

Pathogenicity Data:: Best Score: 0.11120826; CADD: 0.111 (0.512)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.230756247A>G [0/1] rs115203785 (variation viewer)

Variant score: 0.110

Transcripts:: CAB39:ENST00000258418.10:c.-43-3712A>G:p.(=); CAB39:ENST00000409788.7:c.-43-3712A>G:p.(=); CAB39:ENST00000410084.7:c.-43-3712A>G:p.(=)

Pathogenicity Data:: Best Score: 0.17110407; CADD: 0.171 (0.815)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.7757%; UK10K: 1.2960%; gnomAD_G_AFR: 0.2062%; gnomAD_G_AMR: 0.3589%; gnomAD_G_EAS: 0.1233%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 1.0526%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.230773314A>ATATGTGTG [0/1] rs371297550 (variation viewer)

Variant score: 0.087

Transcripts:: CAB39:ENST00000258418.10:c.114+13199_114+13200insTATGTGTG:p.(=); CAB39:ENST00000409788.7:c.114+13199_114+13200insTATGTGTG:p.(=); CAB39:ENST00000410084.7:c.114+13199_114+13200insTATGTGTG:p.(=); CAB39:ENST00000614925.1:c.114+13199_114+13200insTATGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.08651799; CADD: 0.087 (0.393)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.230767795A>C [0/1] rs142147463 (variation viewer)

Variant score: 0.024

Transcripts:: CAB39:ENST00000258418.10:c.114+7680A>C:p.(=); CAB39:ENST00000409788.7:c.114+7680A>C:p.(=); CAB39:ENST00000410084.7:c.114+7680A>C:p.(=); CAB39:ENST00000614925.1:c.114+7680A>C:p.(=)

Pathogenicity Data:: Best Score: 0.026580572; CADD: 0.027 (0.117)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.2931%; UK10K: 0.5025%; gnomAD_G_AFR: 0.0804%; gnomAD_G_NFE: 0.4406%; gnomAD_G_OTH: 0.1027%

FERMT2

Exomiser Score: 0.018

Phenotype Score: 0.504

Variant Score: 0.441

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.197

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.52877574C>CTTTTTT [-/1] rs34676786 (variation viewer)

Variant score: 0.197 CONTRIBUTING VARIANT

Transcripts:: FERMT2:ENST00000341590.8:c.963+1007_963+1008insAAAAAA:p.(=); FERMT2:ENST00000343279.8:c.963+1007_963+1008insAAAAAA:p.(=); FERMT2:ENST00000395631.6:c.963+1007_963+1008insAAAAAA:p.(=); FERMT2:ENST00000399304.7:c.963+1007_963+1008insAAAAAA:p.(=); FERMT2:ENST00000553373.5:c.963+1007_963+1008insAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.19721359; CADD: 0.197 (0.954)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.018

Phenotype Score: 0.504

Variant Score: 0.441

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.52896457A>G [0/1] rs532328031 (variation viewer)

Variant score: 0.613 CONTRIBUTING VARIANT

Transcripts:: FERMT2:ENST00000341590.8:c.392-3030T>C:p.(=); FERMT2:ENST00000343279.8:c.392-3030T>C:p.(=); FERMT2:ENST00000395631.6:c.392-3030T>C:p.(=); FERMT2:ENST00000399304.7:c.392-3030T>C:p.(=); FERMT2:ENST00000553373.5:c.392-3030T>C:p.(=)

Pathogenicity Data:: Best Score: 0.62216693; CADD: 0.622 (4.227)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0127%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.52906768T>C [0/1] rs557824057 (variation viewer)

Variant score: 0.270 CONTRIBUTING VARIANT

Transcripts:: FERMT2:ENST00000341590.8:c.391+12355A>G:p.(=); FERMT2:ENST00000343279.8:c.391+12355A>G:p.(=); FERMT2:ENST00000395631.6:c.391+12355A>G:p.(=); FERMT2:ENST00000399304.7:c.391+12355A>G:p.(=); FERMT2:ENST00000553373.5:c.391+12355A>G:p.(=)

Pathogenicity Data:: Best Score: 0.32516128; CADD: 0.325 (1.708)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4531%; UK10K: 0.6083%; gnomAD_G_AFR: 0.1149%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0288%; gnomAD_G_NFE: 0.6463%; gnomAD_G_OTH: 0.8163%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr14:g.52852433CA>C [1|1] rs71125141 (variation viewer)

Variant score: 0.304

Transcripts:: FERMT2:ENST00000395631.6::; FERMT2:ENST00000556998.1::

Pathogenicity Data:: Best Score: 0.3040148; CADD: 0.304 (1.574)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.52861201G>A [0/1] rs72686364 (variation viewer)

Variant score: 0.175

Transcripts:: FERMT2:ENST00000341590.8:c.1603-736C>T:p.(=); FERMT2:ENST00000343279.8:c.1603-167C>T:p.(=); FERMT2:ENST00000395631.6:c.1603-736C>T:p.(=); FERMT2:ENST00000399304.7:c.1603-167C>T:p.(=); FERMT2:ENST00000553373.5:c.1603-167C>T:p.(=)

Pathogenicity Data:: Best Score: 0.98176104; CADD: 0.982 (17.390)

Frequency Data:: 1000Genomes: 0.9385%; TOPMed: 1.1190%; UK10K: 1.8381%; gnomAD_G_AFR: 0.2749%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.4040%; gnomAD_G_NFE: 1.9557%; gnomAD_G_OTH: 1.8367%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.52892166G>GTT [-/1] rs10547747 (variation viewer)

Variant score: 0.131

Transcripts:: FERMT2:ENST00000341590.8:c.526+1126_526+1127insAA:p.(=); FERMT2:ENST00000343279.8:c.526+1126_526+1127insAA:p.(=); FERMT2:ENST00000395631.6:c.526+1126_526+1127insAA:p.(=); FERMT2:ENST00000399304.7:c.526+1126_526+1127insAA:p.(=); FERMT2:ENST00000553373.5:c.526+1126_526+1127insAA:p.(=)

Pathogenicity Data:: Best Score: 0.13103956; CADD: 0.131 (0.610)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr14:g.52854817C>T [0/1] rs72686360 (variation viewer)

Variant score: 0.117

Transcripts:: FERMT2:ENST00000395631.6::; FERMT2:ENST00000556998.1::

Pathogenicity Data:: Best Score: 0.5106721; CADD: 0.511 (3.104)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 1.0430%; UK10K: 1.7588%; gnomAD_G_AFR: 0.2291%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.3769%; gnomAD_G_NFE: 1.9010%; gnomAD_G_OTH: 1.7312%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.52911576G>A [0/1] rs573214978 (variation viewer)

Variant score: 0.096

Transcripts:: FERMT2:ENST00000341590.8:c.391+7547C>T:p.(=); FERMT2:ENST00000343279.8:c.391+7547C>T:p.(=); FERMT2:ENST00000395631.6:c.391+7547C>T:p.(=); FERMT2:ENST00000399304.7:c.391+7547C>T:p.(=); FERMT2:ENST00000553373.5:c.391+7547C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12097746; CADD: 0.121 (0.560)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.4794%; gnomAD_G_AFR: 0.1497%; gnomAD_G_AMR: 0.4808%; gnomAD_G_FIN: 0.0292%; gnomAD_G_NFE: 0.6752%; gnomAD_G_OTH: 0.9202%

UQCR10

Exomiser Score: 0.018

Phenotype Score: 0.505

Variant Score: 0.438

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.018

Phenotype Score: 0.505

Variant Score: 0.438

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.29778794C>A [0/1] rs1234941497 (variation viewer)

Variant score: 0.438 CONTRIBUTING VARIANT

Transcripts:: UQCR10:ENST00000330029.6::

Pathogenicity Data:: Best Score: 0.4388228; CADD: 0.439 (2.509)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.505

Variant Score: 0.356

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.29778794C>A [0/1] rs1234941497 (variation viewer)

Variant score: 0.438 CONTRIBUTING VARIANT

Transcripts:: UQCR10:ENST00000330029.6::

Pathogenicity Data:: Best Score: 0.4388228; CADD: 0.439 (2.509)

Frequency Data:: TOPMed: 0.0024%; gnomAD_G_NFE: 0.0067%

REGULATORY_REGION_VARIANT chr22:g.30273713C>G [0/1] rs188563973 (variation viewer)

Variant score: 0.273 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.35464305; CADD: 0.355 (1.902)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.1895%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_NFE: 0.2666%; gnomAD_G_OTH: 0.2037%

Other passed variants:

INTERGENIC_VARIANT chr22:g.29780043C>CT [1/1] rs131297 (variation viewer)

Variant score: 0.147

Transcripts:: UQCR10:ENST00000330029.6::

Pathogenicity Data:: Best Score: 0.14709628; CADD: 0.147 (0.691)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr22:g.29773120CA>C [1/1] rs131290 (variation viewer)

Variant score: 0.049

Transcripts:: UQCR10:ENST00000330029.6::; UQCR10:ENST00000542393.5::

Pathogenicity Data:: Best Score: 0.049176276; CADD: 0.049 (0.219)

Frequency Data:: No frequency data

USP13

Exomiser Score: 0.018

Phenotype Score: 0.505

Variant Score: 0.438

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.008

Phenotype Score: 0.505

Variant Score: 0.353

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.179657762CAAAA>C [0/1] rs35377039 (variation viewer)

Variant score: 0.353 CONTRIBUTING VARIANT

Transcripts:: USP13:ENST00000263966.8:c.168+4370_168+4373del:p.(=); USP13:ENST00000496897.5:c.-28+4013_-28+4016del:p.(=)

Pathogenicity Data:: Best Score: 0.35255933; CADD: 0.353 (1.888)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.018

Phenotype Score: 0.505

Variant Score: 0.438

Variants contributing to score:

REGULATORY_REGION_VARIANT chr3:g.180332744C>T [0|1] rs186577357 (variation viewer)

Variant score: 0.523 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.8262599; CADD: 0.826 (7.601)

Frequency Data:: 1000Genomes: 0.8387%; TOPMed: 0.8147%; gnomAD_G_AFR: 1.3106%; gnomAD_G_AMR: 0.7229%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.3299%; gnomAD_G_OTH: 0.1027%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.179657762CAAAA>C [0/1] rs35377039 (variation viewer)

Variant score: 0.353 CONTRIBUTING VARIANT

Transcripts:: USP13:ENST00000263966.8:c.168+4370_168+4373del:p.(=); USP13:ENST00000496897.5:c.-28+4013_-28+4016del:p.(=)

Pathogenicity Data:: Best Score: 0.35255933; CADD: 0.353 (1.888)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.179710663T>C [0|1] rs138879908 (variation viewer)

Variant score: 0.352

Transcripts:: USP13:ENST00000263966.8:c.805+1706T>C:p.(=); USP13:ENST00000496897.5:c.610+1706T>C:p.(=)

Pathogenicity Data:: Best Score: 0.38127166; CADD: 0.381 (2.085)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3154%; UK10K: 0.3570%; gnomAD_G_AFR: 0.1489%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.4529%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.179728542C>T [0/1] rs745344576 (variation viewer)

Variant score: 0.252

Transcripts:: USP13:ENST00000263966.8:c.1089-1647C>T:p.(=); USP13:ENST00000496897.5:c.894-1647C>T:p.(=)

Pathogenicity Data:: Best Score: 0.39993262; CADD: 0.400 (2.218)

Frequency Data:: gnomAD_G_AFR: 0.2211%; gnomAD_G_AMR: 0.4938%; gnomAD_G_EAS: 0.0628%; gnomAD_G_FIN: 0.9543%; gnomAD_G_NFE: 1.1374%; gnomAD_G_OTH: 1.3158%

THREE_PRIME_UTR_EXON_VARIANT chr3:g.179787608CT>C [0/1] rs796952465 (variation viewer)

Variant score: 0.218

Transcripts:: USP13:ENST00000263966.8:c.*3478del:p.(=)

Pathogenicity Data:: Best Score: 0.32157785; CADD: 0.322 (1.685)

Frequency Data:: gnomAD_G_AFR: 0.3210%; gnomAD_G_AMR: 0.1656%; gnomAD_G_ASJ: 0.3817%; gnomAD_G_EAS: 0.0622%; gnomAD_G_FIN: 0.7062%; gnomAD_G_NFE: 1.2185%; gnomAD_G_OTH: 0.3695%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.179715860G>A [0/1] rs141278825 (variation viewer)

Variant score: 0.088

Transcripts:: USP13:ENST00000263966.8:c.806-4080G>A:p.(=); USP13:ENST00000496897.5:c.611-4080G>A:p.(=)

Pathogenicity Data:: Best Score: 0.093432784; CADD: 0.093 (0.426)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.0996%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.1066%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.179705293GTTAT>G [0/1] rs762636915 (variation viewer)

Variant score: 0.019

Transcripts:: USP13:ENST00000263966.8:c.478-1640_478-1637del:p.(=); USP13:ENST00000496897.5:c.283-1640_283-1637del:p.(=)

Pathogenicity Data:: Best Score: 0.12642539; CADD: 0.126 (0.587)

Frequency Data:: 1000Genomes: 0.9398%; TOPMed: 1.1750%; UK10K: 1.4811%; gnomAD_G_AFR: 0.3207%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 1.6667%; gnomAD_G_FIN: 1.9816%; gnomAD_G_NFE: 1.6077%; gnomAD_G_OTH: 1.9388%

DRD2

Exomiser Score: 0.018

Phenotype Score: 0.504

Variant Score: 0.439

Phenotype matches:

Phenotypic similarity 0.470 to Myoclonus-dystonia syndrome associated with DRD2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Phenotypic similarity 0.436 to mouse mutant involving DRD2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: ORPHA:36899 Myoclonus-dystonia syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.018

Phenotype Score: 0.504

Variant Score: 0.439

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.113452469T>TGTGTGC [-/1] rs1210531875 (variation viewer)

Variant score: 0.439 CONTRIBUTING VARIANT

Transcripts:: DRD2:ENST00000346454.7:c.-32+22606_-32+22607insGCACAC:p.(=); DRD2:ENST00000362072.8:c.-32+22606_-32+22607insGCACAC:p.(=)

Pathogenicity Data:: Best Score: 0.4390812; CADD: 0.439 (2.511)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.252

Variant Score: 0.346

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.113452469T>TGTGTGC [-/1] rs1210531875 (variation viewer)

Variant score: 0.439 CONTRIBUTING VARIANT

Transcripts:: DRD2:ENST00000346454.7:c.-32+22606_-32+22607insGCACAC:p.(=); DRD2:ENST00000362072.8:c.-32+22606_-32+22607insGCACAC:p.(=)

Pathogenicity Data:: Best Score: 0.4390812; CADD: 0.439 (2.511)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.113452469TGCGCGCGC>T [-/1] rs150781651 (variation viewer)

Variant score: 0.252 CONTRIBUTING VARIANT

Transcripts:: DRD2:ENST00000346454.7:c.-32+22599_-32+22606del:p.(=); DRD2:ENST00000362072.8:c.-32+22599_-32+22606del:p.(=)

Pathogenicity Data:: Best Score: 0.25200278; CADD: 0.252 (1.261)

Frequency Data:: No frequency data

Other passed variants:

IL18

Exomiser Score: 0.018

Phenotype Score: 0.503

Variant Score: 0.440

Phenotype matches:

Phenotypic similarity 0.389 to mouse mutant involving IL18.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001433, polyphagia

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.101

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.112158521G>GTTTTTTTTTT [0/1] rs71060226 (variation viewer)

Variant score: 0.101 CONTRIBUTING VARIANT

Transcripts:: IL18:ENST00000280357.12:c.-8-3461_-8-3460insAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.10050243; CADD: 0.101 (0.460)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.018

Phenotype Score: 0.503

Variant Score: 0.440

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.112147670G>C [0/1] rs548745531 (variation viewer)

Variant score: 0.780 CONTRIBUTING VARIANT

Transcripts:: IL18:ENST00000280357.12:c.360+933C>G:p.(=); IL18:ENST00000524595.5:c.348+933C>G:p.(=); IL18:ENST00000528832.1:c.360+933C>G:p.(=); IL18:ENST00000532699.1:c.315-22749G>C:p.(=)

Pathogenicity Data:: Best Score: 0.8288409; CADD: 0.829 (7.666)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1465%; UK10K: 0.2380%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.3589%; gnomAD_G_NFE: 0.2331%

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.112158521G>GTTTTTTTTTT [0/1] rs71060226 (variation viewer)

Variant score: 0.101 CONTRIBUTING VARIANT

Transcripts:: IL18:ENST00000280357.12:c.-8-3461_-8-3460insAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.10050243; CADD: 0.101 (0.460)

Frequency Data:: No frequency data

Other passed variants:

REGULATORY_REGION_VARIANT chr11:g.112832286A>G [0|1] rs117169797 (variation viewer)

Variant score: 0.030

Transcripts:

Pathogenicity Data:: Best Score: 0.20200533; CADD: 0.202 (0.980)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.9891%; UK10K: 1.5869%; gnomAD_G_AFR: 0.2633%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.8872%; gnomAD_G_NFE: 1.5869%; gnomAD_G_OTH: 1.4257%

DCK

Exomiser Score: 0.018

Phenotype Score: 0.503

Variant Score: 0.439

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.215

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.71050898AC>A [0/1] rs1275550497 (variation viewer)

Variant score: 0.215 CONTRIBUTING VARIANT

Transcripts:: DCK:ENST00000286648.10::

Pathogenicity Data:: Best Score: 0.21548724; CADD: 0.215 (1.054)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.018

Phenotype Score: 0.503

Variant Score: 0.439

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.71042966T>A [0/1] rs74456118 (variation viewer)

Variant score: 0.663 CONTRIBUTING VARIANT

Transcripts:: DCK:ENST00000286648.10::

Pathogenicity Data:: Best Score: 0.8322355; CADD: 0.832 (7.753)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.3393%; UK10K: 0.0397%; gnomAD_G_AFR: 0.9185%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0134%

INTERGENIC_VARIANT chr4:g.71050898AC>A [0/1] rs1275550497 (variation viewer)

Variant score: 0.215 CONTRIBUTING VARIANT

Transcripts:: DCK:ENST00000286648.10::

Pathogenicity Data:: Best Score: 0.21548724; CADD: 0.215 (1.054)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

Other passed variants:

INTERGENIC_VARIANT chr4:g.71042492A>ATTTTTTTT [1/1] rs71211990 (variation viewer)

Variant score: 0.224

Transcripts:: DCK:ENST00000286648.10::

Pathogenicity Data:: Best Score: 0.2235741; CADD: 0.224 (1.099)

Frequency Data:: No frequency data

LYN

Exomiser Score: 0.017

Phenotype Score: 0.508

Variant Score: 0.431

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.017

Phenotype Score: 0.508

Variant Score: 0.431

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55905719T>A [0/1] rs575307652 (variation viewer)

Variant score: 0.431 CONTRIBUTING VARIANT

Transcripts:: LYN:ENST00000519728.6:c.-6+25616T>A:p.(=); LYN:ENST00000520220.6:c.-6+25616T>A:p.(=)

Pathogenicity Data:: Best Score: 0.43180162; CADD: 0.432 (2.455)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0016%; gnomAD_G_NFE: 0.0134%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.508

Variant Score: 0.401

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55905719T>A [0/1] rs575307652 (variation viewer)

Variant score: 0.431 CONTRIBUTING VARIANT

Transcripts:: LYN:ENST00000519728.6:c.-6+25616T>A:p.(=); LYN:ENST00000520220.6:c.-6+25616T>A:p.(=)

Pathogenicity Data:: Best Score: 0.43180162; CADD: 0.432 (2.455)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0016%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.55994891G>T [0/1] rs182695666 (variation viewer)

Variant score: 0.371 CONTRIBUTING VARIANT

Transcripts:: LYN:ENST00000519728.6:c.1051-3455G>T:p.(=); LYN:ENST00000520220.6:c.988-3455G>T:p.(=)

Pathogenicity Data:: Best Score: 0.39032274; CADD: 0.390 (2.149)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1250%; UK10K: 0.2116%; gnomAD_G_AFR: 0.0574%; gnomAD_G_FIN: 0.1433%; gnomAD_G_NFE: 0.2467%; gnomAD_G_OTH: 0.3055%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55894547T>G [0|1] rs187290593 (variation viewer)

Variant score: 0.333

Transcripts:: LYN:ENST00000519728.6:c.-6+14444T>G:p.(=); LYN:ENST00000520220.6:c.-6+14444T>G:p.(=)

Pathogenicity Data:: Best Score: 0.9540802; CADD: 0.954 (13.380)

Frequency Data:: 1000Genomes: 1.2780%; TOPMed: 0.9262%; gnomAD_G_AFR: 0.1842%; gnomAD_G_AMR: 0.5981%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 1.6841%; gnomAD_G_NFE: 1.2940%; gnomAD_G_OTH: 1.7598%

UPSTREAM_GENE_VARIANT chr8:g.55876035CT>C [0/1] rs902958271 (variation viewer)

Variant score: 0.171

Transcripts:: LYN:ENST00000520220.6::; LYN:ENST00000260129.6::

Pathogenicity Data:: Best Score: 0.17148572; CADD: 0.171 (0.817)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.56008223C>T [0/1] rs186681547 (variation viewer)

Variant score: 0.147

Transcripts:: LYN:ENST00000519728.6:c.1337-1685C>T:p.(=); LYN:ENST00000520220.6:c.1274-1685C>T:p.(=)

Pathogenicity Data:: Best Score: 0.180781; CADD: 0.181 (0.866)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.4595%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1376%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.3460%; gnomAD_G_NFE: 0.7066%; gnomAD_G_OTH: 0.6148%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.55944861G>A [0/1] rs542856186 (variation viewer)

Variant score: 0.144

Transcripts:: LYN:ENST00000519728.6:c.133-1587G>A:p.(=); LYN:ENST00000520220.6:c.70-1587G>A:p.(=)

Pathogenicity Data:: Best Score: 0.14453942; CADD: 0.145 (0.678)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0040%; gnomAD_G_AFR: 0.0458%; gnomAD_G_NFE: 0.0133%

DOWNSTREAM_GENE_VARIANT chr8:g.56017913T>C [0/1] rs191090841 (variation viewer)

Variant score: 0.129

Transcripts:: LYN:ENST00000519728.6::; LYN:ENST00000435260.1::

Pathogenicity Data:: Best Score: 0.15899223; CADD: 0.159 (0.752)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.4571%; UK10K: 0.8728%; gnomAD_G_AFR: 0.1377%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 0.3152%; gnomAD_G_NFE: 0.7086%; gnomAD_G_OTH: 0.6135%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.55987744C>A [0/1] rs185589916 (variation viewer)

Variant score: 0.118

Transcripts:: LYN:ENST00000519728.6:c.1051-10602C>A:p.(=); LYN:ENST00000520220.6:c.988-10602C>A:p.(=)

Pathogenicity Data:: Best Score: 0.7918866; CADD: 0.792 (6.817)

Frequency Data:: 1000Genomes: 1.3780%; TOPMed: 0.9947%; UK10K: 0.9786%; gnomAD_G_AFR: 0.2293%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.6037%; gnomAD_G_NFE: 1.3737%; gnomAD_G_OTH: 1.4257%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55911286T>TA [1/1] rs1491536693 (variation viewer)

Variant score: 0.109

Transcripts:: LYN:ENST00000519728.6:c.-5-30569_-5-30568insA:p.(=); LYN:ENST00000520220.6:c.-5-30569_-5-30568insA:p.(=)

Pathogenicity Data:: Best Score: 0.10874909; CADD: 0.109 (0.500)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr8:g.55861404C>CT [0|1] rs1016981965 (variation viewer)

Variant score: 0.091

Transcripts:: LYN:ENST00000520220.6::

Pathogenicity Data:: Best Score: 0.2328152; CADD: 0.233 (1.151)

Frequency Data:: gnomAD_G_AFR: 0.1949%; gnomAD_G_AMR: 0.7042%; gnomAD_G_FIN: 1.7045%; gnomAD_G_NFE: 0.2592%; gnomAD_G_OTH: 0.5128%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55887575T>TATAC [0/1] rs1554573193 (variation viewer)

Variant score: 0.090

Transcripts:: LYN:ENST00000519728.6:c.-6+7472_-6+7473insATAC:p.(=); LYN:ENST00000520220.6:c.-6+7472_-6+7473insATAC:p.(=)

Pathogenicity Data:: Best Score: 0.08987719; CADD: 0.090 (0.409)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.55978408G>A [0/1] rs144150282 (variation viewer)

Variant score: 0.043

Transcripts:: LYN:ENST00000519728.6:c.1050+8615G>A:p.(=); LYN:ENST00000520220.6:c.987+8615G>A:p.(=)

Pathogenicity Data:: Best Score: 0.069749296; CADD: 0.070 (0.314)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.4723%; UK10K: 0.9257%; gnomAD_G_AFR: 0.1375%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 0.1850%; gnomAD_G_FIN: 1.3452%; gnomAD_G_NFE: 0.8462%; gnomAD_G_OTH: 1.2270%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.55965033AT>A [0/1] rs11450642 (variation viewer)

Variant score: 0.025

Transcripts:: LYN:ENST00000519728.6:c.791-1681del:p.(=); LYN:ENST00000520220.6:c.728-1681del:p.(=)

Pathogenicity Data:: Best Score: 0.09967357; CADD: 0.100 (0.456)

Frequency Data:: gnomAD_G_AFR: 0.2352%; gnomAD_G_AMR: 0.8130%; gnomAD_G_ASJ: 1.7007%; gnomAD_G_EAS: 0.0627%; gnomAD_G_FIN: 1.8812%; gnomAD_G_NFE: 1.5033%; gnomAD_G_OTH: 1.5730%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55909012C>* [-/1]

Variant score: 0.000

Transcripts:: LYN:ENST00000519728.6:c.-6+28909C>*:p.(=); LYN:ENST00000520220.6:c.-6+28909C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55909014C>* [-/1]

Variant score: 0.000

Transcripts:: LYN:ENST00000519728.6:c.-6+28911C>*:p.(=); LYN:ENST00000520220.6:c.-6+28911C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.55911130C>CATACATATATATACGTGTATATATATGTACATATATATACACGTATATATATACATATATATACGTGTATATATATGTACATATATACACGTATATAT [-/1] rs576220810 (variation viewer)

Variant score: 0.000

Transcripts:: LYN:ENST00000519728.6:c.-5-30725_-5-30724insATACATATATATACGTGTATATATATGTACATATATATACACGTATATATATACATATATATACGTGTATATATATGTACATATATACACGTATATAT:p.(=); LYN:ENST00000520220.6:c.-5-30725_-5-30724insATACATATATATACGTGTATATATATGTACATATATATACACGTATATATATACATATATATACGTGTATATATATGTACATATATACACGTATATAT:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: gnomAD_G_NFE: 0.1621%

USH1G

Exomiser Score: 0.017

Phenotype Score: 0.513

Variant Score: 0.423

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 1 associated with USH1G.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:606943 Usher syndrome, type 1G - autosomal recessive; ORPHA:231169 Usher syndrome type 1

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.017

Phenotype Score: 0.513

Variant Score: 0.423

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr17:g.74916996A>AAC [1/1] rs35846955 (variation viewer)

Variant score: 0.423 CONTRIBUTING VARIANT

Transcripts:: USH1G:ENST00000614341.5:c.*1075_*1076dup:p.(=)

Pathogenicity Data:: Best Score: 0.42336637; CADD: 0.423 (2.391)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr17:g.74910239A>T [0/1] rs181384969 (variation viewer)

Variant score: 0.598

Transcripts:: USH1G:ENST00000614341.5::

Pathogenicity Data:: Best Score: 0.64173865; CADD: 0.642 (4.458)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1298%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.1401%; gnomAD_G_OTH: 0.4082%

INTERGENIC_VARIANT chr17:g.74905782CT>C [1/1] rs781970262 (variation viewer)

Variant score: 0.158

Transcripts:: USH1G:ENST00000614341.5::

Pathogenicity Data:: Best Score: 0.15821731; CADD: 0.158 (0.748)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr17:g.74907544G>T [1/1] rs192322733 (variation viewer)

Variant score: 0.131

Transcripts:: USH1G:ENST00000614341.5::

Pathogenicity Data:: Best Score: 0.1785143; CADD: 0.179 (0.854)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.5694%; UK10K: 0.9786%; gnomAD_G_AFR: 0.1718%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1433%; gnomAD_G_NFE: 1.0942%; gnomAD_G_OTH: 0.9165%

FIVE_PRIME_UTR_EXON_VARIANT chr17:g.74923246C>G [0/1] rs570755897 (variation viewer)

ClinVar: UNCERTAIN_SIGNIFICANCE (criteria_provided,_single_submitter)

Variant score: 0.060

Transcripts:: USH1G:ENST00000614341.5:c.-173G>C:p.(=); USH1G:ENST00000580223.2:c.-231+212C>G:p.(=)

Pathogenicity Data:: Best Score: 0.07487589; CADD: 0.075 (0.338)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.3902%; gnomAD_G_AFR: 0.1436%; gnomAD_G_AMR: 0.2421%; gnomAD_G_ASJ: 0.3401%; gnomAD_G_FIN: 0.1458%; gnomAD_G_NFE: 0.8881%; gnomAD_G_OTH: 0.4320%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.74921845C>T [1/1] rs186578638 (variation viewer)

Variant score: 0.002

Transcripts:: USH1G:ENST00000614341.5:c.164+1065G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0032184124; CADD: 0.003 (0.014)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.5710%; UK10K: 0.9521%; gnomAD_G_AFR: 0.1723%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1433%; gnomAD_G_NFE: 1.0965%; gnomAD_G_OTH: 0.9202%

ZNF346

Exomiser Score: 0.017

Phenotype Score: 0.503

Variant Score: 0.433

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO1 and phenotypic similarity 0.864 to MELAS associated with MT-CO1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.017

Phenotype Score: 0.503

Variant Score: 0.433

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr5:g.177084630G>GACAC [0/1] rs59899507 (variation viewer)

Variant score: 0.433 CONTRIBUTING VARIANT

Transcripts:: ZNF346:ENST00000503039.1::

Pathogenicity Data:: Best Score: 0.43389106; CADD: 0.434 (2.471)

Frequency Data:: gnomAD_G_NFE: 0.0140%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.503

Variant Score: 0.293

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr5:g.177084630G>GACAC [0/1] rs59899507 (variation viewer)

Variant score: 0.433 CONTRIBUTING VARIANT

Transcripts:: ZNF346:ENST00000503039.1::

Pathogenicity Data:: Best Score: 0.43389106; CADD: 0.434 (2.471)

Frequency Data:: gnomAD_G_NFE: 0.0140%

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.177053922GC>G [0/1] rs551521342 (variation viewer)

Variant score: 0.154 CONTRIBUTING VARIANT

Transcripts:: ZNF346:ENST00000358149.8:c.703+2987del:p.(=); ZNF346:ENST00000503039.1:c.778+2987del:p.(=); ZNF346:ENST00000503425.5:c.607+2987del:p.(=); ZNF346:ENST00000506693.5:c.409+2987del:p.(=); ZNF346:ENST00000511834.5:c.751+2987del:p.(=); ZNF346:ENST00000512315.5:c.176-8135del:p.(=)

Pathogenicity Data:: Best Score: 0.15666527; CADD: 0.157 (0.740)

Frequency Data:: TOPMed: 0.0932%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0458%; gnomAD_G_NFE: 0.1333%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.177028496T>TTATATA [1/1] rs150044807 (variation viewer)

Variant score: 0.207

Transcripts:: ZNF346:ENST00000358149.8:c.175+5583_175+5584insTATATA:p.(=); ZNF346:ENST00000503039.1:c.250+5262_250+5263insTATATA:p.(=); ZNF346:ENST00000503425.5:c.175+5583_175+5584insTATATA:p.(=); ZNF346:ENST00000506693.5:c.175+5583_175+5584insTATATA:p.(=); ZNF346:ENST00000511834.5:c.175+5583_175+5584insTATATA:p.(=); ZNF346:ENST00000512315.5:c.175+5583_175+5584insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.2067684; CADD: 0.207 (1.006)

Frequency Data:: No frequency data

MARK2

Exomiser Score: 0.016

Phenotype Score: 0.694

Variant Score: 0.215

Phenotype matches:

Proximity score 0.694 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.016

Phenotype Score: 0.694

Variant Score: 0.215

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.63901473C>CTTTT [1/1] rs35231498 (variation viewer)

Variant score: 0.215 CONTRIBUTING VARIANT

Transcripts:: MARK2:ENST00000350490.11:c.1101+404_1101+405insTTTT:p.(=); MARK2:ENST00000361128.9:c.1101+404_1101+405insTTTT:p.(=); MARK2:ENST00000377810.7:c.1002+404_1002+405insTTTT:p.(=); MARK2:ENST00000402010.6:c.1101+404_1101+405insTTTT:p.(=); MARK2:ENST00000408948.7:c.1002+404_1002+405insTTTT:p.(=); MARK2:ENST00000425897.2:c.1002+404_1002+405insTTTT:p.(=); MARK2:ENST00000502399.7:c.1101+404_1101+405insTTTT:p.(=); MARK2:ENST00000508192.5:c.1101+404_1101+405insTTTT:p.(=); MARK2:ENST00000509502.6:c.1002+404_1002+405insTTTT:p.(=); MARK2:ENST00000513765.6:c.1002+404_1002+405insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.21530658; CADD: 0.215 (1.053)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.63856768GTTTTTTTTTTTTTTTTT>G [1/1] rs71039681 (variation viewer)

Variant score: 0.173

Transcripts:: MARK2:ENST00000350490.11:c.54+17209_54+17225del:p.(=); MARK2:ENST00000361128.9:c.54+17209_54+17225del:p.(=); MARK2:ENST00000402010.6:c.54+17209_54+17225del:p.(=); MARK2:ENST00000502399.7:c.54+17209_54+17225del:p.(=); MARK2:ENST00000508192.5:c.54+17209_54+17225del:p.(=); MARK2:ENST00000377810.7:c.-46+17209_-46+17225del:p.(=)

Pathogenicity Data:: Best Score: 0.17339122; CADD: 0.173 (0.827)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.63850315A>AT [1/1] rs34074167 (variation viewer)

Variant score: 0.053

Transcripts:: MARK2:ENST00000350490.11:c.54+10755_54+10756insT:p.(=); MARK2:ENST00000361128.9:c.54+10755_54+10756insT:p.(=); MARK2:ENST00000402010.6:c.54+10755_54+10756insT:p.(=); MARK2:ENST00000502399.7:c.54+10755_54+10756insT:p.(=); MARK2:ENST00000508192.5:c.54+10755_54+10756insT:p.(=); MARK2:ENST00000377810.7:c.-46+10755_-46+10756insT:p.(=)

Pathogenicity Data:: Best Score: 0.053326964; CADD: 0.053 (0.238)

Frequency Data:: No frequency data

GOT2

Exomiser Score: 0.016

Phenotype Score: 0.520

Variant Score: 0.411

Phenotype matches:

Proximity score 0.520 in interactome to SLC25A13 and phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

Known diseases:: OMIM:618721 Epileptic encephalopathy, early infantile, 82 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.260

Variant Score: 0.618

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr16:g.58704986T>C [0/1] rs749546066 (variation viewer)

Variant score: 0.618 CONTRIBUTING VARIANT

Transcripts:: GOT2:ENST00000245206.10::; GOT2:ENST00000564010.5::

Pathogenicity Data:: Best Score: 0.6194603; CADD: 0.619 (4.196)

Frequency Data:: TOPMed: 0.0024%; UK10K: 0.0132%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.016

Phenotype Score: 0.520

Variant Score: 0.411

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr16:g.58704986T>C [0/1] rs749546066 (variation viewer)

Variant score: 0.618 CONTRIBUTING VARIANT

Transcripts:: GOT2:ENST00000245206.10::; GOT2:ENST00000564010.5::

Pathogenicity Data:: Best Score: 0.6194603; CADD: 0.619 (4.196)

Frequency Data:: TOPMed: 0.0024%; UK10K: 0.0132%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.58722026C>T [0/1] rs182760926 (variation viewer)

Variant score: 0.204 CONTRIBUTING VARIANT

Transcripts:: GOT2:ENST00000245206.10:c.375+124G>A:p.(=); GOT2:ENST00000434819.2:c.246+1720G>A:p.(=)

Pathogenicity Data:: Best Score: 0.20585465; CADD: 0.206 (1.001)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0342%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0534%

Other passed variants:

SMPD4

Exomiser Score: 0.016

Phenotype Score: 0.253

Variant Score: 0.714

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618622 Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.016

Phenotype Score: 0.253

Variant Score: 0.714

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.130164331C>T [0/1] rs376121398 (variation viewer)

Variant score: 0.714 CONTRIBUTING VARIANT

Transcripts:: SMPD4:ENST00000351288.10:c.981+43G>A:p.(=); SMPD4:ENST00000409031.5:c.981+43G>A:p.(=); SMPD4:ENST00000431183.6:c.762+43G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7202952; CADD: 0.720 (5.533)

Frequency Data:: TOPMed: 0.0104%; ESP EA: 0.0233%; ESP All: 0.0154%; ExAC NFE: 0.0135%; gnomAD_E_ASJ: 0.0610%; gnomAD_E_FIN: 0.0090%; gnomAD_E_NFE: 0.0143%; gnomAD_E_OTH: 0.0183%; gnomAD_G_AFR: 0.0115%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.009

Phenotype Score: 0.505

Variant Score: 0.361

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.130164331C>T [0/1] rs376121398 (variation viewer)

Variant score: 0.714 CONTRIBUTING VARIANT

Transcripts:: SMPD4:ENST00000351288.10:c.981+43G>A:p.(=); SMPD4:ENST00000409031.5:c.981+43G>A:p.(=); SMPD4:ENST00000431183.6:c.762+43G>A:p.(=)

Pathogenicity Data:: Best Score: 0.7202952; CADD: 0.720 (5.533)

Frequency Data:: TOPMed: 0.0104%; ESP EA: 0.0233%; ESP All: 0.0154%; ExAC NFE: 0.0135%; gnomAD_E_ASJ: 0.0610%; gnomAD_E_FIN: 0.0090%; gnomAD_E_NFE: 0.0143%; gnomAD_E_OTH: 0.0183%; gnomAD_G_AFR: 0.0115%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.130164234T>C [0/1] rs142276527 (variation viewer)

Variant score: 0.007 CONTRIBUTING VARIANT

Transcripts:: SMPD4:ENST00000351288.10:c.981+140A>G:p.(=); SMPD4:ENST00000409031.5:c.981+140A>G:p.(=); SMPD4:ENST00000431183.6:c.762+140A>G:p.(=)

Pathogenicity Data:: Best Score: 0.044787467; CADD: 0.045 (0.199)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 1.0610%; UK10K: 1.9704%; gnomAD_G_AFR: 0.2984%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 1.2593%; gnomAD_G_NFE: 1.6673%; gnomAD_G_OTH: 1.0183%

Other passed variants:

IDH2

Exomiser Score: 0.016

Phenotype Score: 0.503

Variant Score: 0.428

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:613657 D-2-hydroxyglutaric aciduria 2 - autosomal dominant; ORPHA:163634 Maffucci syndrome; ORPHA:296 Ollier disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.016

Phenotype Score: 0.503

Variant Score: 0.428

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.90088906A>AT [0/1] rs57901991 (variation viewer)

Variant score: 0.428 CONTRIBUTING VARIANT

Transcripts:: IDH2:ENST00000330062.7:c.374-160_374-159insA:p.(=); IDH2:ENST00000540499.2:c.218-160_218-159insA:p.(=); IDH2:ENST00000559482.5:c.208-405_208-404insA:p.(=)

Pathogenicity Data:: Best Score: 0.42812645; CADD: 0.428 (2.427)

Frequency Data:: No frequency data

Other passed variants:

NDUFS7

Exomiser Score: 0.016

Phenotype Score: 0.504

Variant Score: 0.426

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFS7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618224 Mitochondrial complex I deficiency, nuclear type 3 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.005

Phenotype Score: 0.252

Variant Score: 0.578

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.1384341G>A [0/1]

Variant score: 0.578 CONTRIBUTING VARIANT

Transcripts:: NDUFS7:ENST00000233627.14:c.16+399G>A:p.(=); NDUFS7:ENST00000313408.11:c.16+399G>A:p.(=); NDUFS7:ENST00000414651.3:c.16+399G>A:p.(=); NDUFS7:ENST00000539480.5:c.16+399G>A:p.(=); NDUFS7:ENST00000546283.5:c.16+399G>A:p.(=); NDUFS7:ENST00000618074.4:c.16+399G>A:p.(=); NDUFS7:ENST00000620479.4:c.16+399G>A:p.(=)

Pathogenicity Data:: Best Score: 0.57791495; CADD: 0.578 (3.746)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.016

Phenotype Score: 0.504

Variant Score: 0.426

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.1384341G>A [0/1]

Variant score: 0.578 CONTRIBUTING VARIANT

Transcripts:: NDUFS7:ENST00000233627.14:c.16+399G>A:p.(=); NDUFS7:ENST00000313408.11:c.16+399G>A:p.(=); NDUFS7:ENST00000414651.3:c.16+399G>A:p.(=); NDUFS7:ENST00000539480.5:c.16+399G>A:p.(=); NDUFS7:ENST00000546283.5:c.16+399G>A:p.(=); NDUFS7:ENST00000618074.4:c.16+399G>A:p.(=); NDUFS7:ENST00000620479.4:c.16+399G>A:p.(=)

Pathogenicity Data:: Best Score: 0.57791495; CADD: 0.578 (3.746)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.1394518CCCTCCCTCCCTGCGGACCGCGCTCCTCCCTCCCTGGGGACCGCGCT>C [0/1] rs1568998244 (variation viewer)

Variant score: 0.273 CONTRIBUTING VARIANT

Transcripts:: NDUFS7:ENST00000233627.14:c.545-872_545-827del:p.(=); NDUFS7:ENST00000618074.4:c.552-872_552-827del:p.(=); NDUFS7:ENST00000620479.4:c.549-872_549-827del:p.(=); NDUFS7:ENST00000313408.11:c.*1136_*1181del:p.(=); NDUFS7:ENST00000539480.5:c.*121_*166del:p.(=)

Pathogenicity Data:: Best Score: 0.28944123; CADD: 0.289 (1.484)

Frequency Data:: gnomAD_G_ASJ: 0.3448%; gnomAD_G_EAS: 0.2778%; gnomAD_G_NFE: 0.0144%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.1387917GGGT>G [0|1] rs1445554650 (variation viewer)

Variant score: 0.197

Transcripts:: NDUFS7:ENST00000233627.14:c.53+71_53+73del:p.(=); NDUFS7:ENST00000313408.11:c.53+71_53+73del:p.(=); NDUFS7:ENST00000414651.3:c.53+71_53+73del:p.(=); NDUFS7:ENST00000539480.5:c.53+71_53+73del:p.(=); NDUFS7:ENST00000546283.5:c.53+71_53+73del:p.(=); NDUFS7:ENST00000618074.4:c.53+71_53+73del:p.(=); NDUFS7:ENST00000620479.4:c.53+71_53+73del:p.(=)

Pathogenicity Data:: Best Score: 0.19739842; CADD: 0.197 (0.955)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr19:g.1396227G>A [0/1] rs146724913 (variation viewer)

Variant score: 0.192

Transcripts:: NDUFS7:ENST00000539480.5::; NDUFS7:ENST00000252288.8::

Pathogenicity Data:: Best Score: 0.20950341; CADD: 0.210 (1.021)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.3608%; UK10K: 0.3438%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.4270%; gnomAD_G_OTH: 0.4073%

UPSTREAM_GENE_VARIANT chr19:g.1380965G>GCAAGGCATGGGAAGGAGGCCGCGGTTCTACTCCACATGGGTCAAGCCGCCTGCGTGCCCGCCCTCTGTAATGGCCAGCTTGCCTCTGAGT [0/1]

Variant score: 0.000

Transcripts:: NDUFS7:ENST00000546283.5::; NDUFS7:ENST00000652273.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CASP3

Exomiser Score: 0.015

Phenotype Score: 0.502

Variant Score: 0.426

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.015

Phenotype Score: 0.502

Variant Score: 0.426

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.184631542T>TCAA [1/1] rs59338037 (variation viewer)

Variant score: 0.426 CONTRIBUTING VARIANT

Transcripts:: CASP3:ENST00000308394.9:c.483+222_483+223insTTG:p.(=); CASP3:ENST00000393585.6:c.483+222_483+223insTTG:p.(=); CASP3:ENST00000393588.8:c.483+222_483+223insTTG:p.(=); CASP3:ENST00000517513.5:c.483+222_483+223insTTG:p.(=); CASP3:ENST00000523916.5:c.483+222_483+223insTTG:p.(=)

Pathogenicity Data:: Best Score: 0.42588353; CADD: 0.426 (2.410)

Frequency Data:: No frequency data

Other passed variants:

AHCY

Exomiser Score: 0.015

Phenotype Score: 0.504

Variant Score: 0.423

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:613752 Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase - autosomal recessive; ORPHA:88618 S-adenosylhomocysteine hydrolase deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.015

Phenotype Score: 0.504

Variant Score: 0.423

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.34297801T>G [0/1] rs141107024 (variation viewer)

Variant score: 0.510 CONTRIBUTING VARIANT

Transcripts:: AHCY:ENST00000217426.7:c.29-2216A>C:p.(=); AHCY:ENST00000538132.1:c.-56-2216A>C:p.(=)

Pathogenicity Data:: Best Score: 0.81344795; CADD: 0.813 (7.292)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1569%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.2800%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.34299107CTT>C [0/1] rs771409357 (variation viewer)

Variant score: 0.336 CONTRIBUTING VARIANT

Transcripts:: AHCY:ENST00000217426.7:c.29-3524_29-3523del:p.(=); AHCY:ENST00000538132.1:c.-56-3524_-56-3523del:p.(=)

Pathogenicity Data:: Best Score: 0.5362328; CADD: 0.536 (3.337)

Frequency Data:: TOPMed: 0.1585%; gnomAD_G_AFR: 0.1032%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.2469%; gnomAD_G_OTH: 0.3061%

Other passed variants:

KLC2

Exomiser Score: 0.015

Phenotype Score: 0.253

Variant Score: 0.707

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:609541 Spastic paraplegia, optic atrophy, and neuropathy - autosomal recessive; ORPHA:320406 Spastic paraplegia-optic atrophy-neuropathy syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.015

Phenotype Score: 0.253

Variant Score: 0.707

Variants contributing to score:

FIVE_PRIME_UTR_EXON_VARIANT chr11:g.66257390CAGTT>C [0/1]

Variant score: 0.707 CONTRIBUTING VARIANT

Transcripts:: KLC2:ENST00000417856.5:c.-143_-140del:p.(=)

Pathogenicity Data:: Best Score: 0.7065055; CADD: 0.707 (5.324)

Frequency Data:: No frequency data

Other passed variants:

CRK

Exomiser Score: 0.015

Phenotype Score: 0.507

Variant Score: 0.419

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.507

Variant Score: 0.329

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr17:g.1417938C>T [0/1]

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: CRK:ENST00000398970.5::; CRK:ENST00000264335.13::

Pathogenicity Data:: Best Score: 0.3287257; CADD: 0.329 (1.731)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.015

Phenotype Score: 0.507

Variant Score: 0.419

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.1429954A>C [0/1] rs546270750 (variation viewer)

Variant score: 0.509 CONTRIBUTING VARIANT

Transcripts:: CRK:ENST00000300574.3:c.778-6304T>G:p.(=); CRK:ENST00000398970.5:c.608-6304T>G:p.(=); CRK:ENST00000574295.1:c.400-6769T>G:p.(=)

Pathogenicity Data:: Best Score: 0.5825543; CADD: 0.583 (3.794)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.0788%; UK10K: 0.0397%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0741%; gnomAD_G_OTH: 0.1035%

DOWNSTREAM_GENE_VARIANT chr17:g.1417938C>T [0/1]

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: CRK:ENST00000398970.5::; CRK:ENST00000264335.13::

Pathogenicity Data:: Best Score: 0.3287257; CADD: 0.329 (1.731)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.1453995G>A [0/1] rs188708806 (variation viewer)

Variant score: 0.189

Transcripts:: CRK:ENST00000300574.3:c.241+1882C>T:p.(=); CRK:ENST00000398970.5:c.241+1882C>T:p.(=); CRK:ENST00000574295.1:c.241+1882C>T:p.(=)

Pathogenicity Data:: Best Score: 0.19015855; CADD: 0.190 (0.916)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0143%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

DOWNSTREAM_GENE_VARIANT chr17:g.1420083CA>C [0/1] rs569784742 (variation viewer)

Variant score: 0.148

Transcripts:: CRK:ENST00000398970.5::; CRK:ENST00000264335.13::

Pathogenicity Data:: Best Score: 0.16938454; CADD: 0.169 (0.806)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0804%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0733%; gnomAD_G_OTH: 0.1018%

RHOB

Exomiser Score: 0.015

Phenotype Score: 0.508

Variant Score: 0.417

Phenotype matches:

Proximity score 0.508 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.009

Phenotype Score: 0.508

Variant Score: 0.362

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr2:g.20442568A>ATT [-/1] rs748929464 (variation viewer)

Variant score: 0.362 CONTRIBUTING VARIANT

Transcripts:: RHOB:ENST00000272233.6::; RHOB:ENST00000390869.1::

Pathogenicity Data:: Best Score: 0.3620304; CADD: 0.362 (1.952)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.015

Phenotype Score: 0.508

Variant Score: 0.417

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.20463154A>T [0/1] rs142501967 (variation viewer)

Variant score: 0.471 CONTRIBUTING VARIANT

Transcripts:: RHOB:ENST00000272233.6::; RHOB:ENST00000624084.2::

Pathogenicity Data:: Best Score: 0.80438596; CADD: 0.804 (7.086)

Frequency Data:: 1000Genomes: 0.6589%; TOPMed: 0.8489%; UK10K: 1.4017%; gnomAD_G_AFR: 0.2633%; gnomAD_G_AMR: 1.3126%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1431%; gnomAD_G_NFE: 1.0389%; gnomAD_G_OTH: 0.7128%

UPSTREAM_GENE_VARIANT chr2:g.20442568A>ATT [-/1] rs748929464 (variation viewer)

Variant score: 0.362 CONTRIBUTING VARIANT

Transcripts:: RHOB:ENST00000272233.6::; RHOB:ENST00000390869.1::

Pathogenicity Data:: Best Score: 0.3620304; CADD: 0.362 (1.952)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr2:g.20442568ATTTT>A [-/1] rs748929464 (variation viewer)

Variant score: 0.163

Transcripts:: RHOB:ENST00000272233.6::; RHOB:ENST00000390869.1::

Pathogenicity Data:: Best Score: 0.16266352; CADD: 0.163 (0.771)

Frequency Data:: No frequency data

NME5

Exomiser Score: 0.014

Phenotype Score: 0.504

Variant Score: 0.414

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.014

Phenotype Score: 0.504

Variant Score: 0.414

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138122441TA>T [1/1] rs70979581 (variation viewer)

Variant score: 0.414 CONTRIBUTING VARIANT

Transcripts:: NME5:ENST00000265191.4:c.437-3506del:p.(=)

Pathogenicity Data:: Best Score: 0.4138618; CADD: 0.414 (2.320)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.138117204CA>C [1/1] rs34623624 (variation viewer)

Variant score: 0.291

Transcripts:: NME5:ENST00000265191.4:c.556-1441del:p.(=)

Pathogenicity Data:: Best Score: 0.29058564; CADD: 0.291 (1.491)

Frequency Data:: No frequency data

SIN3A

Exomiser Score: 0.013

Phenotype Score: 0.520

Variant Score: 0.390

Phenotype matches:

Proximity score 0.520 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.520 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Known diseases:: OMIM:613406 Witteveen-Kolk syndrome - autosomal dominant; ORPHA:500166 SIN3A-related intellectual disability syndrome due to a point mutation; ORPHA:94065 15q24 microdeletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.013

Phenotype Score: 0.520

Variant Score: 0.390

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.75442120CA>C [-/1] rs57418865 (variation viewer)

Variant score: 0.390 CONTRIBUTING VARIANT

Transcripts:: SIN3A:ENST00000360439.8:c.-33-11713del:p.(=); SIN3A:ENST00000394947.8:c.-34+9302del:p.(=); SIN3A:ENST00000394949.8:c.-34+9239del:p.(=); SIN3A:ENST00000567289.5:c.-34+9302del:p.(=)

Pathogenicity Data:: Best Score: 0.39004195; CADD: 0.390 (2.147)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.260

Variant Score: 0.475

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.75449721AAAAAG>A [0/1] rs557171774 (variation viewer)

Variant score: 0.483 CONTRIBUTING VARIANT

Transcripts:: SIN3A:ENST00000360439.8:c.-34+5909_-34+5913del:p.(=); SIN3A:ENST00000394947.8:c.-34+1697_-34+1701del:p.(=); SIN3A:ENST00000394949.8:c.-34+1634_-34+1638del:p.(=); SIN3A:ENST00000567289.5:c.-34+1697_-34+1701del:p.(=)

Pathogenicity Data:: Best Score: 0.6664968; CADD: 0.666 (4.769)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.6634%; UK10K: 1.1108%; gnomAD_G_AFR: 0.1030%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0860%; gnomAD_G_NFE: 0.8592%; gnomAD_G_OTH: 0.2041%

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.75436366G>A [0/1] rs569821703 (variation viewer)

Variant score: 0.468 CONTRIBUTING VARIANT

Transcripts:: SIN3A:ENST00000360439.8:c.-33-5958C>T:p.(=); SIN3A:ENST00000394947.8:c.-33-5958C>T:p.(=); SIN3A:ENST00000394949.8:c.-33-5958C>T:p.(=); SIN3A:ENST00000567289.5:c.-33-5958C>T:p.(=)

Pathogenicity Data:: Best Score: 0.48560113; CADD: 0.486 (2.887)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0733%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.2398%; gnomAD_G_NFE: 0.0734%; gnomAD_G_OTH: 0.1020%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr15:g.75442120CAAAAA>C [-/1] rs57418865 (variation viewer)

Variant score: 0.370

Transcripts:: SIN3A:ENST00000360439.8:c.-33-11717_-33-11713del:p.(=); SIN3A:ENST00000394947.8:c.-34+9298_-34+9302del:p.(=); SIN3A:ENST00000394949.8:c.-34+9235_-34+9239del:p.(=); SIN3A:ENST00000567289.5:c.-34+9298_-34+9302del:p.(=)

Pathogenicity Data:: Best Score: 0.37020385; CADD: 0.370 (2.008)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.75407892CAA>C [1/1] rs775913884 (variation viewer)

Variant score: 0.122

Transcripts:: SIN3A:ENST00000360439.8:c.1318-750_1318-749del:p.(=); SIN3A:ENST00000394947.8:c.1318-750_1318-749del:p.(=); SIN3A:ENST00000394949.8:c.1318-750_1318-749del:p.(=)

Pathogenicity Data:: Best Score: 0.121584475; CADD: 0.122 (0.563)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.75410975C>CAA [-/1] rs542968474 (variation viewer)

Variant score: 0.056

Transcripts:: SIN3A:ENST00000360439.8:c.1008+516_1008+517insTT:p.(=); SIN3A:ENST00000394947.8:c.1008+516_1008+517insTT:p.(=); SIN3A:ENST00000394949.8:c.1008+516_1008+517insTT:p.(=)

Pathogenicity Data:: Best Score: 0.070391655; CADD: 0.070 (0.317)

Frequency Data:: gnomAD_G_AFR: 0.2016%; gnomAD_G_ASJ: 0.9009%; gnomAD_G_EAS: 0.0718%; gnomAD_G_FIN: 0.5917%; gnomAD_G_NFE: 0.2396%

TXN

Exomiser Score: 0.013

Phenotype Score: 0.503

Variant Score: 0.409

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.013

Phenotype Score: 0.503

Variant Score: 0.409

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.110237009CAA>C [0/1] rs55944914 (variation viewer)

Variant score: 0.409 CONTRIBUTING VARIANT

Transcripts:: TXN:ENST00000374517.6::; TXN:ENST00000400613.4::

Pathogenicity Data:: Best Score: 0.40884686; CADD: 0.409 (2.283)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.224

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.110237009CAA>C [0/1] rs55944914 (variation viewer)

Variant score: 0.409 CONTRIBUTING VARIANT

Transcripts:: TXN:ENST00000374517.6::; TXN:ENST00000400613.4::

Pathogenicity Data:: Best Score: 0.40884686; CADD: 0.409 (2.283)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.110251586C>CAAAA [0/1] rs5899890 (variation viewer)

Variant score: 0.039 CONTRIBUTING VARIANT

Transcripts:: TXN:ENST00000374515.9:c.25-125_25-124insTTTT:p.(=); TXN:ENST00000374517.6:c.25-125_25-124insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.03883046; CADD: 0.039 (0.172)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.110245618CTATATA>C [1/1] rs1170640168 (variation viewer)

Variant score: 0.094

Transcripts:: TXN:ENST00000374515.9:c.130-781_130-776del:p.(=); TXN:ENST00000374517.6:c.190-781_190-776del:p.(=)

Pathogenicity Data:: Best Score: 0.09426743; CADD: 0.094 (0.430)

Frequency Data:: No frequency data

CSE1L

Exomiser Score: 0.013

Phenotype Score: 0.503

Variant Score: 0.407

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.503

Variant Score: 0.229

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.49056847C>CTGTGTGTG [-/1] rs3223230 (variation viewer)

Variant score: 0.229 CONTRIBUTING VARIANT

Transcripts:: CSE1L:ENST00000262982.3:c.-11-1606_-11-1605insTGTGTGTG:p.(=); CSE1L:ENST00000396192.7:c.-11-1606_-11-1605insTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.22874147; CADD: 0.229 (1.128)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.503

Variant Score: 0.407

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr20:g.49097494G>C [0/1] rs188214322 (variation viewer)

Variant score: 0.497 CONTRIBUTING VARIANT

Transcripts:: CSE1L:ENST00000396192.7::; CSE1L:ENST00000371856.6::

Pathogenicity Data:: Best Score: 0.69061446; CADD: 0.691 (5.095)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.4277%; UK10K: 0.4364%; gnomAD_G_AFR: 0.0574%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_FIN: 0.5169%; gnomAD_G_NFE: 0.9400%; gnomAD_G_OTH: 1.1224%

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.49050200T>TTTTTATTTTATTTTA [0/1] rs201877558 (variation viewer)

Variant score: 0.317 CONTRIBUTING VARIANT

Transcripts:: CSE1L:ENST00000262982.3:c.-12+3777_-12+3778insTTTTATTTTATTTTA:p.(=); CSE1L:ENST00000396192.7:c.-12+3777_-12+3778insTTTTATTTTATTTTA:p.(=)

Pathogenicity Data:: Best Score: 0.36129546; CADD: 0.361 (1.947)

Frequency Data:: gnomAD_G_AFR: 0.1075%; gnomAD_G_AMR: 0.4792%; gnomAD_G_EAS: 0.6427%; gnomAD_G_FIN: 0.0404%; gnomAD_G_NFE: 0.1503%; gnomAD_G_OTH: 0.2252%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.49094063GTAAC>G [0/1] rs143409482 (variation viewer)

Variant score: 0.279

Transcripts:: CSE1L:ENST00000262982.3:c.2448-76_2448-73del:p.(=); CSE1L:ENST00000396192.7:c.2280-76_2280-73del:p.(=)

Pathogenicity Data:: Best Score: 0.38764966; CADD: 0.388 (2.130)

Frequency Data:: TOPMed: 0.4316%; UK10K: 0.4232%; gnomAD_G_AFR: 0.0573%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.5175%; gnomAD_G_NFE: 0.9403%; gnomAD_G_OTH: 1.1202%

UPSTREAM_GENE_VARIANT chr20:g.49044148C>T [0/1] rs1231766875 (variation viewer)

Variant score: 0.204

Transcripts:: CSE1L:ENST00000396192.7::; CSE1L:ENST00000433229.1::

Pathogenicity Data:: Best Score: 0.20384067; CADD: 0.204 (0.990)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_AFR: 0.0115%

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.49077153C>CT [0/1] rs11439721 (variation viewer)

Variant score: 0.144

Transcripts:: CSE1L:ENST00000262982.3:c.1420+89_1420+90insT:p.(=); CSE1L:ENST00000396192.7:c.1252+89_1252+90insT:p.(=)

Pathogenicity Data:: Best Score: 0.14355397; CADD: 0.144 (0.673)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr20:g.49041679TA>T [0/1] rs556252629 (variation viewer)

Variant score: 0.099

Transcripts:: CSE1L:ENST00000396192.7::; CSE1L:ENST00000433229.1::

Pathogenicity Data:: Best Score: 0.10895425; CADD: 0.109 (0.501)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.4340%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2404%; gnomAD_G_FIN: 0.1207%; gnomAD_G_NFE: 0.5134%; gnomAD_G_OTH: 0.1033%

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.49065312AATT>A [0/1] rs55999600 (variation viewer)

Variant score: 0.057

Transcripts:: CSE1L:ENST00000262982.3:c.229-879_229-877del:p.(=); CSE1L:ENST00000396192.7:c.229-879_229-877del:p.(=)

Pathogenicity Data:: Best Score: 0.057025373; CADD: 0.057 (0.255)

Frequency Data:: No frequency data

FRMPD2

Exomiser Score: 0.013

Phenotype Score: 0.507

Variant Score: 0.403

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.013

Phenotype Score: 0.507

Variant Score: 0.403

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48159142T>C [0/1] rs2652385 (variation viewer)

Variant score: 0.403 CONTRIBUTING VARIANT

Transcripts:: FRMPD2:ENST00000305531.3:c.3807-1772A>G:p.(=); FRMPD2:ENST00000374201.8:c.3882-1772A>G:p.(=); FRMPD2:ENST00000636244.1:c.3882-2768A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4026897; CADD: 0.403 (2.238)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.507

Variant Score: 0.349

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48159142T>C [0/1] rs2652385 (variation viewer)

Variant score: 0.403 CONTRIBUTING VARIANT

Transcripts:: FRMPD2:ENST00000305531.3:c.3807-1772A>G:p.(=); FRMPD2:ENST00000374201.8:c.3882-1772A>G:p.(=); FRMPD2:ENST00000636244.1:c.3882-2768A>G:p.(=)

Pathogenicity Data:: Best Score: 0.4026897; CADD: 0.403 (2.238)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48181097T>G [0/1] rs533643761 (variation viewer)

Variant score: 0.295 CONTRIBUTING VARIANT

Transcripts:: FRMPD2:ENST00000305531.3:c.2510-89A>C:p.(=); FRMPD2:ENST00000374201.8:c.2585-89A>C:p.(=); FRMPD2:ENST00000636244.1:c.2585-89A>C:p.(=)

Pathogenicity Data:: Best Score: 0.31118912; CADD: 0.311 (1.619)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0399%; gnomAD_G_AFR: 0.0116%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0670%; gnomAD_G_OTH: 0.1025%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48173158C>T [0/1] rs534692363 (variation viewer)

Variant score: 0.265

Transcripts:: FRMPD2:ENST00000305531.3:c.3001-65G>A:p.(=); FRMPD2:ENST00000374201.8:c.3076-65G>A:p.(=); FRMPD2:ENST00000636244.1:c.3076-65G>A:p.(=)

Pathogenicity Data:: Best Score: 0.74730307; CADD: 0.747 (5.974)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.4593%; gnomAD_G_AFR: 0.3091%; gnomAD_G_AMR: 1.2097%; gnomAD_G_ASJ: 0.4762%; gnomAD_G_FIN: 1.7528%; gnomAD_G_NFE: 1.3114%; gnomAD_G_OTH: 0.5981%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48169024C>T [0/1] rs1166000676 (variation viewer)

Variant score: 0.205

Transcripts:: FRMPD2:ENST00000305531.3:c.3364-331G>A:p.(=); FRMPD2:ENST00000374201.8:c.3439-331G>A:p.(=); FRMPD2:ENST00000636244.1:c.3439-331G>A:p.(=)

Pathogenicity Data:: Best Score: 0.20493984; CADD: 0.205 (0.996)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48191540G>A [0/1] rs149120885 (variation viewer)

Variant score: 0.157

Transcripts:: FRMPD2:ENST00000305531.3:c.2090+1144C>T:p.(=); FRMPD2:ENST00000374201.8:c.2165+1144C>T:p.(=); FRMPD2:ENST00000636244.1:c.2165+1144C>T:p.(=)

Pathogenicity Data:: Best Score: 0.16555065; CADD: 0.166 (0.786)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0446%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0400%; gnomAD_G_OTH: 0.2037%

DOWNSTREAM_GENE_VARIANT chr10:g.48155391G>A [1/1] rs1462992578 (variation viewer)

Variant score: 0.136

Transcripts:: FRMPD2:ENST00000636244.1::; FRMPD2:ENST00000614090.1::

Pathogenicity Data:: Best Score: 0.13741875; CADD: 0.137 (0.642)

Frequency Data:: gnomAD_G_AFR: 0.0121%; gnomAD_G_NFE: 0.0764%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48169159G>C [0/1] rs2652394 (variation viewer)

Variant score: 0.052

Transcripts:: FRMPD2:ENST00000305531.3:c.3364-466C>G:p.(=); FRMPD2:ENST00000374201.8:c.3439-466C>G:p.(=); FRMPD2:ENST00000636244.1:c.3439-466C>G:p.(=)

Pathogenicity Data:: Best Score: 0.05158156; CADD: 0.052 (0.230)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48239438C>T [0/1] rs544103968 (variation viewer)

Variant score: 0.039

Transcripts:: FRMPD2:ENST00000305531.3:c.716+167G>A:p.(=); FRMPD2:ENST00000374201.8:c.788+167G>A:p.(=); FRMPD2:ENST00000636244.1:c.788+167G>A:p.(=)

Pathogenicity Data:: Best Score: 0.041482627; CADD: 0.041 (0.184)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0398%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0267%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.48186885A>G [0/1] rs117785010 (variation viewer)

Variant score: 0.007

Transcripts:: FRMPD2:ENST00000305531.3:c.2191+307T>C:p.(=); FRMPD2:ENST00000374201.8:c.2266+307T>C:p.(=); FRMPD2:ENST00000636244.1:c.2266+307T>C:p.(=)

Pathogenicity Data:: Best Score: 0.02321273; CADD: 0.023 (0.102)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 1.1310%; UK10K: 1.6794%; gnomAD_G_AFR: 0.2984%; gnomAD_G_AMR: 1.1933%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.8349%; gnomAD_G_NFE: 1.4745%; gnomAD_G_OTH: 0.4073%

TCL1B

Exomiser Score: 0.013

Phenotype Score: 0.504

Variant Score: 0.405

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.013

Phenotype Score: 0.504

Variant Score: 0.405

Variants contributing to score:

INTERGENIC_VARIANT chr14:g.95678815C>CA [0/1] rs10656713 (variation viewer)

Variant score: 0.405 CONTRIBUTING VARIANT

Transcripts:: TCL1B:ENST00000340722.8::

Pathogenicity Data:: Best Score: 0.40529716; CADD: 0.405 (2.257)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.202

Variants contributing to score:

INTERGENIC_VARIANT chr14:g.95708502A>AATATATAT [1/1]

Variant score: 0.202 CONTRIBUTING VARIANT

Transcripts:: TCL1B:ENST00000340722.8::

Pathogenicity Data:: Best Score: 0.20200533; CADD: 0.202 (0.980)

Frequency Data:: No frequency data

Other passed variants:

AK7

Exomiser Score: 0.013

Phenotype Score: 0.503

Variant Score: 0.405

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617965 ?Spermatogenic failure 27 (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.213

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96425480A>AT [-/1] rs35861988 (variation viewer)

Variant score: 0.213 CONTRIBUTING VARIANT

Transcripts:: AK7:ENST00000267584.9:c.609+4548_609+4549insT:p.(=)

Pathogenicity Data:: Best Score: 0.21259165; CADD: 0.213 (1.038)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.503

Variant Score: 0.405

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96437807C>CT [0/1] rs771113927 (variation viewer)

Variant score: 0.598 CONTRIBUTING VARIANT

Transcripts:: AK7:ENST00000267584.9:c.610-28_610-27insT:p.(=)

Pathogenicity Data:: Best Score: 0.70623505; CADD: 0.706 (5.320)

Frequency Data:: ESP AA: 0.7569%; ESP EA: 0.7396%; ESP All: 0.7454%; ExAC AFR: 0.1473%; ExAC AMR: 0.2499%; ExAC EAS: 0.1318%; ExAC FIN: 0.1329%; ExAC NFE: 0.3952%; ExAC OTH: 0.2625%; ExAC SAS: 0.6422%; gnomAD_E_AFR: 0.1179%; gnomAD_E_AMR: 0.4377%; gnomAD_E_ASJ: 0.1634%; gnomAD_E_EAS: 0.2014%; gnomAD_E_FIN: 0.1438%; gnomAD_E_NFE: 0.2761%; gnomAD_E_OTH: 0.5010%; gnomAD_E_SAS: 0.2565%; gnomAD_G_AFR: 0.0231%; gnomAD_G_FIN: 0.1168%; gnomAD_G_NFE: 0.0939%; gnomAD_G_OTH: 0.2075%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96425480A>AT [-/1] rs35861988 (variation viewer)

Variant score: 0.213 CONTRIBUTING VARIANT

Transcripts:: AK7:ENST00000267584.9:c.609+4548_609+4549insT:p.(=)

Pathogenicity Data:: Best Score: 0.21259165; CADD: 0.213 (1.038)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96442148C>T [0/1] rs116856736 (variation viewer)

Variant score: 0.171

Transcripts:: AK7:ENST00000267584.9:c.691-582C>T:p.(=)

Pathogenicity Data:: Best Score: 0.8430722; CADD: 0.843 (8.043)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 1.1360%; UK10K: 1.9307%; gnomAD_G_AFR: 0.2866%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.4009%; gnomAD_G_NFE: 1.7591%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96418322T>TAAAAAAAAAAAAAAAAAAAAAAAAAAAA [1/1]

Variant score: 0.127

Transcripts:: AK7:ENST00000267584.9:c.499-2500_499-2499insAAAAAAAAAAAAAAAAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.1268276; CADD: 0.127 (0.589)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96463491G>A [0/1] rs564052350 (variation viewer)

Variant score: 0.050

Transcripts:: AK7:ENST00000267584.9:c.1357+5279G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09155214; CADD: 0.092 (0.417)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.9190%; gnomAD_G_AFR: 0.3343%; gnomAD_G_AMR: 0.7194%; gnomAD_G_FIN: 0.9855%; gnomAD_G_NFE: 1.4769%; gnomAD_G_OTH: 1.2371%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.96402197A>G [0|1] rs995021011 (variation viewer)

Variant score: 0.032

Transcripts:: AK7:ENST00000267584.9:c.295-2560A>G:p.(=)

Pathogenicity Data:: Best Score: 0.093015194; CADD: 0.093 (0.424)

Frequency Data:: gnomAD_G_AFR: 0.2762%; gnomAD_G_AMR: 0.3597%; gnomAD_G_FIN: 0.4016%; gnomAD_G_NFE: 1.7683%; gnomAD_G_OTH: 0.5112%

SUCLA2

Exomiser Score: 0.013

Phenotype Score: 0.501

Variant Score: 0.406

Phenotype matches:

Proximity score 0.501 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612073 Mitochondrial DNA depletion syndrome 5 (encephalomyopathic with or without methylmalonic aciduria) - autosomal recessive; ORPHA:1933 Mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.251

Variant Score: 0.337

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr13:g.48002675C>A [0/1] rs763868310 (variation viewer)

Variant score: 0.337 CONTRIBUTING VARIANT

Transcripts:: SUCLA2:ENST00000646804.1:c.-84-5652G>T:p.(=)

Pathogenicity Data:: Best Score: 0.337631; CADD: 0.338 (1.789)

Frequency Data:: TOPMed: 0.0135%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.501

Variant Score: 0.406

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr13:g.48026884C>CAAAAAA [1/1] rs59175556 (variation viewer)

Variant score: 0.406 CONTRIBUTING VARIANT

Transcripts:: SUCLA2:ENST00000646804.1:c.-85+10721_-85+10722insTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.40598148; CADD: 0.406 (2.262)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr13:g.48034478CA>C [0/1] rs56211666 (variation viewer)

Variant score: 0.120

Transcripts:: SUCLA2:ENST00000646804.1:c.-85+3127del:p.(=)

Pathogenicity Data:: Best Score: 0.11976224; CADD: 0.120 (0.554)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.47943766G>A [1/1] rs71428266 (variation viewer)

Variant score: 0.014

Transcripts:: SUCLA2:ENST00000642944.1:c.1144-321C>T:p.(=); SUCLA2:ENST00000643023.1:c.1381-321C>T:p.(=); SUCLA2:ENST00000646804.1:c.1144-321C>T:p.(=); SUCLA2:ENST00000646932.1:c.1318-321C>T:p.(=)

Pathogenicity Data:: Best Score: 0.013947606; CADD: 0.014 (0.061)

Frequency Data:: No frequency data

CHRNB3

Exomiser Score: 0.013

Phenotype Score: 0.519

Variant Score: 0.385

Phenotype matches:

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.052

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.42703435A>AAAAAAAAATATATATATATATATATATAT [-/1]

Variant score: 0.052 CONTRIBUTING VARIANT

Transcripts:: CHRNB3:ENST00000289957.3:c.53-5282_53-5281insAAAAAAAATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.051799893; CADD: 0.052 (0.231)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.519

Variant Score: 0.385

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.42708542G>C [0/1] rs72644007 (variation viewer)

Variant score: 0.615 CONTRIBUTING VARIANT

Transcripts:: CHRNB3:ENST00000289957.3:c.53-175G>C:p.(=)

Pathogenicity Data:: Best Score: 0.62433565; CADD: 0.624 (4.252)

Frequency Data:: TOPMed: 0.0860%; gnomAD_G_AFR: 0.0345%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.0734%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.42700616G>A [0/1] rs72644004 (variation viewer)

Variant score: 0.155 CONTRIBUTING VARIANT

Transcripts:: CHRNB3:ENST00000289957.3:c.52+3018G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3863793; CADD: 0.386 (2.121)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.2660%; UK10K: 0.2513%; gnomAD_G_AFR: 0.1146%; gnomAD_G_FIN: 1.6896%; gnomAD_G_NFE: 0.5403%; gnomAD_G_OTH: 0.9221%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.42703435A>AAAAAAATATATATATATATATATATATAT [-/1]

Variant score: 0.052

Transcripts:: CHRNB3:ENST00000289957.3:c.53-5282_53-5281insAAAAAATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.051799893; CADD: 0.052 (0.231)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.42727755C>T [0/1] rs188024921 (variation viewer)

Variant score: 0.048

Transcripts:: CHRNB3:ENST00000289957.3:c.250-2839C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12702864; CADD: 0.127 (0.590)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.2596%; UK10K: 0.2380%; gnomAD_G_AFR: 0.1264%; gnomAD_G_FIN: 1.7192%; gnomAD_G_NFE: 0.5067%; gnomAD_G_OTH: 0.9202%

CERS4

Exomiser Score: 0.013

Phenotype Score: 0.505

Variant Score: 0.400

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.105

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.8245122A>ACAAAAAAAC [-/1] rs755450125 (variation viewer)

Variant score: 0.105 CONTRIBUTING VARIANT

Transcripts:: CERS4:ENST00000251363.10:c.-1-5954_-1-5953insCAAAAAAAC:p.(=); CERS4:ENST00000558331.5:c.-120-5988_-120-5987insCAAAAAAAC:p.(=); CERS4:ENST00000559336.5:c.-1-5954_-1-5953insCAAAAAAAC:p.(=); CERS4:ENST00000559450.5:c.-1-5954_-1-5953insCAAAAAAAC:p.(=)

Pathogenicity Data:: Best Score: 0.10545951; CADD: 0.105 (0.484)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.013

Phenotype Score: 0.505

Variant Score: 0.400

Variants contributing to score:

INTERGENIC_VARIANT chr19:g.8279256G>A [1/1] rs36118792 (variation viewer)

Variant score: 0.400 CONTRIBUTING VARIANT

Transcripts:: CERS4:ENST00000559336.5::; CERS4:ENST00000537716.6::

Pathogenicity Data:: Best Score: 0.49066913; CADD: 0.491 (2.930)

Frequency Data:: gnomAD_G_AFR: 0.5415%; gnomAD_G_NFE: 0.6716%; gnomAD_G_OTH: 0.8621%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.8253449CT>C [1/1] rs35212733 (variation viewer)

Variant score: 0.334

Transcripts:: CERS4:ENST00000251363.10:c.174-1049del:p.(=); CERS4:ENST00000558331.5:c.21-1049del:p.(=); CERS4:ENST00000559336.5:c.174-1049del:p.(=); CERS4:ENST00000559450.5:c.174-1049del:p.(=)

Pathogenicity Data:: Best Score: 0.33426714; CADD: 0.334 (1.767)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr19:g.8281378C>CT [1/1] rs1169945865 (variation viewer)

Variant score: 0.290

Transcripts:: CERS4:ENST00000559336.5::; CERS4:ENST00000537716.6::

Pathogenicity Data:: Best Score: 0.29042226; CADD: 0.290 (1.490)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr19:g.8205725G>T [0/1] rs185138619 (variation viewer)

Variant score: 0.124

Transcripts:: CERS4:ENST00000558331.5::; CERS4:ENST00000595307.1::

Pathogenicity Data:: Best Score: 0.16092652; CADD: 0.161 (0.762)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.1521%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0458%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.1717%; gnomAD_G_NFE: 0.1800%; gnomAD_G_OTH: 0.3055%

DOWNSTREAM_GENE_VARIANT chr19:g.8266863CAA>C [1/1] rs756237359 (variation viewer)

Variant score: 0.091

Transcripts:: CERS4:ENST00000559336.5::; CERS4:ENST00000537716.6::

Pathogenicity Data:: Best Score: 0.09113371; CADD: 0.091 (0.415)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.8260950CA>C [1/1] rs764163177 (variation viewer)

Variant score: 0.081

Transcripts:: CERS4:ENST00000251363.10:c.849-737del:p.(=); CERS4:ENST00000558331.5:c.696-737del:p.(=); CERS4:ENST00000559336.5:c.742-979del:p.(=); CERS4:ENST00000559450.5:c.849-737del:p.(=)

Pathogenicity Data:: Best Score: 0.081455946; CADD: 0.081 (0.369)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.8245122A>AAAAACAAAAAAAAACAAAAAAAAAC [-/1] rs1555777239 (variation viewer)

Variant score: 0.076

Transcripts:: CERS4:ENST00000251363.10:c.-1-5954_-1-5953insAAAACAAAAAAAAACAAAAAAAAAC:p.(=); CERS4:ENST00000558331.5:c.-120-5988_-120-5987insAAAACAAAAAAAAACAAAAAAAAAC:p.(=); CERS4:ENST00000559336.5:c.-1-5954_-1-5953insAAAACAAAAAAAAACAAAAAAAAAC:p.(=); CERS4:ENST00000559450.5:c.-1-5954_-1-5953insAAAACAAAAAAAAACAAAAAAAAAC:p.(=)

Pathogenicity Data:: Best Score: 0.07636583; CADD: 0.076 (0.345)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.8217185C>T [0/1] rs116887167 (variation viewer)

Variant score: 0.060

Transcripts:: CERS4:ENST00000251363.10:c.-2+6323C>T:p.(=); CERS4:ENST00000558331.5:c.-121+6323C>T:p.(=); CERS4:ENST00000559336.5:c.-2+6323C>T:p.(=); CERS4:ENST00000559450.5:c.-2+7691C>T:p.(=)

Pathogenicity Data:: Best Score: 0.08903855; CADD: 0.089 (0.405)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.7279%; UK10K: 1.2166%; gnomAD_G_AFR: 0.2866%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.9732%; gnomAD_G_OTH: 1.1202%

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.8249587A>ATTTTT [1/1] rs869119452 (variation viewer)

Variant score: 0.034

Transcripts:: CERS4:ENST00000251363.10:c.-1-1489_-1-1488insTTTTT:p.(=); CERS4:ENST00000558331.5:c.-120-1523_-120-1522insTTTTT:p.(=); CERS4:ENST00000559336.5:c.-1-1489_-1-1488insTTTTT:p.(=); CERS4:ENST00000559450.5:c.-1-1489_-1-1488insTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.034393907; CADD: 0.034 (0.152)

Frequency Data:: No frequency data

ARHGEF2

Exomiser Score: 0.012

Phenotype Score: 0.501

Variant Score: 0.400

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617523 ?Neurodevelopmental disorder with midbrain and hindbrain malformations (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.220

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.155971579C>CAAAAAAAAAAAA [0/1] rs55942349 (variation viewer)

Variant score: 0.220 CONTRIBUTING VARIANT

Transcripts:: ARHGEF2:ENST00000313667.8:c.64-2280_64-2279insTTTTTTTTTTTT:p.(=); ARHGEF2:ENST00000361247.9:c.64-2280_64-2279insTTTTTTTTTTTT:p.(=); ARHGEF2:ENST00000462460.6:c.199-2280_199-2279insTTTTTTTTTTTT:p.(=); ARHGEF2:ENST00000673475.1:c.493-2280_493-2279insTTTTTTTTTTTT:p.(=); ARHGEF2:ENST00000313695.11:c.-18-2280_-18-2279insTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.21981066; CADD: 0.220 (1.078)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.501

Variant Score: 0.400

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.155964167A>T [1|1] rs377500936 (variation viewer)

Variant score: 0.400 CONTRIBUTING VARIANT

Transcripts:: ARHGEF2:ENST00000313667.8:c.721+821T>A:p.(=); ARHGEF2:ENST00000313695.11:c.640+821T>A:p.(=); ARHGEF2:ENST00000361247.9:c.724+821T>A:p.(=); ARHGEF2:ENST00000462460.6:c.859+821T>A:p.(=); ARHGEF2:ENST00000673475.1:c.1153+821T>A:p.(=)

Pathogenicity Data:: Best Score: 0.40020895; CADD: 0.400 (2.220)

Frequency Data:: No frequency data

Other passed variants:

KAT2B

Exomiser Score: 0.012

Phenotype Score: 0.510

Variant Score: 0.389

Phenotype matches:

Proximity score 0.510 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.510

Variant Score: 0.304

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.20149495CA>C [0/1] rs56091316 (variation viewer)

Variant score: 0.304 CONTRIBUTING VARIANT

Transcripts:: KAT2B:ENST00000263754.5:c.2305+1009del:p.(=)

Pathogenicity Data:: Best Score: 0.3044954; CADD: 0.304 (1.577)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.510

Variant Score: 0.389

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.20020882A>AAAGAT [1|1] rs1553642279 (variation viewer)

Variant score: 0.389 CONTRIBUTING VARIANT

Transcripts:: KAT2B:ENST00000263754.5::; KAT2B:ENST00000450678.1::

Pathogenicity Data:: Best Score: 0.38933927; CADD: 0.389 (2.142)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.20106979GTA>G [1/1]

Variant score: 0.313

Transcripts:: KAT2B:ENST00000263754.5:c.852-4616_852-4615del:p.(=)

Pathogenicity Data:: Best Score: 0.3126151; CADD: 0.313 (1.628)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.20145554G>GTTT [0/1] rs550166293 (variation viewer)

Variant score: 0.149

Transcripts:: KAT2B:ENST00000263754.5:c.2005-762_2005-761insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.14925385; CADD: 0.149 (0.702)

Frequency Data:: No frequency data

HAX1

Exomiser Score: 0.012

Phenotype Score: 0.507

Variant Score: 0.392

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:610738 Neutropenia, severe congenital 3, autosomal recessive - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.125

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr1:g.154277332ATTTTT>A [0/1] rs374846272 (variation viewer)

Variant score: 0.125 CONTRIBUTING VARIANT

Transcripts:: HAX1:ENST00000328703.12::; HAX1:ENST00000612670.1::

Pathogenicity Data:: Best Score: 0.124613166; CADD: 0.125 (0.578)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.507

Variant Score: 0.392

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr1:g.154279867T>C [0|1] rs758401857 (variation viewer)

Variant score: 0.420 CONTRIBUTING VARIANT

Transcripts:: HAX1:ENST00000328703.12::; HAX1:ENST00000612670.1::

Pathogenicity Data:: Best Score: 0.48524565; CADD: 0.485 (2.884)

Frequency Data:: gnomAD_G_AFR: 0.1608%; gnomAD_G_AMR: 0.3589%; gnomAD_G_FIN: 0.2865%; gnomAD_G_NFE: 0.6879%; gnomAD_G_OTH: 0.6110%

DOWNSTREAM_GENE_VARIANT chr1:g.154277339T>A [0/1] rs1366990254 (variation viewer)

Variant score: 0.364 CONTRIBUTING VARIANT

Transcripts:: HAX1:ENST00000328703.12::; HAX1:ENST00000612670.1::

Pathogenicity Data:: Best Score: 0.44319898; CADD: 0.443 (2.543)

Frequency Data:: gnomAD_G_AFR: 0.8396%; gnomAD_G_NFE: 0.0638%; gnomAD_G_OTH: 0.3546%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr1:g.154279862T>TGCG [0|1] rs544918886 (variation viewer)

Variant score: 0.138

Transcripts:: HAX1:ENST00000328703.12::; HAX1:ENST00000612670.1::

Pathogenicity Data:: Best Score: 0.1682362; CADD: 0.168 (0.800)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.2396%; UK10K: 0.8463%; gnomAD_G_AFR: 0.1613%; gnomAD_G_AMR: 0.3597%; gnomAD_G_FIN: 0.2897%; gnomAD_G_NFE: 0.6918%; gnomAD_G_OTH: 0.6148%

DOWNSTREAM_GENE_VARIANT chr1:g.154277336T>* [-/1]

Variant score: 0.000

Transcripts:: HAX1:ENST00000328703.12::; HAX1:ENST00000612670.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ENTPD6

Exomiser Score: 0.012

Phenotype Score: 0.503

Variant Score: 0.396

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.503

Variant Score: 0.396

Variants contributing to score:

INTERGENIC_VARIANT chr20:g.25239844T>TAGA [0|1] rs746138032 (variation viewer)

Variant score: 0.458 CONTRIBUTING VARIANT

Transcripts:: ENTPD6:ENST00000376652.9::

Pathogenicity Data:: Best Score: 0.4757964; CADD: 0.476 (2.805)

Frequency Data:: gnomAD_G_AFR: 0.0802%; gnomAD_G_NFE: 0.2470%; gnomAD_G_OTH: 0.1020%

INTERGENIC_VARIANT chr20:g.25239848C>G [0|1] rs767512639 (variation viewer)

Variant score: 0.334 CONTRIBUTING VARIANT

Transcripts:: ENTPD6:ENST00000376652.9::

Pathogenicity Data:: Best Score: 0.34686947; CADD: 0.347 (1.850)

Frequency Data:: gnomAD_G_AFR: 0.0802%; gnomAD_G_NFE: 0.2468%; gnomAD_G_OTH: 0.1018%

Other passed variants:

INTERGENIC_VARIANT chr20:g.25239845CAT>C [0|1] rs774181843 (variation viewer)

Variant score: 0.206

Transcripts:: ENTPD6:ENST00000376652.9::

Pathogenicity Data:: Best Score: 0.21367878; CADD: 0.214 (1.044)

Frequency Data:: gnomAD_G_AFR: 0.0802%; gnomAD_G_NFE: 0.2468%; gnomAD_G_OTH: 0.1020%

DDC

Exomiser Score: 0.012

Phenotype Score: 0.505

Variant Score: 0.393

Phenotype matches:

Phenotypic similarity 0.479 to Aromatic L-amino acid decarboxylase deficiency associated with DDC.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Phenotypic similarity 0.428 to mouse mutant involving DDC.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:608643 Aromatic L-amino acid decarboxylase deficiency - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.505

Variant Score: 0.393

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr7:g.50548425T>C [0/1] rs117280351 (variation viewer)

Variant score: 0.424 CONTRIBUTING VARIANT

Transcripts:: DDC:ENST00000357936.9:c.-28-4312A>G:p.(=); DDC:ENST00000380984.4:c.-28-4312A>G:p.(=); DDC:ENST00000426377.5:c.-28-4312A>G:p.(=); DDC:ENST00000444124.7:c.-28-4312A>G:p.(=); DDC:ENST00000615193.4:c.-28-4312A>G:p.(=); DDC:ENST00000617822.4:c.-28-4312A>G:p.(=); DDC:ENST00000622873.4:c.-28-4312A>G:p.(=)

Pathogenicity Data:: Best Score: 0.49394232; CADD: 0.494 (2.958)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.5033%; UK10K: 0.7141%; gnomAD_G_AFR: 0.0687%; gnomAD_G_AMR: 0.3589%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4865%; gnomAD_G_NFE: 0.6596%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.50534678A>C [0/1] rs148764326 (variation viewer)

Variant score: 0.362 CONTRIBUTING VARIANT

Transcripts:: DDC:ENST00000357936.9:c.435+3182T>G:p.(=); DDC:ENST00000380984.4:c.435+3182T>G:p.(=); DDC:ENST00000426377.5:c.202-5336T>G:p.(=); DDC:ENST00000431062.5:c.435+3182T>G:p.(=); DDC:ENST00000444124.7:c.435+3182T>G:p.(=); DDC:ENST00000615193.4:c.435+3182T>G:p.(=); DDC:ENST00000617822.4:c.435+3182T>G:p.(=); DDC:ENST00000622873.4:c.321+3182T>G:p.(=); DDC:ENST00000613602.3:c.-11+7840T>G:p.(=)

Pathogenicity Data:: Best Score: 0.57849765; CADD: 0.578 (3.752)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 0.9047%; UK10K: 1.1108%; gnomAD_G_AFR: 0.1720%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.7172%; gnomAD_G_NFE: 1.0946%; gnomAD_G_OTH: 0.6135%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.50474384A>G [0/1] rs182204823 (variation viewer)

Variant score: 0.230

Transcripts:: DDC:ENST00000357936.9:c.1041+2240T>C:p.(=); DDC:ENST00000426377.5:c.807+2240T>C:p.(=); DDC:ENST00000431062.5:c.762+2240T>C:p.(=); DDC:ENST00000444124.7:c.1041+2240T>C:p.(=); DDC:ENST00000615193.4:c.762+2240T>C:p.(=); DDC:ENST00000617822.4:c.897+2240T>C:p.(=); DDC:ENST00000622873.4:c.927+2240T>C:p.(=); DDC:ENST00000613602.3:c.-10-27087T>C:p.(=)

Pathogenicity Data:: Best Score: 0.2639624; CADD: 0.264 (1.331)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.5001%; UK10K: 0.6215%; gnomAD_G_AFR: 0.0574%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4868%; gnomAD_G_NFE: 0.6602%; gnomAD_G_OTH: 0.4073%

FIVE_PRIME_UTR_INTRON_VARIANT chr7:g.50553484C>CT [1/1] rs5884158 (variation viewer)

Variant score: 0.144

Transcripts:: DDC:ENST00000357936.9:c.-29+7529_-29+7530insA:p.(=); DDC:ENST00000380984.4:c.-29+7529_-29+7530insA:p.(=); DDC:ENST00000426377.5:c.-29+7529_-29+7530insA:p.(=); DDC:ENST00000444124.7:c.-28-9372_-28-9371insA:p.(=); DDC:ENST00000615193.4:c.-29+7529_-29+7530insA:p.(=); DDC:ENST00000617822.4:c.-29+7529_-29+7530insA:p.(=); DDC:ENST00000622873.4:c.-29+7529_-29+7530insA:p.(=)

Pathogenicity Data:: Best Score: 0.14434242; CADD: 0.144 (0.677)

Frequency Data:: No frequency data

TJP1

Exomiser Score: 0.012

Phenotype Score: 0.509

Variant Score: 0.388

Phenotype matches:

Proximity score 0.509 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.012

Phenotype Score: 0.509

Variant Score: 0.388

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.29791413CT>C [1/1] rs34201715 (variation viewer)

Variant score: 0.388 CONTRIBUTING VARIANT

Transcripts:: TJP1:ENST00000346128.10:c.84+9232del:p.(=); TJP1:ENST00000356107.10:c.84+9232del:p.(=); TJP1:ENST00000400011.6:c.96+9232del:p.(=); TJP1:ENST00000495972.6:c.84+9232del:p.(=); TJP1:ENST00000545208.6:c.84+9232del:p.(=); TJP1:ENST00000614355.4:c.48+9232del:p.(=)

Pathogenicity Data:: Best Score: 0.38793153; CADD: 0.388 (2.132)

Frequency Data:: No frequency data

Other passed variants:

TRDMT1

Exomiser Score: 0.011

Phenotype Score: 0.504

Variant Score: 0.391

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.011

Phenotype Score: 0.504

Variant Score: 0.391

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr10:g.17141816A>C [0/1] rs191178533 (variation viewer)

Variant score: 0.391 CONTRIBUTING VARIANT

Transcripts:: TRDMT1:ENST00000377799.8:c.*7224T>G:p.(=)

Pathogenicity Data:: Best Score: 0.3929842; CADD: 0.393 (2.168)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0406%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0229%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0333%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.237

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr10:g.17141816A>C [0/1] rs191178533 (variation viewer)

Variant score: 0.391 CONTRIBUTING VARIANT

Transcripts:: TRDMT1:ENST00000377799.8:c.*7224T>G:p.(=)

Pathogenicity Data:: Best Score: 0.3929842; CADD: 0.393 (2.168)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0406%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0229%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0333%

THREE_PRIME_UTR_EXON_VARIANT chr10:g.17139980C>T [0/1] rs117470503 (variation viewer)

Variant score: 0.083 CONTRIBUTING VARIANT

Transcripts:: TRDMT1:ENST00000377799.8:c.*9060G>A:p.(=)

Pathogenicity Data:: Best Score: 0.15355253; CADD: 0.154 (0.724)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.8768%; UK10K: 1.4017%; gnomAD_G_AFR: 0.2664%; gnomAD_G_AMR: 0.6053%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_FIN: 0.8897%; gnomAD_G_NFE: 1.4802%; gnomAD_G_OTH: 1.1411%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr10:g.17136064C>CA [1/1] rs34141782 (variation viewer)

Variant score: 0.131

Transcripts:: TRDMT1:ENST00000377799.8::; TRDMT1:ENST00000377833.10::

Pathogenicity Data:: Best Score: 0.13083947; CADD: 0.131 (0.609)

Frequency Data:: No frequency data

UBE2N

Exomiser Score: 0.011

Phenotype Score: 0.505

Variant Score: 0.388

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.011

Phenotype Score: 0.505

Variant Score: 0.388

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93421207T>TG [0|1] rs1188470851 (variation viewer)

Variant score: 0.388 CONTRIBUTING VARIANT

Transcripts:: UBE2N:ENST00000318066.7:c.31-9909_31-9908insC:p.(=); UBE2N:ENST00000550657.1:c.31-9909_31-9908insC:p.(=); UBE2N:ENST00000552442.1:c.31-9909_31-9908insC:p.(=); UBE2N:ENST00000549833.1:c.-160+3062_-160+3063insC:p.(=)

Pathogenicity Data:: Best Score: 0.38764966; CADD: 0.388 (2.130)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.249

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93421207T>TG [0|1] rs1188470851 (variation viewer)

Variant score: 0.388 CONTRIBUTING VARIANT

Transcripts:: UBE2N:ENST00000318066.7:c.31-9909_31-9908insC:p.(=); UBE2N:ENST00000550657.1:c.31-9909_31-9908insC:p.(=); UBE2N:ENST00000552442.1:c.31-9909_31-9908insC:p.(=); UBE2N:ENST00000549833.1:c.-160+3062_-160+3063insC:p.(=)

Pathogenicity Data:: Best Score: 0.38764966; CADD: 0.388 (2.130)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.93437178G>GA [0/1] rs529180233 (variation viewer)

Variant score: 0.111 CONTRIBUTING VARIANT

Transcripts:: UBE2N:ENST00000318066.7:c.30+4676_30+4677insT:p.(=); UBE2N:ENST00000550657.1:c.30+4676_30+4677insT:p.(=); UBE2N:ENST00000552442.1:c.30+4676_30+4677insT:p.(=); UBE2N:ENST00000549833.1:c.-281+3965_-281+3966insT:p.(=)

Pathogenicity Data:: Best Score: 0.26362336; CADD: 0.264 (1.329)

Frequency Data:: gnomAD_G_AFR: 0.3101%; gnomAD_G_AMR: 0.5650%; gnomAD_G_ASJ: 0.7407%; gnomAD_G_FIN: 0.4960%; gnomAD_G_NFE: 1.6637%; gnomAD_G_OTH: 0.6460%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr12:g.93406275CA>C [0/1] rs58309798 (variation viewer)

Variant score: 0.108

Transcripts:: UBE2N:ENST00000318066.7:c.*3763del:p.(=)

Pathogenicity Data:: Best Score: 0.1077224; CADD: 0.108 (0.495)

Frequency Data:: No frequency data

NANOG

Exomiser Score: 0.011

Phenotype Score: 0.503

Variant Score: 0.388

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.011

Phenotype Score: 0.503

Variant Score: 0.388

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr12:g.7798737T>C [1|1] rs10744050 (variation viewer)

Variant score: 0.388 CONTRIBUTING VARIANT

Transcripts:: NANOG:ENST00000229307.9:c.*3642T>C:p.(=)

Pathogenicity Data:: Best Score: 0.58495045; CADD: 0.585 (3.819)

Frequency Data:: gnomAD_G_AFR: 0.8347%; gnomAD_G_ASJ: 1.2500%; gnomAD_G_EAS: 0.3378%; gnomAD_G_FIN: 0.3555%; gnomAD_G_NFE: 0.5914%

Other passed variants:

INTERGENIC_VARIANT chr12:g.7808908CAAAAAA>C [1/1] rs1166487565 (variation viewer)

Variant score: 0.117

Transcripts:: NANOG:ENST00000229307.9::

Pathogenicity Data:: Best Score: 0.11671674; CADD: 0.117 (0.539)

Frequency Data:: No frequency data

NME1

Exomiser Score: 0.011

Phenotype Score: 0.504

Variant Score: 0.387

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.151

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr17:g.51150839C>CAA [-/1] rs57217311 (variation viewer)

Variant score: 0.151 CONTRIBUTING VARIANT

Transcripts:: NME1:ENST00000393196.7::; NME1:ENST00000262013.12::

Pathogenicity Data:: Best Score: 0.15081954; CADD: 0.151 (0.710)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.011

Phenotype Score: 0.504

Variant Score: 0.387

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.51146448A>C [0|1] rs11651725 (variation viewer)

Variant score: 0.581 CONTRIBUTING VARIANT

Transcripts:: NME1:ENST00000393196.7::

Pathogenicity Data:: Best Score: 0.59987104; CADD: 0.600 (3.978)

Frequency Data:: gnomAD_G_AFR: 0.1518%; gnomAD_G_EAS: 0.2119%; gnomAD_G_FIN: 0.0986%; gnomAD_G_NFE: 0.1391%; gnomAD_G_OTH: 0.1168%

INTERGENIC_VARIANT chr17:g.51139156G>A [0/1] rs139916464 (variation viewer)

Variant score: 0.193 CONTRIBUTING VARIANT

Transcripts:: NME1:ENST00000393196.7::

Pathogenicity Data:: Best Score: 0.225003; CADD: 0.225 (1.107)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.3018%; UK10K: 0.3306%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.7160%; gnomAD_G_FIN: 0.5727%; gnomAD_G_NFE: 0.4264%; gnomAD_G_OTH: 0.6122%

Other passed variants:

UPSTREAM_GENE_VARIANT chr17:g.51150839CA>C [-/1] rs57217311 (variation viewer)

Variant score: 0.122

Transcripts:: NME1:ENST00000393196.7::; NME1:ENST00000262013.12::

Pathogenicity Data:: Best Score: 0.12198889; CADD: 0.122 (0.565)

Frequency Data:: No frequency data

AK8

Exomiser Score: 0.011

Phenotype Score: 0.503

Variant Score: 0.387

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.011

Phenotype Score: 0.503

Variant Score: 0.387

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.132844297C>CAA [0/1] rs35309762 (variation viewer)

Variant score: 0.387 CONTRIBUTING VARIANT

Transcripts:: AK8:ENST00000298545.4:c.402+10559_402+10560insTT:p.(=)

Pathogenicity Data:: Best Score: 0.38694423; CADD: 0.387 (2.125)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.503

Variant Score: 0.252

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.132844297C>CAA [0/1] rs35309762 (variation viewer)

Variant score: 0.387 CONTRIBUTING VARIANT

Transcripts:: AK8:ENST00000298545.4:c.402+10559_402+10560insTT:p.(=)

Pathogenicity Data:: Best Score: 0.38694423; CADD: 0.387 (2.125)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.132812228C>CT [0/1] rs528951216 (variation viewer)

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: AK8:ENST00000298545.4:c.979+2409_979+2410insA:p.(=)

Pathogenicity Data:: Best Score: 0.11671674; CADD: 0.117 (0.539)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.132739441CA>C [0/1] rs768297504 (variation viewer)

Variant score: 0.103

Transcripts:: AK8:ENST00000298545.4:c.1122-11908del:p.(=)

Pathogenicity Data:: Best Score: 0.10257119; CADD: 0.103 (0.470)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.132812530T>TGCCCACTGGGATGACGGGTGAGCCGCCGC [-/1] rs11270703 (variation viewer)

Variant score: 0.043

Transcripts:: AK8:ENST00000298545.4:c.979+2107_979+2108insGCGGCGGCTCACCCGTCATCCCAGTGGGC:p.(=)

Pathogenicity Data:: Best Score: 0.043466926; CADD: 0.043 (0.193)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.132812530T>TACCCACTGGGATGACAGGGGTGAGCCGCCGC [-/1] rs1554795855 (variation viewer)

Variant score: 0.042

Transcripts:: AK8:ENST00000298545.4:c.979+2107_979+2108insGCGGCGGCTCACCCCTGTCATCCCAGTGGGT:p.(=)

Pathogenicity Data:: Best Score: 0.041703284; CADD: 0.042 (0.185)

Frequency Data:: No frequency data

CALU

Exomiser Score: 0.010

Phenotype Score: 0.507

Variant Score: 0.378

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.010

Phenotype Score: 0.507

Variant Score: 0.378

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.128768847CAAAAA>C [0/1] rs1012831963 (variation viewer)

Variant score: 0.378 CONTRIBUTING VARIANT

Transcripts:: CALU:ENST00000249364.9:c.844-215_844-211del:p.(=); CALU:ENST00000449187.6:c.844-215_844-211del:p.(=); CALU:ENST00000479257.5:c.868-215_868-211del:p.(=); CALU:ENST00000535011.6:c.644-215_644-211del:p.(=); CALU:ENST00000542996.6:c.868-215_868-211del:p.(=)

Pathogenicity Data:: Best Score: 0.3782726; CADD: 0.378 (2.064)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.507

Variant Score: 0.287

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.128768847CAAAAA>C [0/1] rs1012831963 (variation viewer)

Variant score: 0.378 CONTRIBUTING VARIANT

Transcripts:: CALU:ENST00000249364.9:c.844-215_844-211del:p.(=); CALU:ENST00000449187.6:c.844-215_844-211del:p.(=); CALU:ENST00000479257.5:c.868-215_868-211del:p.(=); CALU:ENST00000535011.6:c.644-215_644-211del:p.(=); CALU:ENST00000542996.6:c.868-215_868-211del:p.(=)

Pathogenicity Data:: Best Score: 0.3782726; CADD: 0.378 (2.064)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.128755309CAAA>C [0/1] rs59208090 (variation viewer)

Variant score: 0.196 CONTRIBUTING VARIANT

Transcripts:: CALU:ENST00000249364.9:c.415+855_415+857del:p.(=); CALU:ENST00000449187.6:c.415+588_415+590del:p.(=); CALU:ENST00000479257.5:c.439+855_439+857del:p.(=); CALU:ENST00000535011.6:c.415+855_415+857del:p.(=); CALU:ENST00000542996.6:c.439+588_439+590del:p.(=)

Pathogenicity Data:: Best Score: 0.19591862; CADD: 0.196 (0.947)

Frequency Data:: No frequency data

Other passed variants:

SALL3

Exomiser Score: 0.010

Phenotype Score: 0.504

Variant Score: 0.381

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.504

Variant Score: 0.381

Variants contributing to score:

INTERGENIC_VARIANT chr18:g.79006186G>A [0/1] rs112565553 (variation viewer)

Variant score: 0.408 CONTRIBUTING VARIANT

Transcripts:: SALL3:ENST00000537592.6::

Pathogenicity Data:: Best Score: 0.4597435; CADD: 0.460 (2.674)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0599%; UK10K: 0.6083%; gnomAD_G_AFR: 0.1379%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4293%; gnomAD_G_NFE: 0.4945%; gnomAD_G_OTH: 0.2041%

INTERGENIC_VARIANT chr18:g.79008689C>G [0/1] rs111287067 (variation viewer)

Variant score: 0.353 CONTRIBUTING VARIANT

Transcripts:: SALL3:ENST00000537592.6::

Pathogenicity Data:: Best Score: 0.40802956; CADD: 0.408 (2.277)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.4165%; UK10K: 0.6876%; gnomAD_G_AFR: 0.1717%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4293%; gnomAD_G_NFE: 0.6068%; gnomAD_G_OTH: 0.2041%

Other passed variants:

INTERGENIC_VARIANT chr18:g.79018697A>G [0/1] rs539952391 (variation viewer)

Variant score: 0.038

Transcripts:: SALL3:ENST00000537592.6::

Pathogenicity Data:: Best Score: 0.04082024; CADD: 0.041 (0.181)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.1497%; UK10K: 0.3042%; gnomAD_G_AFR: 0.0689%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4014%; gnomAD_G_NFE: 0.2272%; gnomAD_G_OTH: 0.3061%

INTERGENIC_VARIANT chr18:g.79007286G>C [0/1] rs113551876 (variation viewer)

Variant score: 0.034

Transcripts:: SALL3:ENST00000537592.6::

Pathogenicity Data:: Best Score: 0.038387716; CADD: 0.038 (0.170)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.2867%; UK10K: 0.6215%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.4293%; gnomAD_G_NFE: 0.4066%; gnomAD_G_OTH: 0.2037%

TET2

Exomiser Score: 0.010

Phenotype Score: 0.252

Variant Score: 0.666

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:614286 Myelodysplastic syndrome, somatic - somatic; ORPHA:3318 Essential thrombocythemia; ORPHA:729 Polycythemia vera; ORPHA:824 Primary myelofibrosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.008

Phenotype Score: 0.252

Variant Score: 0.632

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105244584A>ATCTTTTTTT [0|1]

Variant score: 0.632 CONTRIBUTING VARIANT

Transcripts:: TET2:ENST00000380013.8:c.3803+806_3803+807insTCTTTTTTT:p.(=); TET2:ENST00000513237.5:c.3866+806_3866+807insTCTTTTTTT:p.(=); TET2:ENST00000540549.5:c.3803+806_3803+807insTCTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.6322099; CADD: 0.632 (4.344)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.252

Variant Score: 0.666

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105205000A>C [0/1] rs577553810 (variation viewer)

Variant score: 0.699 CONTRIBUTING VARIANT

Transcripts:: TET2:ENST00000513237.5:c.17+14514A>C:p.(=); TET2:ENST00000305737.6:c.-47+14495A>C:p.(=); TET2:ENST00000380013.8:c.-47+14495A>C:p.(=); TET2:ENST00000413648.2:c.-46-28897A>C:p.(=); TET2:ENST00000540549.5:c.-47+14514A>C:p.(=)

Pathogenicity Data:: Best Score: 0.75339603; CADD: 0.753 (6.080)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.2071%; UK10K: 0.3174%; gnomAD_G_AFR: 0.0573%; gnomAD_G_FIN: 0.3177%; gnomAD_G_NFE: 0.4269%; gnomAD_G_OTH: 0.4082%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105244584A>ATCTTTTTTT [0|1]

Variant score: 0.632 CONTRIBUTING VARIANT

Transcripts:: TET2:ENST00000380013.8:c.3803+806_3803+807insTCTTTTTTT:p.(=); TET2:ENST00000513237.5:c.3866+806_3866+807insTCTTTTTTT:p.(=); TET2:ENST00000540549.5:c.3803+806_3803+807insTCTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.6322099; CADD: 0.632 (4.344)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr4:g.105291067G>GA [0/1] rs1234584564 (variation viewer)

Variant score: 0.606

Transcripts:: TET2:ENST00000540549.5::

Pathogenicity Data:: Best Score: 0.6169107; CADD: 0.617 (4.167)

Frequency Data:: gnomAD_G_AMR: 0.1214%; gnomAD_G_FIN: 0.0324%; gnomAD_G_NFE: 0.0698%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105231711G>T [0|1] rs552099118 (variation viewer)

Variant score: 0.502

Transcripts:: TET2:ENST00000513237.5:c.18-2186G>T:p.(=); TET2:ENST00000305737.6:c.-46-2186G>T:p.(=); TET2:ENST00000380013.8:c.-46-2186G>T:p.(=); TET2:ENST00000413648.2:c.-46-2186G>T:p.(=); TET2:ENST00000540549.5:c.-46-2186G>T:p.(=)

Pathogenicity Data:: Best Score: 0.54090774; CADD: 0.541 (3.381)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.2063%; UK10K: 0.3174%; gnomAD_G_AFR: 0.0573%; gnomAD_G_FIN: 0.3170%; gnomAD_G_NFE: 0.4283%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105227058G>A [0/1] rs115216836 (variation viewer)

Variant score: 0.425

Transcripts:: TET2:ENST00000513237.5:c.18-6839G>A:p.(=); TET2:ENST00000305737.6:c.-46-6839G>A:p.(=); TET2:ENST00000380013.8:c.-46-6839G>A:p.(=); TET2:ENST00000413648.2:c.-46-6839G>A:p.(=); TET2:ENST00000540549.5:c.-46-6839G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5102212; CADD: 0.510 (3.100)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.5216%; UK10K: 0.7670%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.8018%; gnomAD_G_NFE: 0.7000%; gnomAD_G_OTH: 0.7128%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105224684G>GTCTCTCTCTCTCTC [-/1] rs34870510 (variation viewer)

Variant score: 0.206

Transcripts:: TET2:ENST00000513237.5:c.18-9213_18-9212insTCTCTCTCTCTCTC:p.(=); TET2:ENST00000305737.6:c.-46-9213_-46-9212insTCTCTCTCTCTCTC:p.(=); TET2:ENST00000380013.8:c.-46-9213_-46-9212insTCTCTCTCTCTCTC:p.(=); TET2:ENST00000413648.2:c.-46-9213_-46-9212insTCTCTCTCTCTCTC:p.(=); TET2:ENST00000540549.5:c.-46-9213_-46-9212insTCTCTCTCTCTCTC:p.(=)

Pathogenicity Data:: Best Score: 0.20640302; CADD: 0.206 (1.004)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105225185C>CGTGTGTGTGTGT [0/1] rs79864807 (variation viewer)

Variant score: 0.142

Transcripts:: TET2:ENST00000513237.5:c.18-8712_18-8711insGTGTGTGTGTGT:p.(=); TET2:ENST00000305737.6:c.-46-8712_-46-8711insGTGTGTGTGTGT:p.(=); TET2:ENST00000380013.8:c.-46-8712_-46-8711insGTGTGTGTGTGT:p.(=); TET2:ENST00000413648.2:c.-46-8712_-46-8711insGTGTGTGTGTGT:p.(=); TET2:ENST00000540549.5:c.-46-8712_-46-8711insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.14197487; CADD: 0.142 (0.665)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105228143G>A [0/1] rs184123454 (variation viewer)

Variant score: 0.085

Transcripts:: TET2:ENST00000513237.5:c.18-5754G>A:p.(=); TET2:ENST00000305737.6:c.-46-5754G>A:p.(=); TET2:ENST00000380013.8:c.-46-5754G>A:p.(=); TET2:ENST00000413648.2:c.-46-5754G>A:p.(=); TET2:ENST00000540549.5:c.-46-5754G>A:p.(=)

Pathogenicity Data:: Best Score: 0.10133052; CADD: 0.101 (0.464)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4077%; UK10K: 0.7802%; gnomAD_G_AFR: 0.1261%; gnomAD_G_FIN: 0.3152%; gnomAD_G_NFE: 0.6409%; gnomAD_G_OTH: 0.5092%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105247714CT>C [0/1] rs1206510081 (variation viewer)

Variant score: 0.047

Transcripts:: TET2:ENST00000380013.8:c.3803+3937del:p.(=); TET2:ENST00000513237.5:c.3866+3937del:p.(=); TET2:ENST00000540549.5:c.3803+3937del:p.(=)

Pathogenicity Data:: Best Score: 0.04720384; CADD: 0.047 (0.210)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.105257361T>G [0/1] rs187975676 (variation viewer)

Variant score: 0.013

Transcripts:: TET2:ENST00000380013.8:c.3804-2258T>G:p.(=); TET2:ENST00000513237.5:c.3867-2258T>G:p.(=); TET2:ENST00000540549.5:c.3804-2258T>G:p.(=)

Pathogenicity Data:: Best Score: 0.014855385; CADD: 0.015 (0.065)

Frequency Data:: 1000Genomes: 0.2796%; TOPMed: 0.4101%; UK10K: 0.7405%; gnomAD_G_AFR: 0.1147%; gnomAD_G_FIN: 0.3150%; gnomAD_G_NFE: 0.6333%; gnomAD_G_OTH: 0.5092%

EDN1

Exomiser Score: 0.010

Phenotype Score: 0.507

Variant Score: 0.376

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612798 Question mark ears, isolated - autosomal dominant; OMIM:615706 Auriculocondylar syndrome 3 - autosomal recessive; ORPHA:137888 Auriculocondylar syndrome; ORPHA:137888 Auriculocondylar syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.507

Variant Score: 0.316

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr6:g.12287688C>CCTCT [0/1] rs757039157 (variation viewer)

Variant score: 0.316 CONTRIBUTING VARIANT

Transcripts:: EDN1:ENST00000379375.6::; EDN1:ENST00000379388.7::

Pathogenicity Data:: Best Score: 0.31608832; CADD: 0.316 (1.650)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.507

Variant Score: 0.376

Variants contributing to score:

INTERGENIC_VARIANT chr6:g.12275959G>A [0/1] rs185616679 (variation viewer)

Variant score: 0.436 CONTRIBUTING VARIANT

Transcripts:: EDN1:ENST00000379375.6::; EDN1:ENST00000379388.7::

Pathogenicity Data:: Best Score: 0.4604894; CADD: 0.460 (2.680)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.2158%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0576%; gnomAD_G_AMR: 0.2404%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0618%; gnomAD_G_NFE: 0.2681%; gnomAD_G_OTH: 0.1020%

UPSTREAM_GENE_VARIANT chr6:g.12287688C>CCTCT [0/1] rs757039157 (variation viewer)

Variant score: 0.316 CONTRIBUTING VARIANT

Transcripts:: EDN1:ENST00000379375.6::; EDN1:ENST00000379388.7::

Pathogenicity Data:: Best Score: 0.31608832; CADD: 0.316 (1.650)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr6:g.12287712TCACA>T [0/1] rs66467626 (variation viewer)

Variant score: 0.243

Transcripts:: EDN1:ENST00000379375.6::; EDN1:ENST00000379388.7::

Pathogenicity Data:: Best Score: 0.24334133; CADD: 0.243 (1.211)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr6:g.12278030T>C [0/1] rs189282483 (variation viewer)

Variant score: 0.160

Transcripts:: EDN1:ENST00000379375.6::; EDN1:ENST00000379388.7::

Pathogenicity Data:: Best Score: 0.3743953; CADD: 0.374 (2.037)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.3409%; UK10K: 0.4099%; gnomAD_G_AFR: 0.0916%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.3465%; gnomAD_G_OTH: 0.2037%

UPSTREAM_GENE_VARIANT chr6:g.12287714A>* [-/1]

Variant score: 0.000

Transcripts:: EDN1:ENST00000379375.6::; EDN1:ENST00000379388.7::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

COPG1

Exomiser Score: 0.010

Phenotype Score: 0.504

Variant Score: 0.377

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.010

Phenotype Score: 0.504

Variant Score: 0.377

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.129232892A>ATATATATATT [-/1] rs56016257 (variation viewer)

Variant score: 0.377 CONTRIBUTING VARIANT

Transcripts:: COPG1:ENST00000314797.10::; COPG1:ENST00000464146.1::

Pathogenicity Data:: Best Score: 0.37669587; CADD: 0.377 (2.053)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.504

Variant Score: 0.377

Variants contributing to score:

INTERGENIC_VARIANT chr3:g.129232892A>ATATATATATT [-/1] rs56016257 (variation viewer)

Variant score: 0.377 CONTRIBUTING VARIANT

Transcripts:: COPG1:ENST00000314797.10::; COPG1:ENST00000464146.1::

Pathogenicity Data:: Best Score: 0.37669587; CADD: 0.377 (2.053)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.129232892A>ATATATATTTT [-/1] rs56016257 (variation viewer)

Variant score: 0.377 CONTRIBUTING VARIANT

Transcripts:: COPG1:ENST00000314797.10::; COPG1:ENST00000464146.1::

Pathogenicity Data:: Best Score: 0.37669587; CADD: 0.377 (2.053)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.129267397G>A [0/1] rs190691059 (variation viewer)

Variant score: 0.282

Transcripts:: COPG1:ENST00000314797.10:c.1544+298G>A:p.(=)

Pathogenicity Data:: Best Score: 0.32329404; CADD: 0.323 (1.696)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.3544%; UK10K: 0.6612%; gnomAD_G_AFR: 0.1261%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.2005%; gnomAD_G_NFE: 0.4268%; gnomAD_G_OTH: 0.2041%

APOL6

Exomiser Score: 0.010

Phenotype Score: 0.503

Variant Score: 0.377

Phenotype matches:

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.124

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.35684314A>AGTGTGTGTGTGT [-/1] rs60246428 (variation viewer)

Variant score: 0.124 CONTRIBUTING VARIANT

Transcripts:: APOL6:ENST00000409652.5::; APOL6:ENST00000415961.2::

Pathogenicity Data:: Best Score: 0.123806536; CADD: 0.124 (0.574)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.503

Variant Score: 0.377

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.35633685G>A [1|1] rs889842936 (variation viewer)

Variant score: 0.377 CONTRIBUTING VARIANT

Transcripts:: APOL6:ENST00000409652.5::

Pathogenicity Data:: Best Score: 0.37683934; CADD: 0.377 (2.054)

Frequency Data:: TOPMed: 0.0048%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.35652084G>A [0/1] rs370175184 (variation viewer)

Variant score: 0.216

Transcripts:: APOL6:ENST00000409652.5:c.-48+3461G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3815565; CADD: 0.382 (2.087)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 0.7542%; gnomAD_G_AFR: 0.2294%; gnomAD_G_AMR: 0.7212%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 0.9164%; gnomAD_G_NFE: 1.1351%; gnomAD_G_OTH: 1.4374%

MYO1C

Exomiser Score: 0.010

Phenotype Score: 0.513

Variant Score: 0.365

Phenotype matches:

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.513

Variant Score: 0.042

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.1466153CT>C [0/1] rs71148490 (variation viewer)

Variant score: 0.042 CONTRIBUTING VARIANT

Transcripts:: MYO1C:ENST00000361007.7:c.3061-402del:p.(=); MYO1C:ENST00000545534.6:c.3094-402del:p.(=); MYO1C:ENST00000570984.7:c.3061-402del:p.(=); MYO1C:ENST00000575158.5:c.3061-402del:p.(=); MYO1C:ENST00000646049.1:c.3061-402del:p.(=); MYO1C:ENST00000648446.1:c.3109-402del:p.(=); MYO1C:ENST00000648651.1:c.3166-402del:p.(=)

Pathogenicity Data:: Best Score: 0.041703284; CADD: 0.042 (0.185)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.513

Variant Score: 0.365

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.1488470C>T [0/1] rs150076236 (variation viewer)

Variant score: 0.542 CONTRIBUTING VARIANT

Transcripts:: MYO1C:ENST00000648651.1:c.75+3943G>A:p.(=); MYO1C:ENST00000361007.7:c.-31+3130G>A:p.(=); MYO1C:ENST00000570984.7:c.-31+3540G>A:p.(=); MYO1C:ENST00000646049.1:c.-177-1372G>A:p.(=)

Pathogenicity Data:: Best Score: 0.87332237; CADD: 0.873 (8.973)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.9573%; UK10K: 1.3356%; gnomAD_G_AFR: 0.2980%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.1146%; gnomAD_G_NFE: 1.0874%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.1473946T>C [0/1] rs150120170 (variation viewer)

Variant score: 0.188 CONTRIBUTING VARIANT

Transcripts:: MYO1C:ENST00000361007.7:c.1692+664A>G:p.(=); MYO1C:ENST00000545534.6:c.1725+664A>G:p.(=); MYO1C:ENST00000570984.7:c.1692+664A>G:p.(=); MYO1C:ENST00000575158.5:c.1692+664A>G:p.(=); MYO1C:ENST00000646049.1:c.1692+664A>G:p.(=); MYO1C:ENST00000648446.1:c.1740+664A>G:p.(=); MYO1C:ENST00000648651.1:c.1797+664A>G:p.(=)

Pathogenicity Data:: Best Score: 0.19869107; CADD: 0.199 (0.962)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0844%; UK10K: 0.0529%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0667%; gnomAD_G_OTH: 0.1020%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.1478307G>A [0/1] rs113518060 (variation viewer)

Variant score: 0.057

Transcripts:: MYO1C:ENST00000361007.7:c.1190+103C>T:p.(=); MYO1C:ENST00000545534.6:c.1223+103C>T:p.(=); MYO1C:ENST00000570984.7:c.1190+103C>T:p.(=); MYO1C:ENST00000575158.5:c.1190+103C>T:p.(=); MYO1C:ENST00000646049.1:c.1190+103C>T:p.(=); MYO1C:ENST00000648446.1:c.1238+103C>T:p.(=); MYO1C:ENST00000648651.1:c.1295+103C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0820902; CADD: 0.082 (0.372)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.2596%; UK10K: 0.0529%; gnomAD_G_AFR: 1.1711%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0801%; gnomAD_G_OTH: 0.2041%

YWHAH

Exomiser Score: 0.010

Phenotype Score: 0.501

Variant Score: 0.374

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.010

Phenotype Score: 0.501

Variant Score: 0.374

Variants contributing to score:

INTERGENIC_VARIANT chr22:g.31968274C>T [0/1] rs62240610 (variation viewer)

Variant score: 0.465 CONTRIBUTING VARIANT

Transcripts:: YWHAH:ENST00000248975.6::; YWHAH:ENST00000423610.1::

Pathogenicity Data:: Best Score: 0.93017673; CADD: 0.930 (11.560)

Frequency Data:: 1000Genomes: 0.3594%; TOPMed: 0.6650%; UK10K: 0.9257%; gnomAD_G_AFR: 0.1263%; gnomAD_G_AMR: 0.4785%; gnomAD_G_EAS: 0.0618%; gnomAD_G_FIN: 1.5473%; gnomAD_G_NFE: 0.9366%; gnomAD_G_OTH: 1.4315%

INTERGENIC_VARIANT chr22:g.31965664A>G [0/1] rs193103256 (variation viewer)

Variant score: 0.283 CONTRIBUTING VARIANT

Transcripts:: YWHAH:ENST00000248975.6::; YWHAH:ENST00000423610.1::

Pathogenicity Data:: Best Score: 0.6629456; CADD: 0.663 (4.723)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.8251%; UK10K: 1.1373%; gnomAD_G_AFR: 0.1605%; gnomAD_G_AMR: 0.7229%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 1.6558%; gnomAD_G_NFE: 1.0897%; gnomAD_G_OTH: 1.6529%

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr22:g.31957876A>G [0/1] rs150753294 (variation viewer)

Variant score: 0.174

Transcripts:: YWHAH:ENST00000248975.6::; YWHAH:ENST00000423610.1::

Pathogenicity Data:: Best Score: 0.78432494; CADD: 0.784 (6.662)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.6355%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1260%; gnomAD_G_AMR: 1.9093%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.1432%; gnomAD_G_NFE: 0.6862%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.31951073A>C [0/1] rs2853885 (variation viewer)

Variant score: 0.112

Transcripts:: YWHAH:ENST00000248975.6:c.88-5066A>C:p.(=); YWHAH:ENST00000397492.1:c.202+651A>C:p.(=); YWHAH:ENST00000646701.1:c.1787-5066A>C:p.(=)

Pathogenicity Data:: Best Score: 0.3910243; CADD: 0.391 (2.154)

Frequency Data:: 1000Genomes: 0.7388%; TOPMed: 1.0450%; UK10K: 1.3621%; gnomAD_G_AFR: 0.1835%; gnomAD_G_AMR: 0.9547%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.3708%; gnomAD_G_FIN: 1.4310%; gnomAD_G_NFE: 1.3098%; gnomAD_G_OTH: 1.8367%

INTERGENIC_VARIANT chr22:g.31968837G>GCACACA [-/1] rs112884636 (variation viewer)

Variant score: 0.098

Transcripts:: YWHAH:ENST00000248975.6::; YWHAH:ENST00000423610.1::

Pathogenicity Data:: Best Score: 0.21041298; CADD: 0.210 (1.026)

Frequency Data:: gnomAD_G_AFR: 0.1290%; gnomAD_G_AMR: 0.5155%; gnomAD_G_ASJ: 1.3889%; gnomAD_G_EAS: 0.2500%; gnomAD_G_FIN: 1.5575%; gnomAD_G_NFE: 0.9305%; gnomAD_G_OTH: 1.5991%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.31949902A>G [0/1] rs62240583 (variation viewer)

Variant score: 0.097

Transcripts:: YWHAH:ENST00000248975.6:c.87+5082A>G:p.(=); YWHAH:ENST00000397492.1:c.88-406A>G:p.(=); YWHAH:ENST00000646701.1:c.1787-6237A>G:p.(=)

Pathogenicity Data:: Best Score: 0.22482455; CADD: 0.225 (1.106)

Frequency Data:: 1000Genomes: 0.7388%; TOPMed: 1.0250%; UK10K: 1.3621%; gnomAD_G_AFR: 0.1836%; gnomAD_G_AMR: 0.8537%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0620%; gnomAD_G_FIN: 1.4828%; gnomAD_G_NFE: 1.3061%; gnomAD_G_OTH: 1.6495%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.31955599C>T [0/1] rs2858754 (variation viewer)

Variant score: 0.044

Transcripts:: YWHAH:ENST00000248975.6:c.88-540C>T:p.(=); YWHAH:ENST00000397492.1:c.203-540C>T:p.(=); YWHAH:ENST00000646701.1:c.1787-540C>T:p.(=)

Pathogenicity Data:: Best Score: 0.15218711; CADD: 0.152 (0.717)

Frequency Data:: 1000Genomes: 0.7388%; TOPMed: 1.0190%; UK10K: 1.3621%; gnomAD_G_AFR: 0.1835%; gnomAD_G_AMR: 0.9569%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.4360%; gnomAD_G_NFE: 1.3158%; gnomAD_G_OTH: 1.8330%

DOWNSTREAM_GENE_VARIANT chr22:g.31959028CTG>C [0/1] rs201552933 (variation viewer)

Variant score: 0.030

Transcripts:: YWHAH:ENST00000248975.6::; YWHAH:ENST00000423610.1::

Pathogenicity Data:: Best Score: 0.106900156; CADD: 0.107 (0.491)

Frequency Data:: UK10K: 1.3621%; gnomAD_G_AFR: 0.1844%; gnomAD_G_AMR: 0.8353%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.4048%; gnomAD_G_NFE: 1.2877%; gnomAD_G_OTH: 1.8405%

AGO2

Exomiser Score: 0.009

Phenotype Score: 0.510

Variant Score: 0.363

Phenotype matches:

Proximity score 0.510 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.009

Phenotype Score: 0.510

Variant Score: 0.363

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.140607458TTATATA>T [-/1] rs1167371585 (variation viewer)

Variant score: 0.363 CONTRIBUTING VARIANT

Transcripts:: AGO2:ENST00000220592.10:c.23-22153_23-22148del:p.(=); AGO2:ENST00000519980.5:c.23-22153_23-22148del:p.(=)

Pathogenicity Data:: Best Score: 0.36261773; CADD: 0.363 (1.956)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.510

Variant Score: 0.274

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.140607458TTATATA>T [-/1] rs1167371585 (variation viewer)

Variant score: 0.363 CONTRIBUTING VARIANT

Transcripts:: AGO2:ENST00000220592.10:c.23-22153_23-22148del:p.(=); AGO2:ENST00000519980.5:c.23-22153_23-22148del:p.(=)

Pathogenicity Data:: Best Score: 0.36261773; CADD: 0.363 (1.956)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.140554838C>T [0/1] rs554545035 (variation viewer)

Variant score: 0.186 CONTRIBUTING VARIANT

Transcripts:: AGO2:ENST00000220592.10:c.1269+1058G>A:p.(=); AGO2:ENST00000519980.5:c.1269+1058G>A:p.(=)

Pathogenicity Data:: Best Score: 0.18829167; CADD: 0.188 (0.906)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0804%; UK10K: 0.0793%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.0802%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.140538146A>G [0/1]

Variant score: 0.183

Transcripts:: AGO2:ENST00000220592.10:c.2169+1174T>C:p.(=); AGO2:ENST00000519980.5:c.2169+1174T>C:p.(=)

Pathogenicity Data:: Best Score: 0.18322957; CADD: 0.183 (0.879)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.140561129C>T [0/1] rs917348342 (variation viewer)

Variant score: 0.044

Transcripts:: AGO2:ENST00000220592.10:c.519-619G>A:p.(=); AGO2:ENST00000519980.5:c.519-619G>A:p.(=)

Pathogenicity Data:: Best Score: 0.043687105; CADD: 0.044 (0.194)

Frequency Data:: TOPMed: 0.0199%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0267%

CSNK2A2

Exomiser Score: 0.009

Phenotype Score: 0.502

Variant Score: 0.371

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.079

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.58171980T>TATATATATATATA [-/1] rs1555505772 (variation viewer)

Variant score: 0.079 CONTRIBUTING VARIANT

Transcripts:: CSNK2A2:ENST00000262506.8:c.429+2470_429+2471insTATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.07933849; CADD: 0.079 (0.359)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.009

Phenotype Score: 0.502

Variant Score: 0.371

Variants contributing to score:

THREE_PRIME_UTR_INTRON_VARIANT chr16:g.58160616A>G [0/1] rs140270481 (variation viewer)

Variant score: 0.663 CONTRIBUTING VARIANT

Transcripts:: CSNK2A2:ENST00000262506.8:c.*18-2263T>C:p.(=)

Pathogenicity Data:: Best Score: 0.98883134; CADD: 0.989 (19.520)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.7406%; UK10K: 1.1902%; gnomAD_G_AFR: 0.2179%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.5438%; gnomAD_G_NFE: 1.2348%; gnomAD_G_OTH: 1.2220%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.58171980T>TATATATATATATA [-/1] rs1555505772 (variation viewer)

Variant score: 0.079 CONTRIBUTING VARIANT

Transcripts:: CSNK2A2:ENST00000262506.8:c.429+2470_429+2471insTATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.07933849; CADD: 0.079 (0.359)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.58171980T>TATATATATA [-/1] rs71155247 (variation viewer)

Variant score: 0.055

Transcripts:: CSNK2A2:ENST00000262506.8:c.429+2470_429+2471insTATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.08609724; CADD: 0.086 (0.391)

Frequency Data:: gnomAD_G_AFR: 0.9188%; gnomAD_G_AMR: 1.0638%; gnomAD_G_EAS: 1.3043%; gnomAD_G_NFE: 1.2397%; gnomAD_G_OTH: 0.6410%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.58186352G>A [0/1] rs75693881 (variation viewer)

Variant score: 0.000

Transcripts:: CSNK2A2:ENST00000262506.8:c.318+403C>T:p.(=)

Pathogenicity Data:: Best Score: 6.905198E-4; CADD: 0.001 (0.003)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.7382%; UK10K: 1.1637%; gnomAD_G_AFR: 0.2177%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.5152%; gnomAD_G_NFE: 1.1662%; gnomAD_G_OTH: 1.1202%

SMARCA4

Exomiser Score: 0.009

Phenotype Score: 0.252

Variant Score: 0.650

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:613325 Rhabdoid tumor predisposition syndrome 2 (susceptibility); OMIM:614609 Coffin-Siris syndrome 4 - autosomal dominant; ORPHA:1465 Coffin-Siris syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.504

Variant Score: 0.330

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11061201A>AT [0|1] rs1568568601 (variation viewer)

Variant score: 0.330 CONTRIBUTING VARIANT

Transcripts:: SMARCA4:ENST00000344626.9:c.4912-583_4912-582insT:p.(=); SMARCA4:ENST00000413806.7:c.5014-583_5014-582insT:p.(=); SMARCA4:ENST00000429416.8:c.4912-583_4912-582insT:p.(=); SMARCA4:ENST00000444061.8:c.4810-583_4810-582insT:p.(=); SMARCA4:ENST00000450717.7:c.5008-583_5008-582insT:p.(=); SMARCA4:ENST00000541122.6:c.4822-583_4822-582insT:p.(=); SMARCA4:ENST00000589677.5:c.4819-583_4819-582insT:p.(=); SMARCA4:ENST00000590574.6:c.4813-583_4813-582insT:p.(=); SMARCA4:ENST00000642628.1:c.4909-583_4909-582insT:p.(=); SMARCA4:ENST00000642726.1:c.4909-583_4909-582insT:p.(=); SMARCA4:ENST00000643296.1:c.4822-583_4822-582insT:p.(=); SMARCA4:ENST00000643549.1:c.4918-583_4918-582insT:p.(=); SMARCA4:ENST00000644737.1:c.4822-583_4822-582insT:p.(=); SMARCA4:ENST00000645460.1:c.4810-583_4810-582insT:p.(=); SMARCA4:ENST00000646484.1:c.4813-583_4813-582insT:p.(=); SMARCA4:ENST00000646510.1:c.4813-583_4813-582insT:p.(=); SMARCA4:ENST00000646693.1:c.5008-583_5008-582insT:p.(=); SMARCA4:ENST00000647230.1:c.4813-583_4813-582insT:p.(=)

Pathogenicity Data:: Best Score: 0.32980686; CADD: 0.330 (1.738)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.009

Phenotype Score: 0.252

Variant Score: 0.650

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11061204A>T [1/1] rs12976723 (variation viewer)

Variant score: 0.650 CONTRIBUTING VARIANT

Transcripts:: SMARCA4:ENST00000344626.9:c.4912-580A>T:p.(=); SMARCA4:ENST00000413806.7:c.5014-580A>T:p.(=); SMARCA4:ENST00000429416.8:c.4912-580A>T:p.(=); SMARCA4:ENST00000444061.8:c.4810-580A>T:p.(=); SMARCA4:ENST00000450717.7:c.5008-580A>T:p.(=); SMARCA4:ENST00000541122.6:c.4822-580A>T:p.(=); SMARCA4:ENST00000589677.5:c.4819-580A>T:p.(=); SMARCA4:ENST00000590574.6:c.4813-580A>T:p.(=); SMARCA4:ENST00000642628.1:c.4909-580A>T:p.(=); SMARCA4:ENST00000642726.1:c.4909-580A>T:p.(=); SMARCA4:ENST00000643296.1:c.4822-580A>T:p.(=); SMARCA4:ENST00000643549.1:c.4918-580A>T:p.(=); SMARCA4:ENST00000644737.1:c.4822-580A>T:p.(=); SMARCA4:ENST00000645460.1:c.4810-580A>T:p.(=); SMARCA4:ENST00000646484.1:c.4813-580A>T:p.(=); SMARCA4:ENST00000646510.1:c.4813-580A>T:p.(=); SMARCA4:ENST00000646693.1:c.5008-580A>T:p.(=); SMARCA4:ENST00000647230.1:c.4813-580A>T:p.(=)

Pathogenicity Data:: Best Score: 0.6502965; CADD: 0.650 (4.563)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11061202A>ATAT [0|1] rs1467232116 (variation viewer)

Variant score: 0.318

Transcripts:: SMARCA4:ENST00000344626.9:c.4912-582_4912-581insTAT:p.(=); SMARCA4:ENST00000413806.7:c.5014-582_5014-581insTAT:p.(=); SMARCA4:ENST00000429416.8:c.4912-582_4912-581insTAT:p.(=); SMARCA4:ENST00000444061.8:c.4810-582_4810-581insTAT:p.(=); SMARCA4:ENST00000450717.7:c.5008-582_5008-581insTAT:p.(=); SMARCA4:ENST00000541122.6:c.4822-582_4822-581insTAT:p.(=); SMARCA4:ENST00000589677.5:c.4819-582_4819-581insTAT:p.(=); SMARCA4:ENST00000590574.6:c.4813-582_4813-581insTAT:p.(=); SMARCA4:ENST00000642628.1:c.4909-582_4909-581insTAT:p.(=); SMARCA4:ENST00000642726.1:c.4909-582_4909-581insTAT:p.(=); SMARCA4:ENST00000643296.1:c.4822-582_4822-581insTAT:p.(=); SMARCA4:ENST00000643549.1:c.4918-582_4918-581insTAT:p.(=); SMARCA4:ENST00000644737.1:c.4822-582_4822-581insTAT:p.(=); SMARCA4:ENST00000645460.1:c.4810-582_4810-581insTAT:p.(=); SMARCA4:ENST00000646484.1:c.4813-582_4813-581insTAT:p.(=); SMARCA4:ENST00000646510.1:c.4813-582_4813-581insTAT:p.(=); SMARCA4:ENST00000646693.1:c.5008-582_5008-581insTAT:p.(=); SMARCA4:ENST00000647230.1:c.4813-582_4813-581insTAT:p.(=)

Pathogenicity Data:: Best Score: 0.31750417; CADD: 0.318 (1.659)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.10966130C>T [0/1] rs896214818 (variation viewer)

Variant score: 0.209

Transcripts:: SMARCA4:ENST00000344626.9:c.-32+4956C>T:p.(=); SMARCA4:ENST00000429416.8:c.-108+4956C>T:p.(=); SMARCA4:ENST00000444061.8:c.-29+821C>T:p.(=); SMARCA4:ENST00000541122.6:c.-192+4956C>T:p.(=); SMARCA4:ENST00000589677.5:c.-261+4956C>T:p.(=); SMARCA4:ENST00000590574.6:c.-29+4401C>T:p.(=); SMARCA4:ENST00000642628.1:c.-32+4956C>T:p.(=); SMARCA4:ENST00000642726.1:c.-29+4956C>T:p.(=); SMARCA4:ENST00000643296.1:c.-32+4956C>T:p.(=); SMARCA4:ENST00000643549.1:c.-29+4956C>T:p.(=); SMARCA4:ENST00000644737.1:c.-29+4956C>T:p.(=); SMARCA4:ENST00000645460.1:c.-29+4956C>T:p.(=); SMARCA4:ENST00000646484.1:c.-29+4956C>T:p.(=); SMARCA4:ENST00000646510.1:c.-108+4956C>T:p.(=); SMARCA4:ENST00000646693.1:c.-29+4956C>T:p.(=); SMARCA4:ENST00000647230.1:c.-32+4956C>T:p.(=)

Pathogenicity Data:: Best Score: 0.20968539; CADD: 0.210 (1.022)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

INTERGENIC_VARIANT chr19:g.11068083G>GTA [-/1] rs74180007 (variation viewer)

Variant score: 0.140

Transcripts:: SMARCA4:ENST00000644737.1::; SMARCA4:ENST00000557933.5::

Pathogenicity Data:: Best Score: 0.1403929; CADD: 0.140 (0.657)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr19:g.10951637T>C [0/1] rs549482472 (variation viewer)

Variant score: 0.140

Transcripts:: SMARCA4:ENST00000344626.9::; SMARCA4:ENST00000270502.7::

Pathogenicity Data:: Best Score: 0.16092652; CADD: 0.161 (0.762)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0462%; gnomAD_G_AFR: 0.0230%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_NFE: 0.0201%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11009007C>CTTT [0/1] rs762148337 (variation viewer)

Variant score: 0.140

Transcripts:: SMARCA4:ENST00000344626.9:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000413806.7:c.2315+984_2315+985insTTT:p.(=); SMARCA4:ENST00000429416.8:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000444061.8:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000450717.7:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000541122.6:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000589677.5:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000590574.6:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000642628.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000642726.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000643296.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000643549.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000644737.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000645460.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000646484.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000646510.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000646693.1:c.2123+984_2123+985insTTT:p.(=); SMARCA4:ENST00000647230.1:c.2123+984_2123+985insTTT:p.(=)

Pathogenicity Data:: Best Score: 0.13960081; CADD: 0.140 (0.653)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.10968379A>G [0/1] rs12979487 (variation viewer)

Variant score: 0.135

Transcripts:: SMARCA4:ENST00000344626.9:c.-32+7205A>G:p.(=); SMARCA4:ENST00000429416.8:c.-108+7205A>G:p.(=); SMARCA4:ENST00000444061.8:c.-29+3070A>G:p.(=); SMARCA4:ENST00000541122.6:c.-192+7205A>G:p.(=); SMARCA4:ENST00000589677.5:c.-261+7205A>G:p.(=); SMARCA4:ENST00000590574.6:c.-29+6650A>G:p.(=); SMARCA4:ENST00000642628.1:c.-32+7205A>G:p.(=); SMARCA4:ENST00000642726.1:c.-29+7205A>G:p.(=); SMARCA4:ENST00000643296.1:c.-32+7205A>G:p.(=); SMARCA4:ENST00000643549.1:c.-29+7205A>G:p.(=); SMARCA4:ENST00000644737.1:c.-29+7205A>G:p.(=); SMARCA4:ENST00000645460.1:c.-29+7205A>G:p.(=); SMARCA4:ENST00000646484.1:c.-29+7205A>G:p.(=); SMARCA4:ENST00000646510.1:c.-108+7205A>G:p.(=); SMARCA4:ENST00000646693.1:c.-29+7205A>G:p.(=); SMARCA4:ENST00000647230.1:c.-32+7205A>G:p.(=)

Pathogenicity Data:: Best Score: 0.34596646; CADD: 0.346 (1.844)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 1.1240%; UK10K: 1.7059%; gnomAD_G_AFR: 0.2178%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.9450%; gnomAD_G_NFE: 1.6346%; gnomAD_G_OTH: 1.5337%

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.10964147T>C [0/1] rs1016151958 (variation viewer)

Variant score: 0.108

Transcripts:: SMARCA4:ENST00000344626.9:c.-32+2973T>C:p.(=); SMARCA4:ENST00000429416.8:c.-108+2973T>C:p.(=); SMARCA4:ENST00000444061.8:c.-31-1160T>C:p.(=); SMARCA4:ENST00000541122.6:c.-192+2973T>C:p.(=); SMARCA4:ENST00000589677.5:c.-261+2973T>C:p.(=); SMARCA4:ENST00000590574.6:c.-29+2418T>C:p.(=); SMARCA4:ENST00000642628.1:c.-32+2973T>C:p.(=); SMARCA4:ENST00000642726.1:c.-29+2973T>C:p.(=); SMARCA4:ENST00000643296.1:c.-32+2973T>C:p.(=); SMARCA4:ENST00000643549.1:c.-29+2973T>C:p.(=); SMARCA4:ENST00000644737.1:c.-29+2973T>C:p.(=); SMARCA4:ENST00000645460.1:c.-29+2973T>C:p.(=); SMARCA4:ENST00000646484.1:c.-29+2973T>C:p.(=); SMARCA4:ENST00000646510.1:c.-108+2973T>C:p.(=); SMARCA4:ENST00000646693.1:c.-29+2973T>C:p.(=); SMARCA4:ENST00000647230.1:c.-32+2973T>C:p.(=)

Pathogenicity Data:: Best Score: 0.10977453; CADD: 0.110 (0.505)

Frequency Data:: gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0134%; gnomAD_G_OTH: 0.1025%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11046948C>CA [0/1] rs758955559 (variation viewer)

Variant score: 0.081

Transcripts:: SMARCA4:ENST00000344626.9:c.4424+5388_4424+5389insA:p.(=); SMARCA4:ENST00000413806.7:c.4526+5388_4526+5389insA:p.(=); SMARCA4:ENST00000429416.8:c.4424+5388_4424+5389insA:p.(=); SMARCA4:ENST00000444061.8:c.4325+5388_4325+5389insA:p.(=); SMARCA4:ENST00000450717.7:c.4520+5388_4520+5389insA:p.(=); SMARCA4:ENST00000541122.6:c.4334+5388_4334+5389insA:p.(=); SMARCA4:ENST00000589677.5:c.4334+5388_4334+5389insA:p.(=); SMARCA4:ENST00000590574.6:c.4325+5388_4325+5389insA:p.(=); SMARCA4:ENST00000642628.1:c.4421+5388_4421+5389insA:p.(=); SMARCA4:ENST00000642726.1:c.4421+5388_4421+5389insA:p.(=); SMARCA4:ENST00000643296.1:c.4334+5388_4334+5389insA:p.(=); SMARCA4:ENST00000643549.1:c.4430+5388_4430+5389insA:p.(=); SMARCA4:ENST00000644737.1:c.4334+5388_4334+5389insA:p.(=); SMARCA4:ENST00000645460.1:c.4325+5388_4325+5389insA:p.(=); SMARCA4:ENST00000646484.1:c.4325+5388_4325+5389insA:p.(=); SMARCA4:ENST00000646510.1:c.4325+5388_4325+5389insA:p.(=); SMARCA4:ENST00000646693.1:c.4520+5388_4520+5389insA:p.(=); SMARCA4:ENST00000647230.1:c.4325+5388_4325+5389insA:p.(=)

Pathogenicity Data:: Best Score: 0.12239313; CADD: 0.122 (0.567)

Frequency Data:: gnomAD_G_AFR: 1.2517%; gnomAD_G_AMR: 0.8333%; gnomAD_G_EAS: 1.0496%; gnomAD_G_FIN: 0.4000%; gnomAD_G_NFE: 0.4959%; gnomAD_G_OTH: 0.8523%

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.10974692T>A [1/1] rs57692497 (variation viewer)

Variant score: 0.076

Transcripts:: SMARCA4:ENST00000344626.9:c.-31-9429T>A:p.(=); SMARCA4:ENST00000429416.8:c.-107-6085T>A:p.(=); SMARCA4:ENST00000444061.8:c.-29+9383T>A:p.(=); SMARCA4:ENST00000541122.6:c.-191-2961T>A:p.(=); SMARCA4:ENST00000589677.5:c.-260-8788T>A:p.(=); SMARCA4:ENST00000590574.6:c.-28-9432T>A:p.(=); SMARCA4:ENST00000642628.1:c.-31-9429T>A:p.(=); SMARCA4:ENST00000642726.1:c.-28-9432T>A:p.(=); SMARCA4:ENST00000643296.1:c.-31-9429T>A:p.(=); SMARCA4:ENST00000643549.1:c.-28-9432T>A:p.(=); SMARCA4:ENST00000644737.1:c.-28-9432T>A:p.(=); SMARCA4:ENST00000645460.1:c.-28-9432T>A:p.(=); SMARCA4:ENST00000646484.1:c.-28-9432T>A:p.(=); SMARCA4:ENST00000646510.1:c.-107-6085T>A:p.(=); SMARCA4:ENST00000646693.1:c.-28-9432T>A:p.(=); SMARCA4:ENST00000647230.1:c.-31-9429T>A:p.(=)

Pathogenicity Data:: Best Score: 0.5606607; CADD: 0.561 (3.572)

Frequency Data:: gnomAD_G_AFR: 0.3811%; gnomAD_G_AMR: 1.6667%; gnomAD_G_ASJ: 2.0000%; gnomAD_G_EAS: 0.7576%; gnomAD_G_NFE: 0.6186%; gnomAD_G_OTH: 0.8475%

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.10974689AT>A [1/1] rs74182450 (variation viewer)

Variant score: 0.070

Transcripts:: SMARCA4:ENST00000344626.9:c.-31-9431del:p.(=); SMARCA4:ENST00000429416.8:c.-107-6087del:p.(=); SMARCA4:ENST00000444061.8:c.-29+9381del:p.(=); SMARCA4:ENST00000541122.6:c.-191-2963del:p.(=); SMARCA4:ENST00000589677.5:c.-260-8790del:p.(=); SMARCA4:ENST00000590574.6:c.-28-9434del:p.(=); SMARCA4:ENST00000642628.1:c.-31-9431del:p.(=); SMARCA4:ENST00000642726.1:c.-28-9434del:p.(=); SMARCA4:ENST00000643296.1:c.-31-9431del:p.(=); SMARCA4:ENST00000643549.1:c.-28-9434del:p.(=); SMARCA4:ENST00000644737.1:c.-28-9434del:p.(=); SMARCA4:ENST00000645460.1:c.-28-9434del:p.(=); SMARCA4:ENST00000646484.1:c.-28-9434del:p.(=); SMARCA4:ENST00000646510.1:c.-107-6087del:p.(=); SMARCA4:ENST00000646693.1:c.-28-9434del:p.(=); SMARCA4:ENST00000647230.1:c.-31-9431del:p.(=)

Pathogenicity Data:: Best Score: 0.06953508; CADD: 0.070 (0.313)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr19:g.10952250C>G [0/1] rs556447231 (variation viewer)

Variant score: 0.041

Transcripts:: SMARCA4:ENST00000344626.9::; SMARCA4:ENST00000270502.7::

Pathogenicity Data:: Best Score: 0.04720384; CADD: 0.047 (0.210)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0749%; UK10K: 0.0397%; gnomAD_G_AFR: 0.0575%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0402%; gnomAD_G_OTH: 0.1029%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11019496G>A [0/1] rs977055443 (variation viewer)

Variant score: 0.019

Transcripts:: SMARCA4:ENST00000344626.9:c.2506-95G>A:p.(=); SMARCA4:ENST00000413806.7:c.2698-95G>A:p.(=); SMARCA4:ENST00000429416.8:c.2506-95G>A:p.(=); SMARCA4:ENST00000444061.8:c.2506-95G>A:p.(=); SMARCA4:ENST00000450717.7:c.2506-95G>A:p.(=); SMARCA4:ENST00000541122.6:c.2506-95G>A:p.(=); SMARCA4:ENST00000589677.5:c.2506-95G>A:p.(=); SMARCA4:ENST00000590574.6:c.2506-95G>A:p.(=); SMARCA4:ENST00000642628.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000642726.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000643296.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000643549.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000644737.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000645460.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000646484.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000646510.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000646693.1:c.2506-95G>A:p.(=); SMARCA4:ENST00000647230.1:c.2506-95G>A:p.(=)

Pathogenicity Data:: Best Score: 0.018930018; CADD: 0.019 (0.083)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.11058223C>T [0/1] rs371307719 (variation viewer)

Variant score: 0.001

Transcripts:: SMARCA4:ENST00000344626.9:c.4425-32C>T:p.(=); SMARCA4:ENST00000413806.7:c.4527-32C>T:p.(=); SMARCA4:ENST00000429416.8:c.4425-32C>T:p.(=); SMARCA4:ENST00000444061.8:c.4326-35C>T:p.(=); SMARCA4:ENST00000450717.7:c.4521-32C>T:p.(=); SMARCA4:ENST00000541122.6:c.4335-32C>T:p.(=); SMARCA4:ENST00000589677.5:c.4335-35C>T:p.(=); SMARCA4:ENST00000590574.6:c.4326-32C>T:p.(=); SMARCA4:ENST00000642628.1:c.4422-32C>T:p.(=); SMARCA4:ENST00000642726.1:c.4422-32C>T:p.(=); SMARCA4:ENST00000643296.1:c.4335-32C>T:p.(=); SMARCA4:ENST00000643549.1:c.4431-32C>T:p.(=); SMARCA4:ENST00000644737.1:c.4335-32C>T:p.(=); SMARCA4:ENST00000645460.1:c.4326-35C>T:p.(=); SMARCA4:ENST00000646484.1:c.4326-32C>T:p.(=); SMARCA4:ENST00000646510.1:c.4326-32C>T:p.(=); SMARCA4:ENST00000646693.1:c.4521-32C>T:p.(=); SMARCA4:ENST00000647230.1:c.4326-32C>T:p.(=)

Pathogenicity Data:: Best Score: 9.2059374E-4; CADD: 0.001 (0.004)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0167%; ESP AA: 0.0681%; ESP All: 0.0231%; ExAC AFR: 0.0621%; ExAC NFE: 0.0031%; ExAC SAS: 0.0061%; gnomAD_E_AFR: 0.0337%; gnomAD_E_ASJ: 0.0102%; gnomAD_E_NFE: 0.0037%; gnomAD_E_SAS: 0.0033%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1027%

STRADA

Exomiser Score: 0.009

Phenotype Score: 0.501

Variant Score: 0.368

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:611087 Polyhydramnios, megalencephaly, and symptomatic epilepsy - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.251

Variant Score: 0.565

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.63740107T>C [0|1] rs201206946 (variation viewer)

Variant score: 0.565 CONTRIBUTING VARIANT

Transcripts:: STRADA:ENST00000245865.10:c.-190+1634A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5647888; CADD: 0.565 (3.613)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.009

Phenotype Score: 0.501

Variant Score: 0.368

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.63740107T>C [0|1] rs201206946 (variation viewer)

Variant score: 0.565 CONTRIBUTING VARIANT

Transcripts:: STRADA:ENST00000245865.10:c.-190+1634A>G:p.(=)

Pathogenicity Data:: Best Score: 0.5647888; CADD: 0.565 (3.613)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.63708171G>A [0/1] rs573307607 (variation viewer)

Variant score: 0.171 CONTRIBUTING VARIANT

Transcripts:: STRADA:ENST00000245865.10:c.408-753C>T:p.(=); STRADA:ENST00000336174.12:c.582-753C>T:p.(=); STRADA:ENST00000375840.9:c.408-753C>T:p.(=); STRADA:ENST00000392950.9:c.471-753C>T:p.(=); STRADA:ENST00000447001.8:c.450-753C>T:p.(=); STRADA:ENST00000578008.6:c.495-753C>T:p.(=); STRADA:ENST00000578801.6:c.582-1432C>T:p.(=); STRADA:ENST00000579340.5:c.408-1432C>T:p.(=); STRADA:ENST00000582137.6:c.495-753C>T:p.(=); STRADA:ENST00000617949.4:c.408-753C>T:p.(=); STRADA:ENST00000638193.1:c.582-753C>T:p.(=); STRADA:ENST00000638276.1:c.408-753C>T:p.(=); STRADA:ENST00000638309.1:c.582-753C>T:p.(=); STRADA:ENST00000638698.1:c.582-753C>T:p.(=); STRADA:ENST00000638702.1:c.408-753C>T:p.(=); STRADA:ENST00000638708.1:c.495-753C>T:p.(=); STRADA:ENST00000638888.1:c.582-753C>T:p.(=); STRADA:ENST00000639835.1:c.471-753C>T:p.(=); STRADA:ENST00000640086.1:c.471-753C>T:p.(=); STRADA:ENST00000640397.1:c.582-1432C>T:p.(=); STRADA:ENST00000640679.1:c.582-753C>T:p.(=); STRADA:ENST00000640979.1:c.408-753C>T:p.(=); STRADA:ENST00000640999.1:c.471-753C>T:p.(=); STRADA:ENST00000580553.1:c.*496-753C>T:p.(=)

Pathogenicity Data:: Best Score: 0.17110407; CADD: 0.171 (0.815)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0111%; gnomAD_G_NFE: 0.0134%

Other passed variants:

ACER2

Exomiser Score: 0.009

Phenotype Score: 0.505

Variant Score: 0.361

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.009

Phenotype Score: 0.505

Variant Score: 0.361

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr9:g.19453187CTTTTTTTTTTTTTT>C [0/1] rs397894428 (variation viewer)

Variant score: 0.361 CONTRIBUTING VARIANT

Transcripts:: ACER2:ENST00000340967.3::; ACER2:ENST00000417653.2::

Pathogenicity Data:: Best Score: 0.3614425; CADD: 0.361 (1.948)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.343

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr9:g.19453187CTTTTTTTTTTTTTT>C [0/1] rs397894428 (variation viewer)

Variant score: 0.361 CONTRIBUTING VARIANT

Transcripts:: ACER2:ENST00000340967.3::; ACER2:ENST00000417653.2::

Pathogenicity Data:: Best Score: 0.3614425; CADD: 0.361 (1.948)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.19393304A>G [0/1] rs371525402 (variation viewer)

Variant score: 0.324 CONTRIBUTING VARIANT

Transcripts:: ACER2:ENST00000340967.3::; ACER2:ENST00000449348.2::

Pathogenicity Data:: Best Score: 0.5375125; CADD: 0.538 (3.349)

Frequency Data:: 1000Genomes: 0.6589%; TOPMed: 0.6339%; UK10K: 1.1902%; gnomAD_G_AFR: 0.2081%; gnomAD_G_AMR: 0.1199%; gnomAD_G_FIN: 1.3703%; gnomAD_G_NFE: 0.8471%; gnomAD_G_OTH: 0.4175%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.19433149CT>C [1/1] rs57915019 (variation viewer)

Variant score: 0.103

Transcripts:: ACER2:ENST00000340967.3:c.366-1797del:p.(=)

Pathogenicity Data:: Best Score: 0.10339737; CADD: 0.103 (0.474)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr9:g.19460627A>G [0/1] rs147303425 (variation viewer)

Variant score: 0.063

Transcripts:: ACER2:ENST00000340967.3::

Pathogenicity Data:: Best Score: 0.21584845; CADD: 0.216 (1.056)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.6801%; UK10K: 1.2695%; gnomAD_G_AFR: 0.1717%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.8317%; gnomAD_G_NFE: 1.1256%; gnomAD_G_OTH: 1.1202%

INTERGENIC_VARIANT chr9:g.19398990G>T [0/1] rs769570799 (variation viewer)

Variant score: 0.043

Transcripts:: ACER2:ENST00000340967.3::; ACER2:ENST00000449348.2::

Pathogenicity Data:: Best Score: 0.043026328; CADD: 0.043 (0.191)

Frequency Data:: TOPMed: 0.0111%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0067%

GUK1

Exomiser Score: 0.009

Phenotype Score: 0.504

Variant Score: 0.360

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.009

Phenotype Score: 0.504

Variant Score: 0.360

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr1:g.228138234C>CT [-/1] rs1195463327 (variation viewer)

Variant score: 0.360 CONTRIBUTING VARIANT

Transcripts:: GUK1:ENST00000366730.5::; GUK1:ENST00000413855.2::

Pathogenicity Data:: Best Score: 0.3599705; CADD: 0.360 (1.938)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.504

Variant Score: 0.357

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr1:g.228138234C>CT [-/1] rs1195463327 (variation viewer)

Variant score: 0.360 CONTRIBUTING VARIANT

Transcripts:: GUK1:ENST00000366730.5::; GUK1:ENST00000413855.2::

Pathogenicity Data:: Best Score: 0.3599705; CADD: 0.360 (1.938)

Frequency Data:: No frequency data

UPSTREAM_GENE_VARIANT chr1:g.228138234C>CTT [-/1] rs1195463327 (variation viewer)

Variant score: 0.355 CONTRIBUTING VARIANT

Transcripts:: GUK1:ENST00000366730.5::; GUK1:ENST00000413855.2::

Pathogenicity Data:: Best Score: 0.35464305; CADD: 0.355 (1.902)

Frequency Data:: No frequency data

Other passed variants:

PSMD14

Exomiser Score: 0.009

Phenotype Score: 0.504

Variant Score: 0.359

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.009

Phenotype Score: 0.504

Variant Score: 0.359

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.161297838T>C [0/1] rs565012115 (variation viewer)

Variant score: 0.569 CONTRIBUTING VARIANT

Transcripts:: PSMD14:ENST00000409682.8::; PSMD14:ENST00000429684.1::

Pathogenicity Data:: Best Score: 0.57849765; CADD: 0.578 (3.752)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0056%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.161360753G>T [0/1] rs185930576 (variation viewer)

Variant score: 0.149 CONTRIBUTING VARIANT

Transcripts:: PSMD14:ENST00000409682.8:c.49-6725G>T:p.(=)

Pathogenicity Data:: Best Score: 0.1519919; CADD: 0.152 (0.716)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0111%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.161345236CT>C [1/1] rs869245727 (variation viewer)

Variant score: 0.200

Transcripts:: PSMD14:ENST00000409682.8:c.49-22241del:p.(=)

Pathogenicity Data:: Best Score: 0.19979733; CADD: 0.200 (0.968)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.161311625CT>C [1/1] rs34635738 (variation viewer)

Variant score: 0.183

Transcripts:: PSMD14:ENST00000409682.8:c.-138+3022del:p.(=)

Pathogenicity Data:: Best Score: 0.18285334; CADD: 0.183 (0.877)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.161327946C>CTGTGTGTGTGTG [1|1] rs369674882 (variation viewer)

Variant score: 0.163

Transcripts:: PSMD14:ENST00000409682.8:c.48+9073_48+9074insTGTGTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.16343439; CADD: 0.163 (0.775)

Frequency Data:: No frequency data

NDUFV2

Exomiser Score: 0.008

Phenotype Score: 0.504

Variant Score: 0.357

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFV2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618229 Mitochondrial complex I deficiency, nuclear type 7 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.504

Variant Score: 0.357

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.9118815G>GTT [1/1] rs71168030 (variation viewer)

Variant score: 0.357 CONTRIBUTING VARIANT

Transcripts:: NDUFV2:ENST00000318388.11:c.121-511_121-510insTT:p.(=); NDUFV2:ENST00000400033.1:c.130-511_130-510insTT:p.(=)

Pathogenicity Data:: Best Score: 0.3565719; CADD: 0.357 (1.915)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr18:g.9134754C>CTT [1/1] rs748345204 (variation viewer)

Variant score: 0.217

Transcripts:: NDUFV2:ENST00000400033.1::

Pathogenicity Data:: Best Score: 0.21693105; CADD: 0.217 (1.062)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr18:g.9084929C>CATATAT [1/1] rs1215151563 (variation viewer)

Variant score: 0.041

Transcripts:: NDUFV2:ENST00000497577.2::; NDUFV2:ENST00000460237.2::

Pathogenicity Data:: Best Score: 0.30192834; CADD: 0.302 (1.561)

Frequency Data:: gnomAD_G_AFR: 1.8085%; gnomAD_G_EAS: 1.3333%; gnomAD_G_FIN: 2.0000%; gnomAD_G_NFE: 0.8176%

COX17

Exomiser Score: 0.008

Phenotype Score: 0.503

Variant Score: 0.352

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.008

Phenotype Score: 0.503

Variant Score: 0.352

Variants contributing to score:

THREE_PRIME_UTR_INTRON_VARIANT chr3:g.119670752T>TG [-/1]

Variant score: 0.352 CONTRIBUTING VARIANT

Transcripts:: COX17:ENST00000261070.6:c.*5-1088_*5-1087insC:p.(=); COX17:ENST00000484810.5:c.*5-1088_*5-1087insC:p.(=)

Pathogenicity Data:: Best Score: 0.35226107; CADD: 0.352 (1.886)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.176

Variants contributing to score:

THREE_PRIME_UTR_INTRON_VARIANT chr3:g.119670752T>TG [-/1]

Variant score: 0.352 CONTRIBUTING VARIANT

Transcripts:: COX17:ENST00000261070.6:c.*5-1088_*5-1087insC:p.(=); COX17:ENST00000484810.5:c.*5-1088_*5-1087insC:p.(=)

Pathogenicity Data:: Best Score: 0.35226107; CADD: 0.352 (1.886)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr3:g.119667726CACAG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: COX17:ENST00000261070.6::; COX17:ENST00000493094.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

XRCC6

Exomiser Score: 0.008

Phenotype Score: 0.502

Variant Score: 0.350

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.502

Variant Score: 0.350

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41651361ATTTTTTTTTTTTT>A [1/1] rs764795746 (variation viewer)

Variant score: 0.350 CONTRIBUTING VARIANT

Transcripts:: XRCC6:ENST00000359308.8:c.1129+471_1129+483del:p.(=); XRCC6:ENST00000360079.7:c.1129+471_1129+483del:p.(=); XRCC6:ENST00000402580.7:c.1006+471_1006+483del:p.(=); XRCC6:ENST00000405506.2:c.979+471_979+483del:p.(=); XRCC6:ENST00000405878.5:c.1129+471_1129+483del:p.(=); XRCC6:ENST00000428575.6:c.979+471_979+483del:p.(=)

Pathogenicity Data:: Best Score: 0.39410138; CADD: 0.394 (2.176)

Frequency Data:: gnomAD_G_AFR: 0.1946%; gnomAD_G_EAS: 0.6006%; gnomAD_G_NFE: 0.2840%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.41626631G>GT [1|1] rs921225213 (variation viewer)

Variant score: 0.101

Transcripts:: XRCC6:ENST00000359308.8:c.83-1487_83-1486insT:p.(=); XRCC6:ENST00000360079.7:c.83-1487_83-1486insT:p.(=); XRCC6:ENST00000402580.7:c.83-1487_83-1486insT:p.(=); XRCC6:ENST00000405506.2:c.45+4545_45+4546insT:p.(=); XRCC6:ENST00000405878.5:c.83-1487_83-1486insT:p.(=); XRCC6:ENST00000428575.6:c.45+4545_45+4546insT:p.(=)

Pathogenicity Data:: Best Score: 0.10112357; CADD: 0.101 (0.463)

Frequency Data:: No frequency data

TFDP1

Exomiser Score: 0.008

Phenotype Score: 0.503

Variant Score: 0.347

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.113625476T>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: TFDP1:ENST00000375370.10:c.186+2190T>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.008

Phenotype Score: 0.503

Variant Score: 0.347

Variants contributing to score:

INTERGENIC_VARIANT chr13:g.113648009C>T [0/1] rs545136187 (variation viewer)

Variant score: 0.519 CONTRIBUTING VARIANT

Transcripts:: TFDP1:ENST00000375370.10::

Pathogenicity Data:: Best Score: 0.5948648; CADD: 0.595 (3.924)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0438%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0573%; gnomAD_G_NFE: 0.0400%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.113625476T>C [-/1] rs1191896172 (variation viewer)

Variant score: 0.175 CONTRIBUTING VARIANT

Transcripts:: TFDP1:ENST00000375370.10:c.186+2190T>C:p.(=)

Pathogenicity Data:: Best Score: 0.20200533; CADD: 0.202 (0.980)

Frequency Data:: gnomAD_G_AFR: 0.0989%; gnomAD_G_FIN: 0.5172%; gnomAD_G_NFE: 0.6818%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.113625321TCTCAGGCGTCTCTCACGTGTC>T [0/1] rs751538795 (variation viewer)

Variant score: 0.153

Transcripts:: TFDP1:ENST00000375370.10:c.186+2036_186+2056del:p.(=)

Pathogenicity Data:: Best Score: 0.3164032; CADD: 0.316 (1.652)

Frequency Data:: gnomAD_G_AMR: 0.5917%; gnomAD_G_FIN: 1.5704%; gnomAD_G_NFE: 0.1663%; gnomAD_G_OTH: 0.9881%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.113625445CCTCAGGTGTCTCTCACGTGTCCTCAGGTGTTTCTCAGGTGTCTCTCACGTGTT>C [0/1] rs1566666733 (variation viewer)

Variant score: 0.000

Transcripts:: TFDP1:ENST00000375370.10:c.186+2160_186+2212del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: gnomAD_G_AFR: 0.0995%; gnomAD_G_AMR: 0.7273%; gnomAD_G_EAS: 0.2595%; gnomAD_G_FIN: 0.3994%; gnomAD_G_NFE: 0.0575%; gnomAD_G_OTH: 0.1613%

LRPPRC

Exomiser Score: 0.007

Phenotype Score: 0.503

Variant Score: 0.343

Phenotype matches:

Proximity score 0.503 in interactome to MT-ND5 and phenotypic similarity 0.864 to MELAS associated with MT-ND5.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:220111 Mitochondrial complex IV deficiency, nuclear type 5, (French-Canadian) - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.251

Variant Score: 0.496

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43952003G>A [0/1]

Variant score: 0.496 CONTRIBUTING VARIANT

Transcripts:: LRPPRC:ENST00000260665.12:c.1650-1403C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4958033; CADD: 0.496 (2.974)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.503

Variant Score: 0.343

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43952003G>A [0/1]

Variant score: 0.496 CONTRIBUTING VARIANT

Transcripts:: LRPPRC:ENST00000260665.12:c.1650-1403C>T:p.(=)

Pathogenicity Data:: Best Score: 0.4958033; CADD: 0.496 (2.974)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43932123C>CAA [0/1] rs746600862 (variation viewer)

Variant score: 0.191 CONTRIBUTING VARIANT

Transcripts:: LRPPRC:ENST00000260665.12:c.2736+2066_2736+2067insTT:p.(=)

Pathogenicity Data:: Best Score: 0.1910904; CADD: 0.191 (0.921)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43889314C>CAAAA [1/1] rs780032604 (variation viewer)

Variant score: 0.175

Transcripts:: LRPPRC:ENST00000260665.12:c.4128+419_4128+420insTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.17453247; CADD: 0.175 (0.833)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43944996C>A [0/1] rs550338426 (variation viewer)

Variant score: 0.089

Transcripts:: LRPPRC:ENST00000260665.12:c.2296+336G>T:p.(=)

Pathogenicity Data:: Best Score: 0.08882874; CADD: 0.089 (0.404)

Frequency Data:: TOPMed: 0.0127%; UK10K: 0.0264%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43935621C>G [0/1] rs767685359 (variation viewer)

Variant score: 0.066

Transcripts:: LRPPRC:ENST00000260665.12:c.2505-743G>C:p.(=)

Pathogenicity Data:: Best Score: 0.066100836; CADD: 0.066 (0.297)

Frequency Data:: TOPMed: 0.0120%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43971485T>TAAAAAAAAA [1/1] rs528659622 (variation viewer)

Variant score: 0.038

Transcripts:: LRPPRC:ENST00000260665.12:c.1369+2121_1369+2122insTTTTTTTTT:p.(=); LRPPRC:ENST00000409659.5:c.1369+2121_1369+2122insTTTTTTTTT:p.(=); LRPPRC:ENST00000409946.5:c.1369+2121_1369+2122insTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.037723243; CADD: 0.038 (0.167)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43895869C>CAGTT [0/1] rs532185596 (variation viewer)

Variant score: 0.033

Transcripts:: LRPPRC:ENST00000260665.12:c.3900+764_3900+765insAACT:p.(=)

Pathogenicity Data:: Best Score: 0.042365015; CADD: 0.042 (0.188)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0599%; UK10K: 0.5157%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.2392%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.2799%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.43981909T>* [-/1]

Variant score: 0.000

Transcripts:: LRPPRC:ENST00000260665.12:c.346+329A>:p.(=); LRPPRC:ENST00000409659.5:c.346+329A>:p.(=); LRPPRC:ENST00000409946.5:c.346+329A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SEC16A

Exomiser Score: 0.007

Phenotype Score: 0.504

Variant Score: 0.342

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.504

Variant Score: 0.342

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136452771A>G [1|1] rs1395119690 (variation viewer)

Variant score: 0.342 CONTRIBUTING VARIANT

Transcripts:: SEC16A:ENST00000290037.10:c.6159+657T>C:p.(=); SEC16A:ENST00000313050.11:c.6159+657T>C:p.(=); SEC16A:ENST00000371706.7:c.5625+657T>C:p.(=); SEC16A:ENST00000431893.3:c.5625+657T>C:p.(=)

Pathogenicity Data:: Best Score: 0.611134; CADD: 0.611 (4.102)

Frequency Data:: gnomAD_G_AFR: 0.1340%; gnomAD_G_ASJ: 1.4493%; gnomAD_G_FIN: 0.2188%; gnomAD_G_NFE: 1.1973%; gnomAD_G_OTH: 1.0363%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136452449CAAAA>C [1/1] rs752510860 (variation viewer)

Variant score: 0.187

Transcripts:: SEC16A:ENST00000290037.10:c.6159+975_6159+978del:p.(=); SEC16A:ENST00000313050.11:c.6159+975_6159+978del:p.(=); SEC16A:ENST00000371706.7:c.5625+975_5625+978del:p.(=); SEC16A:ENST00000431893.3:c.5625+975_5625+978del:p.(=)

Pathogenicity Data:: Best Score: 0.18698233; CADD: 0.187 (0.899)

Frequency Data:: No frequency data

IARS1

Exomiser Score: 0.007

Phenotype Score: 0.518

Variant Score: 0.324

Phenotype matches:

Proximity score 0.518 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617093 Growth retardation, impaired intellectual development, hypotonia, and hepatopathy - autosomal recessive; ORPHA:541423 Growth delay-intellectual disability-hepatopathy syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.259

Variant Score: 0.128

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92252764C>CAA [-/1] rs34983021 (variation viewer)

Variant score: 0.128 CONTRIBUTING VARIANT

Transcripts:: IARS1:ENST00000375643.7:c.2229+597_2229+598insTT:p.(=); IARS1:ENST00000443024.6:c.2229+597_2229+598insTT:p.(=); IARS1:ENST00000447699.6:c.1899+597_1899+598insTT:p.(=); IARS1:ENST00000627121.2:c.-613+597_-613+598insTT:p.(=)

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.518

Variant Score: 0.324

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92239458C>A [0/1] rs771234495 (variation viewer)

Variant score: 0.520 CONTRIBUTING VARIANT

Transcripts:: IARS1:ENST00000375627.1:c.491+1185G>T:p.(=); IARS1:ENST00000375643.7:c.3283+1398G>T:p.(=); IARS1:ENST00000443024.6:c.3283+1398G>T:p.(=); IARS1:ENST00000447699.6:c.2953+1398G>T:p.(=); IARS1:ENST00000627121.2:c.491+1185G>T:p.(=)

Pathogenicity Data:: Best Score: 0.5494946; CADD: 0.549 (3.463)

Frequency Data:: TOPMed: 0.0191%; UK10K: 0.0132%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0133%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92252764C>CAA [-/1] rs34983021 (variation viewer)

Variant score: 0.128 CONTRIBUTING VARIANT

Transcripts:: IARS1:ENST00000375643.7:c.2229+597_2229+598insTT:p.(=); IARS1:ENST00000443024.6:c.2229+597_2229+598insTT:p.(=); IARS1:ENST00000447699.6:c.1899+597_1899+598insTT:p.(=); IARS1:ENST00000627121.2:c.-613+597_-613+598insTT:p.(=)

Pathogenicity Data:: Best Score: 0.1278323; CADD: 0.128 (0.594)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92252764CAA>C [-/1] rs34983021 (variation viewer)

Variant score: 0.099

Transcripts:: IARS1:ENST00000375643.7:c.2229+596_2229+597del:p.(=); IARS1:ENST00000443024.6:c.2229+596_2229+597del:p.(=); IARS1:ENST00000447699.6:c.1899+596_1899+597del:p.(=); IARS1:ENST00000627121.2:c.-613+596_-613+597del:p.(=)

Pathogenicity Data:: Best Score: 0.09863645; CADD: 0.099 (0.451)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.92268415G>A [0|1]

Variant score: 0.031

Transcripts:: IARS1:ENST00000375643.7:c.1305-115C>T:p.(=); IARS1:ENST00000443024.6:c.1305-115C>T:p.(=); IARS1:ENST00000447699.6:c.975-115C>T:p.(=); IARS1:ENST00000627121.2:c.-1537-115C>T:p.(=)

Pathogenicity Data:: Best Score: 0.031053066; CADD: 0.031 (0.137)

Frequency Data:: No frequency data

COPE

Exomiser Score: 0.007

Phenotype Score: 0.504

Variant Score: 0.335

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.504

Variant Score: 0.335

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.18910855C>A [0/1] rs540551590 (variation viewer)

Variant score: 0.369 CONTRIBUTING VARIANT

Transcripts:: COPE:ENST00000262812.9:c.290+116G>T:p.(=); COPE:ENST00000349893.8:c.290+116G>T:p.(=); COPE:ENST00000351079.8:c.290+116G>T:p.(=); COPE:ENST00000600932.5:c.290+116G>T:p.(=); COPE:ENST00000596918.5:c.*331+116G>T:p.(=)

Pathogenicity Data:: Best Score: 0.37583417; CADD: 0.376 (2.047)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0358%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.18915350G>C [0/1] rs571720236 (variation viewer)

Variant score: 0.301 CONTRIBUTING VARIANT

Transcripts:: COPE:ENST00000262812.9:c.127-2304C>G:p.(=); COPE:ENST00000349893.8:c.127-2304C>G:p.(=); COPE:ENST00000351079.8:c.127-2304C>G:p.(=); COPE:ENST00000600932.5:c.127-2304C>G:p.(=); COPE:ENST00000596918.5:c.*168-2304C>G:p.(=)

Pathogenicity Data:: Best Score: 0.30641448; CADD: 0.306 (1.589)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0366%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.18911447C>T [0/1] rs576187698 (variation viewer)

Variant score: 0.290

Transcripts:: COPE:ENST00000262812.9:c.190-376G>A:p.(=); COPE:ENST00000349893.8:c.190-376G>A:p.(=); COPE:ENST00000351079.8:c.190-376G>A:p.(=); COPE:ENST00000600932.5:c.190-376G>A:p.(=); COPE:ENST00000596918.5:c.*231-376G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2996744; CADD: 0.300 (1.547)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.1282%; gnomAD_G_AFR: 0.0459%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.1071%; gnomAD_G_OTH: 0.1027%

AP1G2

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.334

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.334

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.23560778CAAAAAAAAA>C [1/1] rs59524126 (variation viewer)

Variant score: 0.334 CONTRIBUTING VARIANT

Transcripts:: AP1G2:ENST00000308724.9:c.1994-369_1994-361del:p.(=); AP1G2:ENST00000397120.8:c.1994-369_1994-361del:p.(=)

Pathogenicity Data:: Best Score: 0.33411384; CADD: 0.334 (1.766)

Frequency Data:: No frequency data

Other passed variants:

PLPP3

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.334

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.334

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.56572043G>GTT [1/1] rs375576842 (variation viewer)

Variant score: 0.334 CONTRIBUTING VARIANT

Transcripts:: PLPP3:ENST00000371250.4:c.139+6834_139+6835insAA:p.(=)

Pathogenicity Data:: Best Score: 0.3336537; CADD: 0.334 (1.763)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.56520910CA>C [1/1] rs1169318077 (variation viewer)

Variant score: 0.166

Transcripts:: PLPP3:ENST00000371250.4:c.633+2912del:p.(=); PLPP3:ENST00000642129.1:c.277+2912del:p.(=)

Pathogenicity Data:: Best Score: 0.16555065; CADD: 0.166 (0.786)

Frequency Data:: No frequency data

MTCL1

Exomiser Score: 0.007

Phenotype Score: 0.501

Variant Score: 0.338

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.501

Variant Score: 0.338

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.8823470C>T [0/1]

Variant score: 0.338 CONTRIBUTING VARIANT

Transcripts:: MTCL1:ENST00000306329.15:c.4146-1229C>T:p.(=); MTCL1:ENST00000359865.7:c.3189-1229C>T:p.(=); MTCL1:ENST00000400050.7:c.3189-1229C>T:p.(=); MTCL1:ENST00000517570.5:c.3066-1229C>T:p.(=); MTCL1:ENST00000518815.1:c.1164-1229C>T:p.(=)

Pathogenicity Data:: Best Score: 0.33793598; CADD: 0.338 (1.791)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.501

Variant Score: 0.228

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.8823470C>T [0/1]

Variant score: 0.338 CONTRIBUTING VARIANT

Transcripts:: MTCL1:ENST00000306329.15:c.4146-1229C>T:p.(=); MTCL1:ENST00000359865.7:c.3189-1229C>T:p.(=); MTCL1:ENST00000400050.7:c.3189-1229C>T:p.(=); MTCL1:ENST00000517570.5:c.3066-1229C>T:p.(=); MTCL1:ENST00000518815.1:c.1164-1229C>T:p.(=)

Pathogenicity Data:: Best Score: 0.33793598; CADD: 0.338 (1.791)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.8788158C>T [0/1] rs766048142 (variation viewer)

Variant score: 0.118 CONTRIBUTING VARIANT

Transcripts:: MTCL1:ENST00000306329.15:c.2967+2067C>T:p.(=); MTCL1:ENST00000359865.7:c.1887+2067C>T:p.(=); MTCL1:ENST00000400050.7:c.1887+2067C>T:p.(=); MTCL1:ENST00000517570.5:c.1887+2067C>T:p.(=)

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: TOPMed: 0.0271%; UK10K: 0.0661%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.1233%; gnomAD_G_NFE: 0.0333%; gnomAD_G_OTH: 0.1018%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.8710457CT>C [0/1] rs59830434 (variation viewer)

Variant score: 0.116

Transcripts:: MTCL1:ENST00000306329.15:c.1053+3745del:p.(=); MTCL1:ENST00000517570.5:c.-28+2893del:p.(=)

Pathogenicity Data:: Best Score: 0.11610639; CADD: 0.116 (0.536)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.8729673A>AAT [0/1] rs3051533 (variation viewer)

Variant score: 0.062

Transcripts:: MTCL1:ENST00000306329.15:c.1437+9177_1437+9178insAT:p.(=); MTCL1:ENST00000359865.7:c.357+9177_357+9178insAT:p.(=); MTCL1:ENST00000400050.7:c.357+9177_357+9178insAT:p.(=); MTCL1:ENST00000517570.5:c.357+9177_357+9178insAT:p.(=)

Pathogenicity Data:: Best Score: 0.062222064; CADD: 0.062 (0.279)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.8726286CT>C [1/1] rs77665680 (variation viewer)

Variant score: 0.036

Transcripts:: MTCL1:ENST00000306329.15:c.1437+5791del:p.(=); MTCL1:ENST00000359865.7:c.357+5791del:p.(=); MTCL1:ENST00000400050.7:c.357+5791del:p.(=); MTCL1:ENST00000517570.5:c.357+5791del:p.(=)

Pathogenicity Data:: Best Score: 0.035727024; CADD: 0.036 (0.158)

Frequency Data:: No frequency data

CACNA1A

Exomiser Score: 0.007

Phenotype Score: 0.510

Variant Score: 0.327

Phenotype matches:

Phenotypic similarity 0.435 to Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia associated with CACNA1A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000739, Anxiety

Proximity score 0.510 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:108500 Episodic ataxia, type 2 - autosomal dominant; OMIM:141500 Migraine, familial hemiplegic, 1, with progressive cerebellar ataxia - autosomal dominant; OMIM:183086 Spinocerebellar ataxia 6 - autosomal dominant; OMIM:617106 Developemental and epileptic encephalopathy 42 - autosomal dominant; ORPHA:442835 Undetermined early-onset epileptic encephalopathy; ORPHA:569 Familial or sporadic hemiplegic migraine; ORPHA:97 Familial paroxysmal ataxia; ORPHA:98758 Spinocerebellar ataxia type 6

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.510

Variant Score: 0.327

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13556188G>A [0/1] rs536653373 (variation viewer)

Variant score: 0.327 CONTRIBUTING VARIANT

Transcripts:: CACNA1A:ENST00000592864.3:c.195-36685C>T:p.(=); CACNA1A:ENST00000664864.1:c.194+43565C>T:p.(=)

Pathogenicity Data:: Best Score: 0.33011538; CADD: 0.330 (1.740)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0096%; gnomAD_G_FIN: 0.0573%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.255

Variant Score: 0.387

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13460234C>T [0/1] rs138381686 (variation viewer)

Variant score: 0.447 CONTRIBUTING VARIANT

Transcripts:: CACNA1A:ENST00000360228.11:c.294-5022G>A:p.(=); CACNA1A:ENST00000573710.7:c.294-5022G>A:p.(=); CACNA1A:ENST00000614285.4:c.295-5023G>A:p.(=); CACNA1A:ENST00000635727.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000635895.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000636012.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000636389.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000636549.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000637276.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000637432.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000637736.1:c.259-7219G>A:p.(=); CACNA1A:ENST00000637769.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000637927.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000638009.2:c.294-5022G>A:p.(=); CACNA1A:ENST00000638029.1:c.294-5022G>A:p.(=); CACNA1A:ENST00000664864.1:c.489-5022G>A:p.(=)

Pathogenicity Data:: Best Score: 0.75362307; CADD: 0.754 (6.084)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 1.0810%; UK10K: 1.3885%; gnomAD_G_AFR: 0.2978%; gnomAD_G_AMR: 0.9569%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.5155%; gnomAD_G_NFE: 1.2345%; gnomAD_G_OTH: 1.2220%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13556188G>A [0/1] rs536653373 (variation viewer)

Variant score: 0.327 CONTRIBUTING VARIANT

Transcripts:: CACNA1A:ENST00000592864.3:c.195-36685C>T:p.(=); CACNA1A:ENST00000664864.1:c.194+43565C>T:p.(=)

Pathogenicity Data:: Best Score: 0.33011538; CADD: 0.330 (1.740)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0096%; gnomAD_G_FIN: 0.0573%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13579340T>C [0/1] rs151323779 (variation viewer)

Variant score: 0.239

Transcripts:: CACNA1A:ENST00000592864.3:c.194+20413A>G:p.(=); CACNA1A:ENST00000664864.1:c.194+20413A>G:p.(=)

Pathogenicity Data:: Best Score: 0.3564238; CADD: 0.356 (1.914)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.4746%; UK10K: 1.0050%; gnomAD_G_AFR: 0.1259%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.2321%; gnomAD_G_NFE: 0.6997%; gnomAD_G_OTH: 0.6110%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13592168C>CAA [0/1] rs370983093 (variation viewer)

Variant score: 0.204

Transcripts:: CACNA1A:ENST00000592864.3:c.194+7584_194+7585insTT:p.(=); CACNA1A:ENST00000664864.1:c.194+7584_194+7585insTT:p.(=)

Pathogenicity Data:: Best Score: 0.20420718; CADD: 0.204 (0.992)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13513657C>CAAAAAAAAAAAAAA [0/1] rs57026194 (variation viewer)

Variant score: 0.200

Transcripts:: CACNA1A:ENST00000664864.1:c.195-7433_195-7432insTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.20016575; CADD: 0.200 (0.970)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13393795T>TTCCC [1/1] rs752179743 (variation viewer)

Variant score: 0.172

Transcripts:: CACNA1A:ENST00000360228.11:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000573710.7:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000614285.4:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000635727.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000635895.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000636012.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000636389.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000636549.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000637276.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000637432.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000637736.1:c.399-22017_399-22016insGGGA:p.(=); CACNA1A:ENST00000637769.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000637927.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000638009.2:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000638029.1:c.540-22017_540-22016insGGGA:p.(=); CACNA1A:ENST00000664864.1:c.735-22017_735-22016insGGGA:p.(=)

Pathogenicity Data:: Best Score: 0.17167646; CADD: 0.172 (0.818)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13383990A>AT [0/1] rs987472326 (variation viewer)

Variant score: 0.158

Transcripts:: CACNA1A:ENST00000360228.11:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000573710.7:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000614285.4:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000635727.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000635895.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000636012.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000636389.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000636549.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000637276.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000637432.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000637736.1:c.399-12212_399-12211insA:p.(=); CACNA1A:ENST00000637769.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000637927.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000638009.2:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000638029.1:c.540-12212_540-12211insA:p.(=); CACNA1A:ENST00000664864.1:c.735-12212_735-12211insA:p.(=)

Pathogenicity Data:: Best Score: 0.15957296; CADD: 0.160 (0.755)

Frequency Data:: TOPMed: 0.0398%; gnomAD_G_AFR: 0.0690%; gnomAD_G_FIN: 0.0289%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13367294CAAAAAA>C [1/1] rs71168702 (variation viewer)

Variant score: 0.118

Transcripts:: CACNA1A:ENST00000360228.11:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000573710.7:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000614285.4:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000635727.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000635895.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000636012.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000636389.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000636549.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000637276.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000637432.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000637736.1:c.491-1831_491-1826del:p.(=); CACNA1A:ENST00000637769.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000637927.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000638009.2:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000638029.1:c.632-1831_632-1826del:p.(=); CACNA1A:ENST00000664864.1:c.827-1831_827-1826del:p.(=)

Pathogenicity Data:: Best Score: 0.117936194; CADD: 0.118 (0.545)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13264699T>A [0/1]

Variant score: 0.113

Transcripts:: CACNA1A:ENST00000360228.11:c.3990-1866A>T:p.(=); CACNA1A:ENST00000573710.7:c.3996-1866A>T:p.(=); CACNA1A:ENST00000614285.4:c.4002-1866A>T:p.(=); CACNA1A:ENST00000635727.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000635895.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000636012.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000636389.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000636549.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000637276.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000637432.1:c.4002-1866A>T:p.(=); CACNA1A:ENST00000637736.1:c.3852-1866A>T:p.(=); CACNA1A:ENST00000637769.1:c.3993-1866A>T:p.(=); CACNA1A:ENST00000637927.1:c.3996-1866A>T:p.(=); CACNA1A:ENST00000638009.2:c.3993-1866A>T:p.(=); CACNA1A:ENST00000638029.1:c.4002-1866A>T:p.(=); CACNA1A:ENST00000664864.1:c.4188-1866A>T:p.(=)

Pathogenicity Data:: Best Score: 0.113048255; CADD: 0.113 (0.521)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.13610749A>AT [-/1] rs71170542 (variation viewer)

Variant score: 0.110

Transcripts:: CACNA1A:ENST00000592864.3:c.-110-10694_-110-10693insA:p.(=)

Pathogenicity Data:: Best Score: 0.10997951; CADD: 0.110 (0.506)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13336594G>GGA [1/1] rs547329827 (variation viewer)

Variant score: 0.109

Transcripts:: CACNA1A:ENST00000360228.11:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000573710.7:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000614285.4:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000635727.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000635895.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000636012.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000636389.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000636549.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000637276.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000637432.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000637736.1:c.838-686_838-685insTC:p.(=); CACNA1A:ENST00000637769.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000637927.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000638009.2:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000638029.1:c.979-686_979-685insTC:p.(=); CACNA1A:ENST00000664864.1:c.1174-686_1174-685insTC:p.(=)

Pathogenicity Data:: Best Score: 0.10895425; CADD: 0.109 (0.501)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13437691CA>C [0/1] rs35266881 (variation viewer)

Variant score: 0.099

Transcripts:: CACNA1A:ENST00000360228.11:c.539+15184del:p.(=); CACNA1A:ENST00000573710.7:c.539+15184del:p.(=); CACNA1A:ENST00000614285.4:c.539+15184del:p.(=); CACNA1A:ENST00000635727.1:c.539+15184del:p.(=); CACNA1A:ENST00000635895.1:c.539+15184del:p.(=); CACNA1A:ENST00000636012.1:c.539+15184del:p.(=); CACNA1A:ENST00000636389.1:c.539+15184del:p.(=); CACNA1A:ENST00000636549.1:c.539+15184del:p.(=); CACNA1A:ENST00000637276.1:c.539+15184del:p.(=); CACNA1A:ENST00000637432.1:c.539+15184del:p.(=); CACNA1A:ENST00000637736.1:c.398+15184del:p.(=); CACNA1A:ENST00000637769.1:c.539+15184del:p.(=); CACNA1A:ENST00000637927.1:c.539+15184del:p.(=); CACNA1A:ENST00000638009.2:c.539+15184del:p.(=); CACNA1A:ENST00000638029.1:c.539+15184del:p.(=); CACNA1A:ENST00000664864.1:c.734+15184del:p.(=)

Pathogenicity Data:: Best Score: 0.099466264; CADD: 0.099 (0.455)

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.13610749AT>A [-/1] rs71170542 (variation viewer)

Variant score: 0.087

Transcripts:: CACNA1A:ENST00000592864.3:c.-110-10694del:p.(=)

Pathogenicity Data:: Best Score: 0.086728275; CADD: 0.087 (0.394)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13346642ATATATATATATATATATATATATATTTTTTT>A [0/1] rs546414513 (variation viewer)

Variant score: 0.030

Transcripts:: CACNA1A:ENST00000360228.11:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000573710.7:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000614285.4:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000635727.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000635895.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000636012.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000636389.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000636549.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000637276.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000637432.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000637736.1:c.838-10764_838-10734del:p.(=); CACNA1A:ENST00000637769.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000637927.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000638009.2:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000638029.1:c.979-10764_979-10734del:p.(=); CACNA1A:ENST00000664864.1:c.1174-10764_1174-10734del:p.(=)

Pathogenicity Data:: Best Score: 0.086307645; CADD: 0.086 (0.392)

Frequency Data:: gnomAD_G_AFR: 0.2506%; gnomAD_G_EAS: 1.1364%; gnomAD_G_NFE: 0.9479%; gnomAD_G_OTH: 1.7544%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13406465T>TTATATA [0/1] rs61273249 (variation viewer)

Variant score: 0.023

Transcripts:: CACNA1A:ENST00000360228.11:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000573710.7:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000614285.4:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000635727.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000635895.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000636012.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000636389.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000636549.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000637276.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000637432.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000637736.1:c.399-34687_399-34686insTATATA:p.(=); CACNA1A:ENST00000637769.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000637927.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000638009.2:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000638029.1:c.540-34687_540-34686insTATATA:p.(=); CACNA1A:ENST00000664864.1:c.735-34687_735-34686insTATATA:p.(=)

Pathogenicity Data:: Best Score: 0.02321273; CADD: 0.023 (0.102)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13499446GT>G [0/1] rs1441099981 (variation viewer)

Variant score: 0.002

Transcripts:: CACNA1A:ENST00000360228.11:c.293+6485del:p.(=); CACNA1A:ENST00000573710.7:c.293+6485del:p.(=); CACNA1A:ENST00000614285.4:c.294+6484del:p.(=); CACNA1A:ENST00000635727.1:c.293+6485del:p.(=); CACNA1A:ENST00000635895.1:c.293+6485del:p.(=); CACNA1A:ENST00000636012.1:c.293+6485del:p.(=); CACNA1A:ENST00000636389.1:c.293+6485del:p.(=); CACNA1A:ENST00000636549.1:c.293+6485del:p.(=); CACNA1A:ENST00000637276.1:c.293+6485del:p.(=); CACNA1A:ENST00000637432.1:c.293+6485del:p.(=); CACNA1A:ENST00000637736.1:c.258+6520del:p.(=); CACNA1A:ENST00000637769.1:c.293+6485del:p.(=); CACNA1A:ENST00000637927.1:c.293+6485del:p.(=); CACNA1A:ENST00000638009.2:c.293+6485del:p.(=); CACNA1A:ENST00000638029.1:c.293+6485del:p.(=); CACNA1A:ENST00000664864.1:c.488+6485del:p.(=)

Pathogenicity Data:: Best Score: 0.0071126223; CADD: 0.007 (0.031)

Frequency Data:: gnomAD_G_AFR: 1.8926%; gnomAD_G_AMR: 1.5050%; gnomAD_G_ASJ: 1.8868%; gnomAD_G_FIN: 0.0807%; gnomAD_G_NFE: 1.1712%; gnomAD_G_OTH: 0.6536%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13260338G>* [-/1]

Variant score: 0.000

Transcripts:: CACNA1A:ENST00000360228.11:c.4251-637C>:p.(=); CACNA1A:ENST00000573710.7:c.4257-637C>:p.(=); CACNA1A:ENST00000614285.4:c.4263-637C>:p.(=); CACNA1A:ENST00000635727.1:c.4254-637C>:p.(=); CACNA1A:ENST00000635895.1:c.4254-637C>:p.(=); CACNA1A:ENST00000636012.1:c.4254-637C>:p.(=); CACNA1A:ENST00000636389.1:c.4254-637C>:p.(=); CACNA1A:ENST00000636549.1:c.4254-637C>:p.(=); CACNA1A:ENST00000637276.1:c.4254-637C>:p.(=); CACNA1A:ENST00000637432.1:c.4263-637C>:p.(=); CACNA1A:ENST00000637736.1:c.4113-637C>:p.(=); CACNA1A:ENST00000637769.1:c.4254-637C>:p.(=); CACNA1A:ENST00000637927.1:c.4257-637C>:p.(=); CACNA1A:ENST00000638009.2:c.4254-637C>:p.(=); CACNA1A:ENST00000638029.1:c.4263-637C>:p.(=); CACNA1A:ENST00000664864.1:c.4449-637C>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.13575725T>* [-/1]

Variant score: 0.000

Transcripts:: CACNA1A:ENST00000592864.3:c.194+24028A>:p.(=); CACNA1A:ENST00000664864.1:c.194+24028A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NAA35

Exomiser Score: 0.007

Phenotype Score: 0.503

Variant Score: 0.335

Phenotype matches:

Proximity score 0.503 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.223

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.85962490C>CAAAA [-/1] rs781302881 (variation viewer)

Variant score: 0.223 CONTRIBUTING VARIANT

Transcripts:: NAA35:ENST00000361671.10:c.516+310_516+311insAAAA:p.(=); NAA35:ENST00000376040.2:c.516+310_516+311insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.22321647; CADD: 0.223 (1.097)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.007

Phenotype Score: 0.503

Variant Score: 0.335

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.85955360A>T [1/1] rs28378629 (variation viewer)

Variant score: 0.335 CONTRIBUTING VARIANT

Transcripts:: NAA35:ENST00000361671.10:c.125-1000A>T:p.(=); NAA35:ENST00000376040.2:c.125-1000A>T:p.(=)

Pathogenicity Data:: Best Score: 0.33472687; CADD: 0.335 (1.770)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr9:g.85940874G>C [0/1] rs142062871 (variation viewer)

Variant score: 0.362

Transcripts:: NAA35:ENST00000361671.10::; NAA35:ENST00000442109.2::

Pathogenicity Data:: Best Score: 0.41169846; CADD: 0.412 (2.304)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.3807%; UK10K: 0.6348%; gnomAD_G_AFR: 0.1030%; gnomAD_G_AMR: 0.2392%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.5996%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.85962490C>CAAAAA [-/1] rs781302881 (variation viewer)

Variant score: 0.219

Transcripts:: NAA35:ENST00000361671.10:c.516+310_516+311insAAAAA:p.(=); NAA35:ENST00000376040.2:c.516+310_516+311insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.21927154; CADD: 0.219 (1.075)

Frequency Data:: No frequency data

AP2A1

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.329

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.007

Phenotype Score: 0.505

Variant Score: 0.329

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.49779487C>CA [-/1] rs370114853 (variation viewer)

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: AP2A1:ENST00000354293.9:c.68-2270_68-2269insA:p.(=); AP2A1:ENST00000359032.9:c.68-2270_68-2269insA:p.(=)

Pathogenicity Data:: Best Score: 0.32857114; CADD: 0.329 (1.730)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.192

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.49779487C>CA [-/1] rs370114853 (variation viewer)

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: AP2A1:ENST00000354293.9:c.68-2270_68-2269insA:p.(=); AP2A1:ENST00000359032.9:c.68-2270_68-2269insA:p.(=)

Pathogenicity Data:: Best Score: 0.32857114; CADD: 0.329 (1.730)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.49779487CA>C [-/1] rs370114853 (variation viewer)

Variant score: 0.056 CONTRIBUTING VARIANT

Transcripts:: AP2A1:ENST00000354293.9:c.68-2269del:p.(=); AP2A1:ENST00000359032.9:c.68-2269del:p.(=)

Pathogenicity Data:: Best Score: 0.056373775; CADD: 0.056 (0.252)

Frequency Data:: No frequency data

Other passed variants:

RAB11FIP2

Exomiser Score: 0.006

Phenotype Score: 0.501

Variant Score: 0.329

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.501

Variant Score: 0.329

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.118019665T>C [0/1] rs747233686 (variation viewer)

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: RAB11FIP2:ENST00000355624.8:c.1266-4555A>G:p.(=); RAB11FIP2:ENST00000369199.5:c.1326-4555A>G:p.(=)

Pathogenicity Data:: Best Score: 0.33303964; CADD: 0.333 (1.759)

Frequency Data:: TOPMed: 0.0565%; gnomAD_G_FIN: 0.0306%; gnomAD_G_NFE: 0.0827%

Other passed variants:

TTC13

Exomiser Score: 0.006

Phenotype Score: 0.507

Variant Score: 0.322

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.507

Variant Score: 0.322

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.230971345C>CA [0/1] rs11453211 (variation viewer)

Variant score: 0.322 CONTRIBUTING VARIANT

Transcripts:: TTC13:ENST00000366661.9:c.271+7214_271+7215insT:p.(=); TTC13:ENST00000366662.8:c.271+7214_271+7215insT:p.(=)

Pathogenicity Data:: Best Score: 0.32220244; CADD: 0.322 (1.689)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.507

Variant Score: 0.283

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.230971345C>CA [0/1] rs11453211 (variation viewer)

Variant score: 0.322 CONTRIBUTING VARIANT

Transcripts:: TTC13:ENST00000366661.9:c.271+7214_271+7215insT:p.(=); TTC13:ENST00000366662.8:c.271+7214_271+7215insT:p.(=)

Pathogenicity Data:: Best Score: 0.32220244; CADD: 0.322 (1.689)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.230949871A>C [0|1] rs538809050 (variation viewer)

Variant score: 0.244 CONTRIBUTING VARIANT

Transcripts:: TTC13:ENST00000366661.9:c.514-4417T>G:p.(=); TTC13:ENST00000366662.8:c.513+4462T>G:p.(=)

Pathogenicity Data:: Best Score: 0.248204; CADD: 0.248 (1.239)

Frequency Data:: TOPMed: 0.0287%; gnomAD_G_AFR: 0.0230%; gnomAD_G_EAS: 0.1238%; gnomAD_G_FIN: 0.0289%; gnomAD_G_NFE: 0.0334%; gnomAD_G_OTH: 0.1025%

Other passed variants:

SERPINB5

Exomiser Score: 0.006

Phenotype Score: 0.504

Variant Score: 0.325

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.006

Phenotype Score: 0.504

Variant Score: 0.325

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63494321C>CA [1/1] rs372412366 (variation viewer)

Variant score: 0.325 CONTRIBUTING VARIANT

Transcripts:: SERPINB5:ENST00000382771.9:c.567+1226_567+1227insA:p.(=)

Pathogenicity Data:: Best Score: 0.324695; CADD: 0.325 (1.705)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.63484741C>CTTTTTTTTTTT [1/1] rs869236018 (variation viewer)

Variant score: 0.105

Transcripts:: SERPINB5:ENST00000382771.9:c.168+145_168+146insTTTTTTTTTTT:p.(=); SERPINB5:ENST00000489441.5:c.168+145_168+146insTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.10484135; CADD: 0.105 (0.481)

Frequency Data:: No frequency data

UGT1A6

Exomiser Score: 0.006

Phenotype Score: 0.505

Variant Score: 0.323

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.505

Variant Score: 0.323

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233695130C>CTTTCTTTTT [0/1] rs1364557158 (variation viewer)

Variant score: 0.323 CONTRIBUTING VARIANT

Transcripts:: UGT1A6:ENST00000305139.11:c.861+1265_861+1266insTTTCTTTTT:p.(=); UGT1A6:ENST00000373424.5:c.60+1265_60+1266insTTTCTTTTT:p.(=); UGT1A6:ENST00000406651.1:c.60+1265_60+1266insTTTCTTTTT:p.(=); UGT1A6:ENST00000354728.5:c.855+22341_855+22342insTTTCTTTTT:p.(=); UGT1A6:ENST00000373450.4:c.856-71904_856-71903insTTTCTTTTT:p.(=); UGT1A6:ENST00000344644.9:c.855+57753_855+57754insTTTCTTTTT:p.(=); UGT1A6:ENST00000373445.1:c.855+57753_855+57754insTTTCTTTTT:p.(=); UGT1A6:ENST00000373426.3:c.855+12338_855+12339insTTTCTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.32313824; CADD: 0.323 (1.695)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.254

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233695130C>CTTTCTTTTT [0/1] rs1364557158 (variation viewer)

Variant score: 0.323 CONTRIBUTING VARIANT

Transcripts:: UGT1A6:ENST00000305139.11:c.861+1265_861+1266insTTTCTTTTT:p.(=); UGT1A6:ENST00000373424.5:c.60+1265_60+1266insTTTCTTTTT:p.(=); UGT1A6:ENST00000406651.1:c.60+1265_60+1266insTTTCTTTTT:p.(=); UGT1A6:ENST00000354728.5:c.855+22341_855+22342insTTTCTTTTT:p.(=); UGT1A6:ENST00000373450.4:c.856-71904_856-71903insTTTCTTTTT:p.(=); UGT1A6:ENST00000344644.9:c.855+57753_855+57754insTTTCTTTTT:p.(=); UGT1A6:ENST00000373445.1:c.855+57753_855+57754insTTTCTTTTT:p.(=); UGT1A6:ENST00000373426.3:c.855+12338_855+12339insTTTCTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.32313824; CADD: 0.323 (1.695)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233731857C>T [0/1] rs191763365 (variation viewer)

Variant score: 0.185 CONTRIBUTING VARIANT

Transcripts:: UGT1A6:ENST00000305139.11:c.862-35177C>T:p.(=); UGT1A6:ENST00000373424.5:c.61-35177C>T:p.(=); UGT1A6:ENST00000406651.1:c.61-35177C>T:p.(=); UGT1A6:ENST00000373414.3:c.867+17999C>T:p.(=); UGT1A6:ENST00000354728.5:c.856-35177C>T:p.(=); UGT1A6:ENST00000373450.4:c.856-35177C>T:p.(=); UGT1A6:ENST00000344644.9:c.856-35177C>T:p.(=); UGT1A6:ENST00000373445.1:c.856-35177C>T:p.(=); UGT1A6:ENST00000482026.5:c.867+1864C>T:p.(=); UGT1A6:ENST00000373426.3:c.856-35177C>T:p.(=); UGT1A6:ENST00000373409.7:c.867+12170C>T:p.(=)

Pathogenicity Data:: Best Score: 0.21530658; CADD: 0.215 (1.053)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 0.1402%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.3580%; gnomAD_G_NFE: 0.1666%; gnomAD_G_OTH: 0.2041%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233725179GAGAGGCAGAGGC>G [1/1] rs879478240 (variation viewer)

Variant score: 0.209

Transcripts:: UGT1A6:ENST00000305139.11:c.861+31315_861+31326del:p.(=); UGT1A6:ENST00000373424.5:c.60+31315_60+31326del:p.(=); UGT1A6:ENST00000406651.1:c.60+31315_60+31326del:p.(=); UGT1A6:ENST00000373414.3:c.867+11322_867+11333del:p.(=); UGT1A6:ENST00000354728.5:c.856-41854_856-41843del:p.(=); UGT1A6:ENST00000373450.4:c.856-41854_856-41843del:p.(=); UGT1A6:ENST00000344644.9:c.856-41854_856-41843del:p.(=); UGT1A6:ENST00000373445.1:c.856-41854_856-41843del:p.(=); UGT1A6:ENST00000373426.3:c.856-41854_856-41843del:p.(=); UGT1A6:ENST00000373409.7:c.867+5493_867+5504del:p.(=)

Pathogenicity Data:: Best Score: 0.25663865; CADD: 0.257 (1.288)

Frequency Data:: gnomAD_G_AFR: 0.4223%; gnomAD_G_AMR: 0.8523%; gnomAD_G_EAS: 0.1953%; gnomAD_G_FIN: 0.0627%; gnomAD_G_NFE: 0.4439%; gnomAD_G_OTH: 0.8621%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233757535A>AATATATATACATATACATATATATATATATAT [0/1]

Variant score: 0.108

Transcripts:: UGT1A6:ENST00000305139.11:c.862-9499_862-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000373424.5:c.61-9499_61-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000406651.1:c.61-9499_61-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000373414.3:c.868-9499_868-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000354728.5:c.856-9499_856-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000373450.4:c.856-9499_856-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000344644.9:c.856-9499_856-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000373445.1:c.856-9499_856-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000482026.5:c.868-9499_868-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000373426.3:c.856-9499_856-9498insATATATATACATATACATATATATATATATAT:p.(=); UGT1A6:ENST00000373409.7:c.868-9499_868-9498insATATATATACATATACATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.1077224; CADD: 0.108 (0.495)

Frequency Data:: No frequency data

NDUFS5

Exomiser Score: 0.006

Phenotype Score: 0.504

Variant Score: 0.320

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.006

Phenotype Score: 0.504

Variant Score: 0.320

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.39050221A>G [0/1] rs142874981 (variation viewer)

Variant score: 0.440 CONTRIBUTING VARIANT

Transcripts:: NDUFS5:ENST00000372967.3::

Pathogenicity Data:: Best Score: 0.8080005; CADD: 0.808 (7.167)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.8649%; UK10K: 1.4282%; gnomAD_G_AFR: 0.2982%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0618%; gnomAD_G_FIN: 0.4296%; gnomAD_G_NFE: 1.4727%; gnomAD_G_OTH: 1.0246%

INTERGENIC_VARIANT chr1:g.39040069C>CT [-/1] rs200616251 (variation viewer)

Variant score: 0.200 CONTRIBUTING VARIANT

Transcripts:: NDUFS5:ENST00000372967.3::

Pathogenicity Data:: Best Score: 0.24403793; CADD: 0.244 (1.215)

Frequency Data:: gnomAD_G_AFR: 0.1744%; gnomAD_G_EAS: 0.1014%; gnomAD_G_NFE: 0.8457%; gnomAD_G_OTH: 0.2688%

Other passed variants:

INTERGENIC_VARIANT chr1:g.39039802A>AAT [0/1] rs551855553 (variation viewer)

Variant score: 0.043

Transcripts:: NDUFS5:ENST00000372967.3::

Pathogenicity Data:: Best Score: 0.18266517; CADD: 0.183 (0.876)

Frequency Data:: UK10K: 0.7009%; gnomAD_G_AFR: 0.1526%; gnomAD_G_AMR: 0.4065%; gnomAD_G_ASJ: 1.3793%; gnomAD_G_FIN: 1.7391%; gnomAD_G_NFE: 1.7234%; gnomAD_G_OTH: 1.8931%

NOS3

Exomiser Score: 0.006

Phenotype Score: 0.502

Variant Score: 0.316

Phenotype matches:

Phenotypic similarity 0.436 to mouse mutant involving NOS3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.502 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:104300 Alzheimer disease, late-onset, susceptibility to (susceptibility); OMIM:145500 Hypertension, susceptibility to (susceptibility); OMIM:189800 Hypertension, pregnancy-induced (susceptibility); OMIM:601367 Ischemic stroke, susceptibility to (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.502

Variant Score: 0.316

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.151002383AAC>A [0/1] rs3138808 (variation viewer)

Variant score: 0.316 CONTRIBUTING VARIANT

Transcripts:: NOS3:ENST00000297494.8:c.1752+80_1752+81del:p.(=); NOS3:ENST00000461406.5:c.1134+80_1134+81del:p.(=); NOS3:ENST00000467517.1:c.1752+80_1752+81del:p.(=); NOS3:ENST00000484524.5:c.1752+80_1752+81del:p.(=)

Pathogenicity Data:: Best Score: 0.3164032; CADD: 0.316 (1.652)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.273

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.151002383AAC>A [0/1] rs3138808 (variation viewer)

Variant score: 0.316 CONTRIBUTING VARIANT

Transcripts:: NOS3:ENST00000297494.8:c.1752+80_1752+81del:p.(=); NOS3:ENST00000461406.5:c.1134+80_1134+81del:p.(=); NOS3:ENST00000467517.1:c.1752+80_1752+81del:p.(=); NOS3:ENST00000484524.5:c.1752+80_1752+81del:p.(=)

Pathogenicity Data:: Best Score: 0.3164032; CADD: 0.316 (1.652)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr7:g.150755609T>TAGAGAGAGAGAGAGAG [-/1] rs58155618 (variation viewer)

Variant score: 0.229 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.22909653; CADD: 0.229 (1.130)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr7:g.150987803TGTGA>* [-/1]

Variant score: 0.000

Transcripts:: NOS3:ENST00000297494.8::; NOS3:ENST00000262186.10::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NDUFB2

Exomiser Score: 0.006

Phenotype Score: 0.504

Variant Score: 0.312

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.006

Phenotype Score: 0.504

Variant Score: 0.312

Variants contributing to score:

REGULATORY_REGION_VARIANT chr7:g.140219509CA>C [0/1] rs71170957 (variation viewer)

Variant score: 0.312 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.3121401; CADD: 0.312 (1.625)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.156

Variants contributing to score:

REGULATORY_REGION_VARIANT chr7:g.140219509CA>C [0/1] rs71170957 (variation viewer)

Variant score: 0.312 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.3121401; CADD: 0.312 (1.625)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr7:g.140324893GT>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

SETDB1

Exomiser Score: 0.005

Phenotype Score: 0.504

Variant Score: 0.309

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.150916043C>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: SETDB1:ENST00000271640.9::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.504

Variant Score: 0.309

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.150932052T>C [0/1] rs139793505 (variation viewer)

Variant score: 0.618 CONTRIBUTING VARIANT

Transcripts:: SETDB1:ENST00000271640.9:c.412+1934T>C:p.(=); SETDB1:ENST00000368962.6:c.412+1934T>C:p.(=); SETDB1:ENST00000368963.5:c.412+1934T>C:p.(=); SETDB1:ENST00000368969.8:c.412+1934T>C:p.(=)

Pathogenicity Data:: Best Score: 0.6563629; CADD: 0.656 (4.639)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.0725%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_AMR: 0.3589%; gnomAD_G_NFE: 0.1002%

INTERGENIC_VARIANT chr1:g.150916043C>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: SETDB1:ENST00000271640.9::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.150930519C>CTT [1/1] rs61548246 (variation viewer)

Variant score: 0.180

Transcripts:: SETDB1:ENST00000271640.9:c.412+401_412+402insTT:p.(=); SETDB1:ENST00000368962.6:c.412+401_412+402insTT:p.(=); SETDB1:ENST00000368963.5:c.412+401_412+402insTT:p.(=); SETDB1:ENST00000368969.8:c.412+401_412+402insTT:p.(=)

Pathogenicity Data:: Best Score: 0.18040371; CADD: 0.180 (0.864)

Frequency Data:: No frequency data

EIF4A2

Exomiser Score: 0.005

Phenotype Score: 0.502

Variant Score: 0.311

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.005

Phenotype Score: 0.502

Variant Score: 0.311

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr3:g.186781333G>A [0/1] rs986011922 (variation viewer)

Variant score: 0.311 CONTRIBUTING VARIANT

Transcripts:: EIF4A2:ENST00000323963.10::; EIF4A2:ENST00000430745.1::

Pathogenicity Data:: Best Score: 0.31277335; CADD: 0.313 (1.629)

Frequency Data:: TOPMed: 0.0104%; gnomAD_G_NFE: 0.0400%

Other passed variants:

COX4I2

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.307

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612714 Exocrine pancreatic insufficiency, dyserythropoietic anemia, and calvarial hyperostosis - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.307

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr20:g.31649608A>G [0/1] rs139559092 (variation viewer)

Variant score: 0.407 CONTRIBUTING VARIANT

Transcripts:: COX4I2:ENST00000376075.4::; COX4I2:ENST00000376062.6::

Pathogenicity Data:: Best Score: 0.46997058; CADD: 0.470 (2.757)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 0.4285%; UK10K: 0.6876%; gnomAD_G_AFR: 0.0923%; gnomAD_G_AMR: 0.4785%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0861%; gnomAD_G_NFE: 0.6292%; gnomAD_G_OTH: 0.6135%

INTERGENIC_VARIANT chr20:g.31625601G>A [0/1] rs527745843 (variation viewer)

Variant score: 0.206 CONTRIBUTING VARIANT

Transcripts:: COX4I2:ENST00000376075.4::

Pathogenicity Data:: Best Score: 0.21801215; CADD: 0.218 (1.068)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1601%; gnomAD_G_AFR: 0.0465%; gnomAD_G_AMR: 0.1202%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_NFE: 0.1640%; gnomAD_G_OTH: 0.2132%

Other passed variants:

INTERGENIC_VARIANT chr20:g.31654687A>G [0/1] rs117545313 (variation viewer)

Variant score: 0.199

Transcripts:: COX4I2:ENST00000376075.4::; COX4I2:ENST00000376062.6::

Pathogenicity Data:: Best Score: 0.23104662; CADD: 0.231 (1.141)

Frequency Data:: 1000Genomes: 0.5990%; TOPMed: 0.4396%; UK10K: 0.6876%; gnomAD_G_AFR: 0.0917%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0861%; gnomAD_G_NFE: 0.6606%; gnomAD_G_OTH: 0.7128%

CNBD2

Exomiser Score: 0.005

Phenotype Score: 0.507

Variant Score: 0.298

Phenotype matches:

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.147

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.36028685G>GTTTTTTTTTTTTTT [0/1] rs148778050 (variation viewer)

Variant score: 0.147 CONTRIBUTING VARIANT

Transcripts:: CNBD2:ENST00000349339.5:c.1428-1672_1428-1671insTTTTTTTTTTTTTT:p.(=); CNBD2:ENST00000373973.7:c.1440-1672_1440-1671insTTTTTTTTTTTTTT:p.(=); CNBD2:ENST00000538900.1:c.1270-1672_1270-1671insTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.1465069; CADD: 0.147 (0.688)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.507

Variant Score: 0.298

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.36029506A>G [0/1] rs569653815 (variation viewer)

Variant score: 0.332 CONTRIBUTING VARIANT

Transcripts:: CNBD2:ENST00000349339.5:c.1428-851A>G:p.(=); CNBD2:ENST00000373973.7:c.1440-851A>G:p.(=); CNBD2:ENST00000538900.1:c.1270-851A>G:p.(=)

Pathogenicity Data:: Best Score: 0.3470198; CADD: 0.347 (1.851)

Frequency Data:: TOPMed: 0.0812%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0344%; gnomAD_G_NFE: 0.1333%; gnomAD_G_OTH: 0.1018%

INTERGENIC_VARIANT chr20:g.35962399C>T [0|1] rs140770153 (variation viewer)

Variant score: 0.264 CONTRIBUTING VARIANT

Transcripts:: CNBD2:ENST00000373973.7::

Pathogenicity Data:: Best Score: 0.30224973; CADD: 0.302 (1.563)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.5240%; UK10K: 0.6612%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0862%; gnomAD_G_NFE: 0.6409%; gnomAD_G_OTH: 0.3074%

Other passed variants:

UPSTREAM_GENE_VARIANT chr20:g.35966556A>G [0/1] rs144626888 (variation viewer)

Variant score: 0.124

Transcripts:: CNBD2:ENST00000373973.7::; CNBD2:ENST00000373991.3::

Pathogenicity Data:: Best Score: 0.12943739; CADD: 0.129 (0.602)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.1115%; UK10K: 0.2777%; gnomAD_G_AFR: 0.0229%; gnomAD_G_NFE: 0.1535%; gnomAD_G_OTH: 0.1022%

UPSTREAM_GENE_VARIANT chr20:g.35967620A>AGGT [0/1] rs1379975235 (variation viewer)

Variant score: 0.000

Transcripts:: CNBD2:ENST00000373973.7::; CNBD2:ENST00000373991.3::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: TOPMed: 0.0008%

B3GALT5

Exomiser Score: 0.005

Phenotype Score: 0.502

Variant Score: 0.302

Phenotype matches:

Proximity score 0.502 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.502

Variant Score: 0.029

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr21:g.39586220G>GTGTATATATATATATATATATATATATATATATA [0/1] rs1555920998 (variation viewer)

Variant score: 0.029 CONTRIBUTING VARIANT

Transcripts:: B3GALT5:ENST00000380620.8:c.-523-18874_-523-18873insTGTATATATATATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.028595746; CADD: 0.029 (0.126)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.502

Variant Score: 0.302

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr21:g.39583839C>T [1|1] rs370449972 (variation viewer)

Variant score: 0.302 CONTRIBUTING VARIANT

Transcripts:: B3GALT5:ENST00000380620.8:c.-523-21255C>T:p.(=)

Pathogenicity Data:: Best Score: 0.30224973; CADD: 0.302 (1.563)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr21:g.39642873CA>C [0/1] rs1210751363 (variation viewer)

Variant score: 0.023

Transcripts:: B3GALT5:ENST00000380620.8:c.-391-3518del:p.(=); B3GALT5:ENST00000615480.4:c.-160-16879del:p.(=)

Pathogenicity Data:: Best Score: 0.063516796; CADD: 0.064 (0.285)

Frequency Data:: gnomAD_G_AFR: 0.4469%; gnomAD_G_AMR: 1.7241%; gnomAD_G_EAS: 0.0850%; gnomAD_G_FIN: 1.7341%; gnomAD_G_NFE: 0.7048%; gnomAD_G_OTH: 0.8021%

UPSTREAM_GENE_VARIANT chr21:g.39554976ATATATATATATATAAAATATATATATATATATAAAATATATATATATATATATTT>* [-/1]

Variant score: 0.000

Transcripts:: B3GALT5:ENST00000380620.8::; B3GALT5:ENST00000411867.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr21:g.39557680C>* [-/1]

Variant score: 0.000

Transcripts:: B3GALT5:ENST00000380620.8:c.-524+1170C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

FIVE_PRIME_UTR_INTRON_VARIANT chr21:g.39571323ATGTGTG>* [-/1]

Variant score: 0.000

Transcripts:: B3GALT5:ENST00000380620.8:c.-524+14813_-524+14819delATGTGTGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SP1

Exomiser Score: 0.005

Phenotype Score: 0.503

Variant Score: 0.297

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.005

Phenotype Score: 0.503

Variant Score: 0.297

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.53395776G>A [0/1] rs914052057 (variation viewer)

Variant score: 0.297 CONTRIBUTING VARIANT

Transcripts:: SP1:ENST00000327443.9:c.1676-10809G>A:p.(=); SP1:ENST00000426431.2:c.1655-10809G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2985447; CADD: 0.299 (1.540)

Frequency Data:: gnomAD_G_NFE: 0.0405%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.056

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.53406065C>CT [1/1] rs1170832065 (variation viewer)

Variant score: 0.056 CONTRIBUTING VARIANT

Transcripts:: SP1:ENST00000327443.9:c.1676-520_1676-519insT:p.(=); SP1:ENST00000426431.2:c.1655-520_1655-519insT:p.(=)

Pathogenicity Data:: Best Score: 0.0557217; CADD: 0.056 (0.249)

Frequency Data:: No frequency data

Other passed variants:

ALDH1A3

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.294

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:615113 Microphthalmia, isolated 8 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.251

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.100908016T>G [0/1] rs747628813 (variation viewer)

Variant score: 0.251 CONTRIBUTING VARIANT

Transcripts:: ALDH1A3:ENST00000329841.10:c.1392-392T>G:p.(=); ALDH1A3:ENST00000346623.6:c.1071-392T>G:p.(=)

Pathogenicity Data:: Best Score: 0.2513135; CADD: 0.251 (1.257)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.294

Variants contributing to score:

REGULATORY_REGION_VARIANT chr15:g.100721147T>TTG [1/1] rs151054934 (variation viewer)

Variant score: 0.294 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.2941702; CADD: 0.294 (1.513)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr15:g.100861824C>T [0/1] rs192698513 (variation viewer)

Variant score: 0.251

Transcripts:: ALDH1A3:ENST00000329841.10::; ALDH1A3:ENST00000559380.1::

Pathogenicity Data:: Best Score: 0.5394254; CADD: 0.539 (3.367)

Frequency Data:: 1000Genomes: 0.4393%; TOPMed: 1.1050%; UK10K: 1.6001%; gnomAD_G_AFR: 0.3206%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.6297%; gnomAD_G_NFE: 1.5335%; gnomAD_G_OTH: 0.7128%

CERK

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.293

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.139

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46691056T>TACACACACACAC [-/1] rs141210280 (variation viewer)

Variant score: 0.139 CONTRIBUTING VARIANT

Transcripts:: CERK:ENST00000216264.13:c.1332+515_1332+516insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.13880795; CADD: 0.139 (0.649)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.293

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46713791G>C [0/1] rs547879121 (variation viewer)

Variant score: 0.446 CONTRIBUTING VARIANT

Transcripts:: CERK:ENST00000216264.13:c.380-1498C>G:p.(=)

Pathogenicity Data:: Best Score: 0.45424217; CADD: 0.454 (2.630)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0319%; gnomAD_G_AMR: 0.1196%; gnomAD_G_NFE: 0.0400%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46691056T>TACACACACACAC [-/1] rs141210280 (variation viewer)

Variant score: 0.139 CONTRIBUTING VARIANT

Transcripts:: CERK:ENST00000216264.13:c.1332+515_1332+516insGTGTGTGTGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.13880795; CADD: 0.139 (0.649)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46709708C>A [0/1] rs934360567 (variation viewer)

Variant score: 0.118

Transcripts:: CERK:ENST00000216264.13:c.569+1378G>T:p.(=)

Pathogenicity Data:: Best Score: 0.11813927; CADD: 0.118 (0.546)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46726548G>A [0/1] rs181430064 (variation viewer)

Variant score: 0.117

Transcripts:: CERK:ENST00000216264.13:c.143-5533C>T:p.(=)

Pathogenicity Data:: Best Score: 0.13003856; CADD: 0.130 (0.605)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.5384%; UK10K: 0.4232%; gnomAD_G_AFR: 0.0803%; gnomAD_G_AMR: 0.3580%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.5401%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.46712536G>A [0/1] rs117937275 (variation viewer)

Variant score: 0.040

Transcripts:: CERK:ENST00000216264.13:c.380-243C>T:p.(=)

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: 1000Genomes: 0.8586%; TOPMed: 1.2430%; UK10K: 1.6266%; gnomAD_G_AFR: 0.2755%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.4585%; gnomAD_G_NFE: 1.5654%; gnomAD_G_OTH: 1.5337%

CSNK2A1

Exomiser Score: 0.005

Phenotype Score: 0.251

Variant Score: 0.580

Phenotype matches:

Proximity score 0.502 in interactome to HIRA and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with HIRA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:617062 Okur-Chung neurodevelopmental syndrome - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.251

Variant Score: 0.580

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.539327C>T [0/1] rs117308522 (variation viewer)

Variant score: 0.814 CONTRIBUTING VARIANT

Transcripts:: CSNK2A1:ENST00000217244.9:c.-227+4345G>A:p.(=); CSNK2A1:ENST00000349736.10:c.-308+4345G>A:p.(=); CSNK2A1:ENST00000400217.7:c.-55+4345G>A:p.(=); CSNK2A1:ENST00000400227.8:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000642160.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000642689.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000643600.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000643660.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000644003.1:c.-414+4345G>A:p.(=); CSNK2A1:ENST00000644710.1:c.-357+4345G>A:p.(=); CSNK2A1:ENST00000644885.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000645187.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000645234.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000645260.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000645623.1:c.-227+4345G>A:p.(=); CSNK2A1:ENST00000646305.1:c.-474+4345G>A:p.(=); CSNK2A1:ENST00000646477.1:c.-559+4345G>A:p.(=); CSNK2A1:ENST00000646561.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000646814.1:c.-357+4345G>A:p.(=); CSNK2A1:ENST00000647026.1:c.-110+4345G>A:p.(=); CSNK2A1:ENST00000647348.1:c.-110+1563G>A:p.(=)

Pathogenicity Data:: Best Score: 0.9396051; CADD: 0.940 (12.190)

Frequency Data:: TOPMed: 0.4269%; UK10K: 0.6876%; gnomAD_G_AFR: 0.0802%; gnomAD_G_FIN: 0.4293%; gnomAD_G_NFE: 0.4398%; gnomAD_G_OTH: 0.4073%

FIVE_PRIME_UTR_INTRON_VARIANT chr20:g.518083A>T [0/1] rs75834664 (variation viewer)

Variant score: 0.346 CONTRIBUTING VARIANT

Transcripts:: CSNK2A1:ENST00000217244.9:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000349736.10:c.-307-12854T>A:p.(=); CSNK2A1:ENST00000400217.7:c.-54-9478T>A:p.(=); CSNK2A1:ENST00000400227.8:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000642160.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000642689.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000643600.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000643660.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000644003.1:c.-413-12854T>A:p.(=); CSNK2A1:ENST00000644710.1:c.-110+8613T>A:p.(=); CSNK2A1:ENST00000644885.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000645187.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000645234.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000645260.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000645623.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000646305.1:c.-110+8613T>A:p.(=); CSNK2A1:ENST00000646477.1:c.-442+9850T>A:p.(=); CSNK2A1:ENST00000646561.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000646814.1:c.-110+8613T>A:p.(=); CSNK2A1:ENST00000647026.1:c.-109-9423T>A:p.(=); CSNK2A1:ENST00000647348.1:c.-109-9423T>A:p.(=)

Pathogenicity Data:: Best Score: 0.9345364; CADD: 0.935 (11.840)

Frequency Data:: 1000Genomes: 0.5591%; TOPMed: 1.0770%; UK10K: 1.7323%; gnomAD_G_AFR: 0.2522%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.6583%; gnomAD_G_NFE: 1.4596%; gnomAD_G_OTH: 0.8147%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr20:g.475494C>CCA [0/1] rs200228258 (variation viewer)

Variant score: 0.010

Transcripts:: CSNK2A1:ENST00000217244.9:c.*8465_*8466dup:p.(=); CSNK2A1:ENST00000646561.1:c.*8465_*8466dup:p.(=); CSNK2A1:ENST00000643660.1:c.*34-1545_*34-1544insTG:p.(=); CSNK2A1:ENST00000645623.1:c.*34-1545_*34-1544insTG:p.(=)

Pathogenicity Data:: Best Score: 0.0770036; CADD: 0.077 (0.348)

Frequency Data:: 1000Genomes: 0.6589%; TOPMed: 0.6589%; UK10K: 1.9175%; gnomAD_G_AFR: 0.2315%; gnomAD_G_AMR: 0.5102%; gnomAD_G_ASJ: 2.0000%; gnomAD_G_FIN: 0.7186%; gnomAD_G_NFE: 1.5117%; gnomAD_G_OTH: 1.1411%

PLPP2

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.292

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.505

Variant Score: 0.292

Variants contributing to score:

INTERGENIC_VARIANT chr19:g.274786CTT>C [1/1] rs59968582 (variation viewer)

Variant score: 0.292 CONTRIBUTING VARIANT

Transcripts:: PLPP2:ENST00000327790.7::; PLPP2:ENST00000632795.1::

Pathogenicity Data:: Best Score: 0.291565; CADD: 0.292 (1.497)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr19:g.298356A>ATGACACCAGTGACTGGAGAGACTGTGGGACACCCAGGGCCG [1/1] rs1568207878 (variation viewer)

Variant score: 0.071

Transcripts:: PLPP2:ENST00000434325.7::

Pathogenicity Data:: Best Score: 0.070605695; CADD: 0.071 (0.318)

Frequency Data:: No frequency data

TFAM

Exomiser Score: 0.005

Phenotype Score: 0.517

Variant Score: 0.278

Phenotype matches:

Proximity score 0.517 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617156 ?Mitochondrial DNA depletion syndrome 15 (hepatocerebral type) (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.259

Variant Score: 0.241

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr10:g.58384933T>C [0/1] rs187107005 (variation viewer)

Variant score: 0.241 CONTRIBUTING VARIANT

Transcripts:: TFAM:ENST00000487519.6::; TFAM:ENST00000615793.1::

Pathogenicity Data:: Best Score: 0.24264413; CADD: 0.243 (1.207)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0048%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.005

Phenotype Score: 0.517

Variant Score: 0.278

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr10:g.58401980G>A [0/1] rs12761094 (variation viewer)

Variant score: 0.314 CONTRIBUTING VARIANT

Transcripts:: TFAM:ENST00000487519.6::; TFAM:ENST00000373886.8::

Pathogenicity Data:: Best Score: 0.67618275; CADD: 0.676 (4.897)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.8235%; UK10K: 1.6001%; gnomAD_G_AFR: 0.2634%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.2864%; gnomAD_G_NFE: 1.3253%; gnomAD_G_OTH: 0.9184%

UPSTREAM_GENE_VARIANT chr10:g.58384933T>C [0/1] rs187107005 (variation viewer)

Variant score: 0.241 CONTRIBUTING VARIANT

Transcripts:: TFAM:ENST00000487519.6::; TFAM:ENST00000615793.1::

Pathogenicity Data:: Best Score: 0.24264413; CADD: 0.243 (1.207)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0048%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr10:g.58395968A>G [0/1] rs74587271 (variation viewer)

Variant score: 0.149

Transcripts:: TFAM:ENST00000487519.6:c.*894A>G:p.(=)

Pathogenicity Data:: Best Score: 0.1597665; CADD: 0.160 (0.756)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.1250%; gnomAD_G_AFR: 0.3324%

CAMSAP3

Exomiser Score: 0.005

Phenotype Score: 0.507

Variant Score: 0.287

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.005

Phenotype Score: 0.507

Variant Score: 0.287

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.7614259C>CAA [0/1] rs1173068955 (variation viewer)

Variant score: 0.287 CONTRIBUTING VARIANT

Transcripts:: CAMSAP3:ENST00000160298.8:c.2671-924_2671-923insAA:p.(=); CAMSAP3:ENST00000446248.4:c.2752-924_2752-923insAA:p.(=)

Pathogenicity Data:: Best Score: 0.28731108; CADD: 0.287 (1.471)

Frequency Data:: No frequency data

Other passed variants:

CDC14A

Exomiser Score: 0.004

Phenotype Score: 0.510

Variant Score: 0.282

Phenotype matches:

Proximity score 0.510 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:608653 Deafness, autosomal recessive 32, with or without immotile sperm - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.255

Variant Score: 0.035

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100420063C>CATATATATATATATATATATAT [-/1] rs1553180578 (variation viewer)

Variant score: 0.035 CONTRIBUTING VARIANT

Transcripts:: CDC14A:ENST00000336454.5:c.310-4159_310-4158insATATATATATATATATATATAT:p.(=); CDC14A:ENST00000361544.11:c.310-4159_310-4158insATATATATATATATATATATAT:p.(=); CDC14A:ENST00000370124.8:c.310-4159_310-4158insATATATATATATATATATATAT:p.(=); CDC14A:ENST00000635056.2:c.136-4159_136-4158insATATATATATATATATATATAT:p.(=); CDC14A:ENST00000644676.1:c.313-4159_313-4158insATATATATATATATATATATAT:p.(=); CDC14A:ENST00000644813.1:c.310-4159_310-4158insATATATATATATATATATATAT:p.(=); CDC14A:ENST00000647005.1:c.136-4159_136-4158insATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.034616232; CADD: 0.035 (0.153)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.510

Variant Score: 0.282

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100387224T>G [0/1] rs564458817 (variation viewer)

Variant score: 0.425 CONTRIBUTING VARIANT

Transcripts:: CDC14A:ENST00000336454.5:c.217-3508T>G:p.(=); CDC14A:ENST00000361544.11:c.217-3508T>G:p.(=); CDC14A:ENST00000370124.8:c.217-3508T>G:p.(=); CDC14A:ENST00000635056.2:c.43-3508T>G:p.(=); CDC14A:ENST00000644676.1:c.220-3508T>G:p.(=); CDC14A:ENST00000644813.1:c.217-3508T>G:p.(=); CDC14A:ENST00000647005.1:c.43-3508T>G:p.(=)

Pathogenicity Data:: Best Score: 0.48666602; CADD: 0.487 (2.896)

Frequency Data:: TOPMed: 0.0796%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0229%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1133%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100516557A>T [0/1] rs549496554 (variation viewer)

Variant score: 0.138 CONTRIBUTING VARIANT

Transcripts:: CDC14A:ENST00000336454.5:c.1756-1694A>T:p.(=); CDC14A:ENST00000644813.1:c.*47-1694A>T:p.(=); CDC14A:ENST00000647005.1:c.*47-1694A>T:p.(=)

Pathogenicity Data:: Best Score: 0.15841109; CADD: 0.158 (0.749)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0836%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0229%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1265%; gnomAD_G_OTH: 0.1020%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100482639G>T [0/1] rs773569761 (variation viewer)

Variant score: 0.131

Transcripts:: CDC14A:ENST00000336454.5:c.978-1653G>T:p.(=); CDC14A:ENST00000361544.11:c.978-1653G>T:p.(=); CDC14A:ENST00000370124.8:c.978-1653G>T:p.(=); CDC14A:ENST00000635056.2:c.804-1653G>T:p.(=); CDC14A:ENST00000644676.1:c.981-1653G>T:p.(=); CDC14A:ENST00000644813.1:c.978-1653G>T:p.(=); CDC14A:ENST00000647005.1:c.804-1653G>T:p.(=)

Pathogenicity Data:: Best Score: 0.13283849; CADD: 0.133 (0.619)

Frequency Data:: TOPMed: 0.0358%; UK10K: 0.0264%; gnomAD_G_FIN: 0.0288%; gnomAD_G_NFE: 0.0534%; gnomAD_G_OTH: 0.1027%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100491568A>AT [0/1] rs1255539504 (variation viewer)

Variant score: 0.096

Transcripts:: CDC14A:ENST00000336454.5:c.1138-3250_1138-3249insT:p.(=); CDC14A:ENST00000361544.11:c.1138-3250_1138-3249insT:p.(=); CDC14A:ENST00000635056.2:c.964-3250_964-3249insT:p.(=); CDC14A:ENST00000644676.1:c.1141-3250_1141-3249insT:p.(=); CDC14A:ENST00000644813.1:c.1138-3250_1138-3249insT:p.(=); CDC14A:ENST00000647005.1:c.964-3250_964-3249insT:p.(=)

Pathogenicity Data:: Best Score: 0.12138218; CADD: 0.121 (0.562)

Frequency Data:: gnomAD_G_AFR: 0.2613%; gnomAD_G_ASJ: 0.9259%; gnomAD_G_NFE: 0.3692%

INTERGENIC_VARIANT chr1:g.100334747A>G [0/1] rs767190655 (variation viewer)

Variant score: 0.056

Transcripts:: CDC14A:ENST00000635056.2::

Pathogenicity Data:: Best Score: 0.056373775; CADD: 0.056 (0.252)

Frequency Data:: TOPMed: 0.0358%; UK10K: 0.0661%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0533%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100420063C>CACACATATATATATATATATATATATAT [-/1]

Variant score: 0.031

Transcripts:: CDC14A:ENST00000336454.5:c.310-4159_310-4158insACACATATATATATATATATATATATAT:p.(=); CDC14A:ENST00000361544.11:c.310-4159_310-4158insACACATATATATATATATATATATATAT:p.(=); CDC14A:ENST00000370124.8:c.310-4159_310-4158insACACATATATATATATATATATATATAT:p.(=); CDC14A:ENST00000635056.2:c.136-4159_136-4158insACACATATATATATATATATATATATAT:p.(=); CDC14A:ENST00000644676.1:c.313-4159_313-4158insACACATATATATATATATATATATATAT:p.(=); CDC14A:ENST00000644813.1:c.310-4159_310-4158insACACATATATATATATATATATATATAT:p.(=); CDC14A:ENST00000647005.1:c.136-4159_136-4158insACACATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.030829906; CADD: 0.031 (0.136)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100491572A>T [1/1] rs4520435 (variation viewer)

Variant score: 0.024

Transcripts:: CDC14A:ENST00000336454.5:c.1138-3246A>T:p.(=); CDC14A:ENST00000361544.11:c.1138-3246A>T:p.(=); CDC14A:ENST00000635056.2:c.964-3246A>T:p.(=); CDC14A:ENST00000644676.1:c.1141-3246A>T:p.(=); CDC14A:ENST00000644813.1:c.1138-3246A>T:p.(=); CDC14A:ENST00000647005.1:c.964-3246A>T:p.(=)

Pathogenicity Data:: Best Score: 0.023887217; CADD: 0.024 (0.105)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.100435824A>* [-/1]

Variant score: 0.000

Transcripts:: CDC14A:ENST00000336454.5:c.390-4108A>*:p.(=); CDC14A:ENST00000361544.11:c.390-4108A>*:p.(=); CDC14A:ENST00000370124.8:c.390-4108A>*:p.(=); CDC14A:ENST00000635056.2:c.216-4108A>*:p.(=); CDC14A:ENST00000644676.1:c.393-4108A>*:p.(=); CDC14A:ENST00000644813.1:c.390-4108A>*:p.(=); CDC14A:ENST00000647005.1:c.216-4108A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

HLA-C

Exomiser Score: 0.004

Phenotype Score: 0.252

Variant Score: 0.573

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:177900 Psoriasis susceptibility 1 (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.252

Variant Score: 0.573

Variants contributing to score:

REGULATORY_REGION_VARIANT chr6:g.30806507A>G [0|1] rs141494988 (variation viewer)

Variant score: 0.573 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.57322395; CADD: 0.573 (3.698)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.252

Variant Score: 0.450

Variants contributing to score:

REGULATORY_REGION_VARIANT chr6:g.30806507A>G [0|1] rs141494988 (variation viewer)

Variant score: 0.573 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.57322395; CADD: 0.573 (3.698)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr6:g.30806512T>A [0|1]

Variant score: 0.328 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.32764292; CADD: 0.328 (1.724)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31269806GCT>G [0/1] rs281860586 (variation viewer)

Variant score: 0.142

Transcripts:: HLA-C:ENST00000376228.9:c.1015+158_1015+159del:p.(=); HLA-C:ENST00000383329.7:c.1015+158_1015+159del:p.(=); HLA-C:ENST00000640219.1:c.652+158_652+159del:p.(=); HLA-C:ENST00000640615.1:c.206-283_206-282del:p.(=)

Pathogenicity Data:: Best Score: 0.58960694; CADD: 0.590 (3.868)

Frequency Data:: 1000Genomes: 1.3180%; TOPMed: 1.3180%; UK10K: 0.1587%; gnomAD_G_AFR: 1.8890%; gnomAD_G_AMR: 0.7229%; gnomAD_G_ASJ: 0.6897%; gnomAD_G_FIN: 0.0861%; gnomAD_G_NFE: 0.2617%; gnomAD_G_OTH: 0.4141%

REGULATORY_REGION_VARIANT chr6:g.30806495AGG>A [0|1] rs9281051 (variation viewer)

Variant score: 0.037

Transcripts:

Pathogenicity Data:: Best Score: 0.039272964; CADD: 0.039 (0.174)

Frequency Data:: gnomAD_G_AFR: 0.0126%; gnomAD_G_AMR: 0.1629%; gnomAD_G_ASJ: 0.3876%; gnomAD_G_EAS: 0.0784%; gnomAD_G_FIN: 0.0483%; gnomAD_G_NFE: 0.1841%; gnomAD_G_OTH: 0.2681%

DCX

Exomiser Score: 0.004

Phenotype Score: 0.501

Variant Score: 0.288

Phenotype matches:

Proximity score 0.501 in interactome to CEP85L and phenotypic similarity 0.913 to Lissencephaly 10 associated with CEP85L.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300067 Subcortical laminal heterotopia, X-linked - X-linked; ORPHA:2148 Lissencephaly type 1 due to doublecortin gene mutation

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.501

Variant Score: 0.288

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.111366575C>T [1/1]

Variant score: 0.288 CONTRIBUTING VARIANT

Transcripts:: DCX:ENST00000356220.8:c.706-33422G>A:p.(=); DCX:ENST00000358070.9:c.706-33422G>A:p.(=); DCX:ENST00000371993.6:c.706-33422G>A:p.(=); DCX:ENST00000488120.2:c.706-33422G>A:p.(=); DCX:ENST00000496551.2:c.706-33422G>A:p.(=); DCX:ENST00000635795.1:c.706-33422G>A:p.(=); DCX:ENST00000636035.1:c.706-33422G>A:p.(=); DCX:ENST00000637453.1:c.706-33422G>A:p.(=); DCX:ENST00000637570.1:c.706-33422G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2879672; CADD: 0.288 (1.475)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.501

Variant Score: 0.288

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.111366575C>T [1/1]

Variant score: 0.288 CONTRIBUTING VARIANT

Transcripts:: DCX:ENST00000356220.8:c.706-33422G>A:p.(=); DCX:ENST00000358070.9:c.706-33422G>A:p.(=); DCX:ENST00000371993.6:c.706-33422G>A:p.(=); DCX:ENST00000488120.2:c.706-33422G>A:p.(=); DCX:ENST00000496551.2:c.706-33422G>A:p.(=); DCX:ENST00000635795.1:c.706-33422G>A:p.(=); DCX:ENST00000636035.1:c.706-33422G>A:p.(=); DCX:ENST00000637453.1:c.706-33422G>A:p.(=); DCX:ENST00000637570.1:c.706-33422G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2879672; CADD: 0.288 (1.475)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.111342339T>TTATATATA [1/1] rs60045433 (variation viewer)

Variant score: 0.141

Transcripts:: DCX:ENST00000356220.8:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000358070.9:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000371993.6:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000488120.2:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000496551.2:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000635795.1:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000636035.1:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000637453.1:c.706-9187_706-9186insTATATATA:p.(=); DCX:ENST00000637570.1:c.706-9187_706-9186insTATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.14059079; CADD: 0.141 (0.658)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.111307170TA>T [1/1] rs746691520 (variation viewer)

Variant score: 0.094

Transcripts:: DCX:ENST00000356220.8:c.1045-5428del:p.(=); DCX:ENST00000358070.9:c.1027-5428del:p.(=); DCX:ENST00000371993.6:c.1027-5428del:p.(=); DCX:ENST00000488120.2:c.1027-5428del:p.(=); DCX:ENST00000496551.2:c.1042-5428del:p.(=); DCX:ENST00000635795.1:c.1042-5428del:p.(=); DCX:ENST00000636035.1:c.1045-5428del:p.(=); DCX:ENST00000637453.1:c.1045-5428del:p.(=); DCX:ENST00000637570.1:c.1030-5428del:p.(=)

Pathogenicity Data:: Best Score: 0.10463524; CADD: 0.105 (0.480)

Frequency Data:: 1000Genomes: 0.0795%; TOPMed: 0.3209%; UK10K: 0.5154%; gnomAD_G_AFR: 0.0346%; gnomAD_G_ASJ: 0.5319%; gnomAD_G_FIN: 0.2075%; gnomAD_G_NFE: 0.5047%; gnomAD_G_OTH: 0.5674%

DBH

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.280

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:223360 Orthostatic hypotension 1, due to DBH deficiency - autosomal recessive; ORPHA:230 Dopamine beta-hydroxylase deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.280

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.133628031G>T [0/1] rs571815604 (variation viewer)

Variant score: 0.496 CONTRIBUTING VARIANT

Transcripts:: DBH:ENST00000393056.8::; DBH:ENST00000673969.1::

Pathogenicity Data:: Best Score: 0.5064854; CADD: 0.506 (3.067)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.0860%; UK10K: 0.1190%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.1199%

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.133645241GTTT>G [-/1] rs754586962 (variation viewer)

Variant score: 0.064 CONTRIBUTING VARIANT

Transcripts:: DBH:ENST00000393056.8:c.1024+922_1024+924del:p.(=)

Pathogenicity Data:: Best Score: 0.19443607; CADD: 0.194 (0.939)

Frequency Data:: UK10K: 1.7852%; gnomAD_G_AFR: 0.1865%; gnomAD_G_EAS: 0.1921%; gnomAD_G_FIN: 0.3179%; gnomAD_G_NFE: 0.8004%; gnomAD_G_OTH: 0.3778%

Other passed variants:

INTERGENIC_VARIANT chr9:g.133621860G>A [0/1] rs144614262 (variation viewer)

Variant score: 0.022

Transcripts:: DBH:ENST00000393056.8::; DBH:ENST00000673969.1::

Pathogenicity Data:: Best Score: 0.037723243; CADD: 0.038 (0.167)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.9509%; UK10K: 1.1902%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_FIN: 0.5447%; gnomAD_G_NFE: 1.4143%; gnomAD_G_OTH: 0.7143%

INTERGENIC_VARIANT chr9:g.133628748A>G [0/1] rs117053657 (variation viewer)

Variant score: 0.014

Transcripts:: DBH:ENST00000393056.8::; DBH:ENST00000673969.1::

Pathogenicity Data:: Best Score: 0.03283626; CADD: 0.033 (0.145)

Frequency Data:: 1000Genomes: 0.7788%; TOPMed: 1.2910%; gnomAD_G_AFR: 0.3435%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 1.0876%; gnomAD_G_NFE: 1.6591%; gnomAD_G_OTH: 0.7128%

NDUFB10

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.281

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:619003 ?Mitochondrial complex I deficiency, nuclear type 35 (unconfirmed); ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.000

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr16:g.1956157AT>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NDUFB10:ENST00000268668.11::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.281

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr16:g.1958609G>A [0/1] rs188768534 (variation viewer)

Variant score: 0.561 CONTRIBUTING VARIANT

Transcripts:: NDUFB10:ENST00000268668.11::

Pathogenicity Data:: Best Score: 0.57907957; CADD: 0.579 (3.758)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0382%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.0735%; gnomAD_G_OTH: 0.2045%

UPSTREAM_GENE_VARIANT chr16:g.1956157AT>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NDUFB10:ENST00000268668.11::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

NAT8

Exomiser Score: 0.004

Phenotype Score: 0.532

Variant Score: 0.248

Phenotype matches:

Proximity score 0.532 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.532

Variant Score: 0.248

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.73629172CT>C [1/1] rs34570629 (variation viewer)

Variant score: 0.248 CONTRIBUTING VARIANT

Transcripts:: NAT8:ENST00000272425.4::

Pathogenicity Data:: Best Score: 0.24837708; CADD: 0.248 (1.240)

Frequency Data:: No frequency data

Other passed variants:

CYP1B1

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.274

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:231300 Glaucoma 3A, primary open angle, congenital, juvenile, or adult onset - autosomal recessive; OMIM:617315 Anterior segment dysgenesis 6, multiple subtypes - autosomal recessive; ORPHA:708 Peters anomaly; ORPHA:98976 Congenital glaucoma; ORPHA:98977 Juvenile glaucoma

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.274

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.38085374C>G [1|1]

Variant score: 0.274 CONTRIBUTING VARIANT

Transcripts:: CYP1B1:ENST00000494864.1:c.-70-14064G>C:p.(=)

Pathogenicity Data:: Best Score: 0.27355957; CADD: 0.274 (1.388)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.38107382CTT>C [1/1] rs1166475675 (variation viewer)

Variant score: 0.164

Transcripts:: CYP1B1:ENST00000494864.1:c.-71+2285_-71+2286del:p.(=)

Pathogenicity Data:: Best Score: 0.16401207; CADD: 0.164 (0.778)

Frequency Data:: No frequency data

NDUFC2

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.274

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.056

Variants contributing to score:

CUSTOM chr11:g.78033901G>GTGTGTGTGTACATATATATATATATA [0/1] rs781027862 (variation viewer)

Variant score: 0.056 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.0557217; CADD: 0.056 (0.249)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.504

Variant Score: 0.274

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.78078728C>CTTTTTTTTTTTTTTTT [1/1] rs71046953 (variation viewer)

Variant score: 0.274 CONTRIBUTING VARIANT

Transcripts:: NDUFC2:ENST00000281031.5:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000525085.1:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000527806.1:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000528164.1:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000534029.5:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000528251.1:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000530054.1:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000612612.5:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=); NDUFC2:ENST00000614236.2:c.166+850_166+851insAAAAAAAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.27422833; CADD: 0.274 (1.392)

Frequency Data:: No frequency data

Other passed variants:

CUSTOM chr11:g.78018600G>A [0/1] rs149724010 (variation viewer)

Variant score: 0.013

Transcripts:

Pathogenicity Data:: Best Score: 0.04082024; CADD: 0.041 (0.181)

Frequency Data:: 1000Genomes: 0.5791%; TOPMed: 1.1740%; UK10K: 1.8117%; gnomAD_G_AFR: 0.6444%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.6315%; gnomAD_G_NFE: 1.0554%; gnomAD_G_OTH: 0.4098%

CUSTOM chr11:g.78025086G>* [-/1]

Variant score: 0.000

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

GATA4

Exomiser Score: 0.004

Phenotype Score: 0.258

Variant Score: 0.546

Phenotype matches:

Proximity score 0.517 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.517 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

Known diseases:: OMIM:187500 Tetralogy of Fallot - autosomal dominant; OMIM:607941 Atrial septal defect 2 - autosomal dominant; OMIM:614429 Ventricular septal defect 1 - autosomal dominant; OMIM:614430 Atrioventricular septal defect 4 - autosomal dominant; OMIM:615542 ?Testicular anomalies with or without congenital heart disease (unconfirmed); ORPHA:251510 46,XY partial gonadal dysgenesis; ORPHA:3303 Tetralogy of Fallot; ORPHA:99103 Atrial septal defect, ostium secundum type

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.517

Variant Score: 0.000

Variants contributing to score:

INTERGENIC_VARIANT chr8:g.11660206C>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: GATA4:ENST00000528712.5::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.258

Variant Score: 0.546

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.11680464G>A [0/1] rs770999720 (variation viewer)

Variant score: 0.763 CONTRIBUTING VARIANT

Transcripts:: GATA4:ENST00000528712.5:c.-274+3401G>A:p.(=)

Pathogenicity Data:: Best Score: 0.8060454; CADD: 0.806 (7.123)

Frequency Data:: TOPMed: 0.0342%; UK10K: 0.0132%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0267%

UPSTREAM_GENE_VARIANT chr8:g.11674262G>C [0/1] rs866103069 (variation viewer)

Variant score: 0.329 CONTRIBUTING VARIANT

Transcripts:: GATA4:ENST00000528712.5::; GATA4:ENST00000259089.9::

Pathogenicity Data:: Best Score: 0.34762096; CADD: 0.348 (1.855)

Frequency Data:: TOPMed: 0.0366%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.0333%

Other passed variants:

INTERGENIC_VARIANT chr8:g.11766159C>G [0/1] rs181202291 (variation viewer)

Variant score: 0.319

Transcripts:: GATA4:ENST00000335135.8::

Pathogenicity Data:: Best Score: 0.36261773; CADD: 0.363 (1.956)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.4651%; UK10K: 0.6348%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.2579%; gnomAD_G_NFE: 0.6215%

FIVE_PRIME_UTR_INTRON_VARIANT chr8:g.11679179C>* [-/1]

Variant score: 0.000

Transcripts:: GATA4:ENST00000528712.5:c.-274+2116C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CYC1

Exomiser Score: 0.004

Phenotype Score: 0.506

Variant Score: 0.265

Phenotype matches:

Proximity score 0.506 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615453 Mitochondrial complex III deficiency, nuclear type 6 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.506

Variant Score: 0.265

Variants contributing to score:

INTERGENIC_VARIANT chr8:g.144089588G>A [1/1] rs7832798 (variation viewer)

Variant score: 0.265 CONTRIBUTING VARIANT

Transcripts:: CYC1:ENST00000318911.5::

Pathogenicity Data:: Best Score: 0.2651478; CADD: 0.265 (1.338)

Frequency Data:: No frequency data

Other passed variants:

AMFR

Exomiser Score: 0.004

Phenotype Score: 0.506

Variant Score: 0.265

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.506

Variant Score: 0.265

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.56395135T>C [0/1] rs868078974 (variation viewer)

Variant score: 0.265 CONTRIBUTING VARIANT

Transcripts:: AMFR:ENST00000290649.10:c.1086-5760A>G:p.(=)

Pathogenicity Data:: Best Score: 0.26565522; CADD: 0.266 (1.341)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_NFE: 0.0134%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.506

Variant Score: 0.234

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.56395135T>C [0/1] rs868078974 (variation viewer)

Variant score: 0.265 CONTRIBUTING VARIANT

Transcripts:: AMFR:ENST00000290649.10:c.1086-5760A>G:p.(=)

Pathogenicity Data:: Best Score: 0.26565522; CADD: 0.266 (1.341)

Frequency Data:: TOPMed: 0.0080%; gnomAD_G_NFE: 0.0134%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.56406202CT>C [0/1] rs746757607 (variation viewer)

Variant score: 0.203 CONTRIBUTING VARIANT

Transcripts:: AMFR:ENST00000290649.10:c.667-959del:p.(=)

Pathogenicity Data:: Best Score: 0.20255637; CADD: 0.203 (0.983)

Frequency Data:: No frequency data

Other passed variants:

EED

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.265

Phenotype matches:

Proximity score 0.505 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617561 Cohen-Gibson syndrome - autosomal dominant; ORPHA:3447 Weaver syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.265

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.86254048C>CAAAAA [0/1] rs201298345 (variation viewer)

Variant score: 0.265 CONTRIBUTING VARIANT

Transcripts:: EED:ENST00000263360.11:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000327320.8:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000351625.10:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000528180.5:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000672825.1:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000673233.1:c.541-1174_541-1173insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.26531696; CADD: 0.265 (1.339)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.303

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.86248119T>G [0/1] rs11606696 (variation viewer)

Variant score: 0.341 CONTRIBUTING VARIANT

Transcripts:: EED:ENST00000263360.11:c.115-2177T>G:p.(=); EED:ENST00000327320.8:c.115-2177T>G:p.(=); EED:ENST00000351625.10:c.115-2177T>G:p.(=); EED:ENST00000528180.5:c.115-2177T>G:p.(=); EED:ENST00000672825.1:c.115-2177T>G:p.(=); EED:ENST00000673233.1:c.295-2177T>G:p.(=)

Pathogenicity Data:: Best Score: 0.73288393; CADD: 0.733 (5.733)

Frequency Data:: 1000Genomes: 1.1180%; TOPMed: 0.8633%; UK10K: 1.6001%; gnomAD_G_AFR: 0.3322%; gnomAD_G_AMR: 0.9569%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.0017%; gnomAD_G_NFE: 0.9394%; gnomAD_G_OTH: 1.0204%

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.86254048C>CAAAAA [0/1] rs201298345 (variation viewer)

Variant score: 0.265 CONTRIBUTING VARIANT

Transcripts:: EED:ENST00000263360.11:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000327320.8:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000351625.10:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000528180.5:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000672825.1:c.361-1174_361-1173insAAAAA:p.(=); EED:ENST00000673233.1:c.541-1174_541-1173insAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.26531696; CADD: 0.265 (1.339)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr11:g.86236982AAG>A [0/1] rs1491227819 (variation viewer)

Variant score: 0.142

Transcripts:: EED:ENST00000528180.5::; EED:ENST00000530657.1::

Pathogenicity Data:: Best Score: 0.15511036; CADD: 0.155 (0.732)

Frequency Data:: gnomAD_G_AFR: 0.1590%; gnomAD_G_FIN: 0.0740%; gnomAD_G_NFE: 0.4950%; gnomAD_G_OTH: 0.1241%

INTERGENIC_VARIANT chr11:g.86238061C>T [0/1] rs116969642 (variation viewer)

Variant score: 0.068

Transcripts:: EED:ENST00000528180.5::; EED:ENST00000530657.1::

Pathogenicity Data:: Best Score: 0.14631039; CADD: 0.146 (0.687)

Frequency Data:: 1000Genomes: 1.1180%; TOPMed: 0.8649%; UK10K: 1.6001%; gnomAD_G_AFR: 0.3439%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 1.0017%; gnomAD_G_NFE: 0.9469%; gnomAD_G_OTH: 1.0183%

F11

Exomiser Score: 0.004

Phenotype Score: 0.508

Variant Score: 0.260

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612416 Factor XI deficiency, autosomal dominant - autosomal dominant/recessive; ORPHA:329 Congenital factor XI deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.004

Phenotype Score: 0.508

Variant Score: 0.260

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr4:g.186265513AAAAG>A [0/1] rs4253813 (variation viewer)

Variant score: 0.260 CONTRIBUTING VARIANT

Transcripts:: F11:ENST00000403665.7::; F11:ENST00000264690.11::

Pathogenicity Data:: Best Score: 0.26124573; CADD: 0.261 (1.315)

Frequency Data:: gnomAD_G_AFR: 0.0462%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.508

Variant Score: 0.202

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr4:g.186265513AAAAG>A [0/1] rs4253813 (variation viewer)

Variant score: 0.260 CONTRIBUTING VARIANT

Transcripts:: F11:ENST00000403665.7::; F11:ENST00000264690.11::

Pathogenicity Data:: Best Score: 0.26124573; CADD: 0.261 (1.315)

Frequency Data:: gnomAD_G_AFR: 0.0462%; gnomAD_G_NFE: 0.0067%

DOWNSTREAM_GENE_VARIANT chr4:g.186294268C>T [0/1] rs1310786788 (variation viewer)

Variant score: 0.145 CONTRIBUTING VARIANT

Transcripts:: F11:ENST00000403665.7::; F11:ENST00000515328.1::

Pathogenicity Data:: Best Score: 0.14532697; CADD: 0.145 (0.682)

Frequency Data:: TOPMed: 0.0008%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186276939G>T [0/1] rs140543332 (variation viewer)

Variant score: 0.090

Transcripts:: F11:ENST00000264692.8:c.593+549G>T:p.(=); F11:ENST00000403665.7:c.755+549G>T:p.(=)

Pathogenicity Data:: Best Score: 0.11100358; CADD: 0.111 (0.511)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 0.6029%; UK10K: 0.7802%; gnomAD_G_AFR: 0.1718%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_EAS: 0.0618%; gnomAD_G_FIN: 0.6885%; gnomAD_G_NFE: 0.8798%; gnomAD_G_OTH: 0.7128%

INTERGENIC_VARIANT chr4:g.186259689C>T [0/1] rs563878211 (variation viewer)

Variant score: 0.019

Transcripts:: F11:ENST00000403665.7::

Pathogenicity Data:: Best Score: 0.021186411; CADD: 0.021 (0.093)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.1999%; UK10K: 0.2909%; gnomAD_G_AFR: 0.0344%; gnomAD_G_FIN: 0.4868%; gnomAD_G_NFE: 0.3197%; gnomAD_G_OTH: 0.3055%

CDK3

Exomiser Score: 0.004

Phenotype Score: 0.503

Variant Score: 0.265

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.503

Variant Score: 0.265

Variants contributing to score:

CUSTOM chr17:g.75991149C>CA [1/1] rs71361699 (variation viewer)

Variant score: 0.265 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.26464003; CADD: 0.265 (1.335)

Frequency Data:: No frequency data

Other passed variants:

COX6A1

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.261

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616039 Charcot-Marie-Tooth disease, recessive intermediate D - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.004

Phenotype Score: 0.505

Variant Score: 0.261

Variants contributing to score:

REGULATORY_REGION_VARIANT chr12:g.120202435CTTTTTTTTTT>C [1/1] rs71072595 (variation viewer)

Variant score: 0.261 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.26073527; CADD: 0.261 (1.312)

Frequency Data:: No frequency data

Other passed variants:

NOTCH1

Exomiser Score: 0.003

Phenotype Score: 0.254

Variant Score: 0.544

Phenotype matches:

Proximity score 0.508 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:109730 Aortic valve disease 1 - autosomal dominant; OMIM:616028 Adams-Oliver syndrome 5 - autosomal dominant; ORPHA:402075 Familial bicuspid aortic valve; ORPHA:974 Adams-Oliver syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.254

Variant Score: 0.544

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr9:g.136490154CTTTTTTTTTTTTTT>C [1/1] rs71384084 (variation viewer)

Variant score: 0.544 CONTRIBUTING VARIANT

Transcripts:: NOTCH1:ENST00000651671.1::; NOTCH1:ENST00000290037.10::

Pathogenicity Data:: Best Score: 0.54354286; CADD: 0.544 (3.406)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136535621G>C [1|1] rs55857022 (variation viewer)

Variant score: 0.399

Transcripts:: NOTCH1:ENST00000651671.1:c.140+8403C>G:p.(=)

Pathogenicity Data:: Best Score: 0.3992414; CADD: 0.399 (2.213)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.136535622GAGA>G [1|1] rs751009512 (variation viewer)

Variant score: 0.133

Transcripts:: NOTCH1:ENST00000651671.1:c.140+8399_140+8401del:p.(=)

Pathogenicity Data:: Best Score: 0.26616234; CADD: 0.266 (1.344)

Frequency Data:: UK10K: 1.5472%

ACER1

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.259

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.259

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.6316483G>T [0/1]

Variant score: 0.259 CONTRIBUTING VARIANT

Transcripts:: ACER1:ENST00000301452.5:c.94-3984C>A:p.(=)

Pathogenicity Data:: Best Score: 0.25868976; CADD: 0.259 (1.300)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.152

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.6316483G>T [0/1]

Variant score: 0.259 CONTRIBUTING VARIANT

Transcripts:: ACER1:ENST00000301452.5:c.94-3984C>A:p.(=)

Pathogenicity Data:: Best Score: 0.25868976; CADD: 0.259 (1.300)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.6323736C>T [0/1] rs183654008 (variation viewer)

Variant score: 0.045 CONTRIBUTING VARIANT

Transcripts:: ACER1:ENST00000301452.5:c.93+9723G>A:p.(=)

Pathogenicity Data:: Best Score: 0.045007408; CADD: 0.045 (0.200)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0111%; gnomAD_G_NFE: 0.0067%

Other passed variants:

TIMM22

Exomiser Score: 0.003

Phenotype Score: 0.501

Variant Score: 0.263

Phenotype matches:

Proximity score 0.501 in interactome to SLC25A13 and phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

Known diseases:: OMIM:618851 ?Combined oxidative phosphorylation deficiency 43 (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.251

Variant Score: 0.339

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.999323C>CTATATATATATATATATATATATA [-/1]

Variant score: 0.339 CONTRIBUTING VARIANT

Transcripts:: TIMM22:ENST00000327158.5:c.436-189_436-188insTATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.33869773; CADD: 0.339 (1.796)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.501

Variant Score: 0.263

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.999323C>CTATATATATATATATATATATATA [-/1]

Variant score: 0.339 CONTRIBUTING VARIANT

Transcripts:: TIMM22:ENST00000327158.5:c.436-189_436-188insTATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.33869773; CADD: 0.339 (1.796)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr17:g.983611T>TACACAC [-/1] rs1555523750 (variation viewer)

Variant score: 0.187 CONTRIBUTING VARIANT

Transcripts:: TIMM22:ENST00000327158.5::

Pathogenicity Data:: Best Score: 0.18716949; CADD: 0.187 (0.900)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr17:g.996144AT>A [0/1] rs56123942 (variation viewer)

Variant score: 0.187

Transcripts:: TIMM22:ENST00000327158.5::; TIMM22:ENST00000336868.8::

Pathogenicity Data:: Best Score: 0.18716949; CADD: 0.187 (0.900)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr17:g.1002149A>* [-/1]

Variant score: 0.000

Transcripts:: TIMM22:ENST00000327158.5:c.*1061A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CERS5

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.258

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.258

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.50148927A>T [0/1] rs58887399 (variation viewer)

Variant score: 0.258 CONTRIBUTING VARIANT

Transcripts:: CERS5:ENST00000317551.12:c.198-4870T>A:p.(=); CERS5:ENST00000422340.6:c.-178-3958T>A:p.(=)

Pathogenicity Data:: Best Score: 0.25817752; CADD: 0.258 (1.297)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.170

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.50148927A>T [0/1] rs58887399 (variation viewer)

Variant score: 0.258 CONTRIBUTING VARIANT

Transcripts:: CERS5:ENST00000317551.12:c.198-4870T>A:p.(=); CERS5:ENST00000422340.6:c.-178-3958T>A:p.(=)

Pathogenicity Data:: Best Score: 0.25817752; CADD: 0.258 (1.297)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.50148921A>ATATATATAT [0|1] rs1218104568 (variation viewer)

Variant score: 0.083 CONTRIBUTING VARIANT

Transcripts:: CERS5:ENST00000317551.12:c.198-4865_198-4864insATATATATA:p.(=); CERS5:ENST00000422340.6:c.-178-3953_-178-3952insATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.192765; CADD: 0.193 (0.930)

Frequency Data:: gnomAD_G_AFR: 0.2547%; gnomAD_G_AMR: 1.1111%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_EAS: 0.3922%; gnomAD_G_NFE: 1.6520%; gnomAD_G_OTH: 1.2658%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.50156437T>TATATATATATATATATATATATATATATATATAA [0/1] rs1197474516 (variation viewer)

Variant score: 0.081

Transcripts:: CERS5:ENST00000317551.12:c.197+10663_197+10664insTTATATATATATATATATATATATATATATATAT:p.(=); CERS5:ENST00000422340.6:c.-179+10663_-179+10664insTTATATATATATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.08103281; CADD: 0.081 (0.367)

Frequency Data:: No frequency data

CHM

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.256

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:303100 Choroideremia - X-linked dominant; ORPHA:180 Choroideremia

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.252

Variant Score: 0.358

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.85911159A>G [1|1] rs868627450 (variation viewer)

Variant score: 0.358 CONTRIBUTING VARIANT

Transcripts:: CHM:ENST00000357749.7:c.1244+102T>C:p.(=)

Pathogenicity Data:: Best Score: 0.36642212; CADD: 0.366 (1.982)

Frequency Data:: gnomAD_G_AFR: 0.1185%; gnomAD_G_NFE: 0.1535%

X_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.256

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.85911163G>A [1|1] rs4998528 (variation viewer)

Variant score: 0.256 CONTRIBUTING VARIANT

Transcripts:: CHM:ENST00000357749.7:c.1244+98C>T:p.(=)

Pathogenicity Data:: Best Score: 0.2564674; CADD: 0.256 (1.287)

Frequency Data:: No frequency data

Other passed variants:

POLR2G

Exomiser Score: 0.003

Phenotype Score: 0.511

Variant Score: 0.243

Phenotype matches:

Proximity score 0.511 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.511

Variant Score: 0.243

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.62763355C>T [0/1] rs1268664526 (variation viewer)

Variant score: 0.243 CONTRIBUTING VARIANT

Transcripts:: POLR2G:ENST00000301788.12:c.282+329C>T:p.(=)

Pathogenicity Data:: Best Score: 0.24334133; CADD: 0.243 (1.211)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.511

Variant Score: 0.213

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.62763355C>T [0/1] rs1268664526 (variation viewer)

Variant score: 0.243 CONTRIBUTING VARIANT

Transcripts:: POLR2G:ENST00000301788.12:c.282+329C>T:p.(=)

Pathogenicity Data:: Best Score: 0.24334133; CADD: 0.243 (1.211)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.62764751G>A [0/1] rs533936488 (variation viewer)

Variant score: 0.182 CONTRIBUTING VARIANT

Transcripts:: POLR2G:ENST00000301788.12:c.283-431G>A:p.(=)

Pathogenicity Data:: Best Score: 0.19239312; CADD: 0.192 (0.928)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.1481%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0574%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.2001%

Other passed variants:

UPSTREAM_GENE_VARIANT chr11:g.62756673G>A [0/1] rs558763527 (variation viewer)

Variant score: 0.137

Transcripts:: POLR2G:ENST00000301788.12::; POLR2G:ENST00000673933.1::

Pathogenicity Data:: Best Score: 0.15101504; CADD: 0.151 (0.711)

Frequency Data:: UK10K: 0.5290%; gnomAD_G_AFR: 0.0804%; gnomAD_G_AMR: 0.3597%; gnomAD_G_FIN: 0.5172%; gnomAD_G_NFE: 0.4683%; gnomAD_G_OTH: 0.3080%

DAOA

Exomiser Score: 0.003

Phenotype Score: 0.503

Variant Score: 0.249

Phenotype matches:

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:181500 Schizophrenia (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.503

Variant Score: 0.249

Variants contributing to score:

REGULATORY_REGION_VARIANT chr13:g.106418000G>GTTT [-/1] rs5806578 (variation viewer)

Variant score: 0.249 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.2494148; CADD: 0.249 (1.246)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.146

Variants contributing to score:

REGULATORY_REGION_VARIANT chr13:g.106418000G>GTTT [-/1] rs5806578 (variation viewer)

Variant score: 0.249 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.2494148; CADD: 0.249 (1.246)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr13:g.105493444A>ATATATATATATATATG [0/1] rs35461996 (variation viewer)

Variant score: 0.043 CONTRIBUTING VARIANT

Transcripts:: DAOA:ENST00000375936.7::; DAOA:ENST00000410750.1::

Pathogenicity Data:: Best Score: 0.043026328; CADD: 0.043 (0.191)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr13:g.105493422C>CTCTCTCTCTCTATATATATATATATA [0/1] rs1390870155 (variation viewer)

Variant score: 0.036

Transcripts:: DAOA:ENST00000375936.7::; DAOA:ENST00000410750.1::

Pathogenicity Data:: Best Score: 0.03617096; CADD: 0.036 (0.160)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.105486621C>* [-/1]

Variant score: 0.000

Transcripts:: DAOA:ENST00000329625.9:c.69-3280C>*:p.(=); DAOA:ENST00000375936.7:c.282-3280C>*:p.(=); DAOA:ENST00000595812.2:c.89-3171C>*:p.(=); DAOA:ENST00000618629.1:c.282-3280C>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AMBN

Exomiser Score: 0.003

Phenotype Score: 0.512

Variant Score: 0.237

Phenotype matches:

Proximity score 0.512 in interactome to CLCN4 and phenotypic similarity 0.864 to Raynaud-Claes syndrome associated with CLCN4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616270 Amelogenesis imperfecta, type IF - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.256

Variant Score: 0.072

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr4:g.70588707C>A [0|1] rs28476549 (variation viewer)

Variant score: 0.072 CONTRIBUTING VARIANT

Transcripts:: AMBN:ENST00000322937.10::; AMBN:ENST00000339336.9::

Pathogenicity Data:: Best Score: 0.07231617; CADD: 0.072 (0.326)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.512

Variant Score: 0.237

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.70596934G>A [0/1] rs955532764 (variation viewer)

Variant score: 0.402 CONTRIBUTING VARIANT

Transcripts:: AMBN:ENST00000322937.10:c.85-65G>A:p.(=); AMBN:ENST00000449493.2:c.85-65G>A:p.(=); AMBN:ENST00000613447.4:c.85-65G>A:p.(=)

Pathogenicity Data:: Best Score: 0.4142666; CADD: 0.414 (2.323)

Frequency Data:: TOPMed: 0.0056%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.2041%

UPSTREAM_GENE_VARIANT chr4:g.70588707C>A [0|1] rs28476549 (variation viewer)

Variant score: 0.072 CONTRIBUTING VARIANT

Transcripts:: AMBN:ENST00000322937.10::; AMBN:ENST00000339336.9::

Pathogenicity Data:: Best Score: 0.07231617; CADD: 0.072 (0.326)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr4:g.70583403G>* [-/1]

Variant score: 0.000

Transcripts:: AMBN:ENST00000322937.10::; AMBN:ENST00000339336.9::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TNFSF10

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.246

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.238

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr3:g.172505289CA>C [-/1] rs372169927 (variation viewer)

Variant score: 0.238 CONTRIBUTING VARIANT

Transcripts:: TNFSF10:ENST00000241261.7::; TNFSF10:ENST00000241256.3::

Pathogenicity Data:: Best Score: 0.23774546; CADD: 0.238 (1.179)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.246

Variants contributing to score:

REGULATORY_REGION_VARIANT chr3:g.171967352A>G [0/1] rs114242245 (variation viewer)

Variant score: 0.255 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.9601893; CADD: 0.960 (14.000)

Frequency Data:: 1000Genomes: 0.4193%; TOPMed: 0.9262%; UK10K: 1.6794%; gnomAD_G_AFR: 0.2407%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.8603%; gnomAD_G_NFE: 1.5856%; gnomAD_G_OTH: 0.6110%

DOWNSTREAM_GENE_VARIANT chr3:g.172505289CA>C [-/1] rs372169927 (variation viewer)

Variant score: 0.238 CONTRIBUTING VARIANT

Transcripts:: TNFSF10:ENST00000241261.7::; TNFSF10:ENST00000241256.3::

Pathogenicity Data:: Best Score: 0.23774546; CADD: 0.238 (1.179)

Frequency Data:: No frequency data

Other passed variants:

FOXK1

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.246

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.246

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.4697075C>CA [0/1] rs993284027 (variation viewer)

Variant score: 0.246 CONTRIBUTING VARIANT

Transcripts:: FOXK1:ENST00000328914.5:c.560+14207_560+14208insA:p.(=)

Pathogenicity Data:: Best Score: 0.24595022; CADD: 0.246 (1.226)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0068%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.176

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.4697075C>CA [0/1] rs993284027 (variation viewer)

Variant score: 0.246 CONTRIBUTING VARIANT

Transcripts:: FOXK1:ENST00000328914.5:c.560+14207_560+14208insA:p.(=)

Pathogenicity Data:: Best Score: 0.24595022; CADD: 0.246 (1.226)

Frequency Data:: TOPMed: 0.0048%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0068%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.4721589CT>C [0/1] rs200132324 (variation viewer)

Variant score: 0.107 CONTRIBUTING VARIANT

Transcripts:: FOXK1:ENST00000328914.5:c.561-19248del:p.(=)

Pathogenicity Data:: Best Score: 0.106900156; CADD: 0.107 (0.491)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.4748803C>G [0/1] rs112347937 (variation viewer)

Variant score: 0.026

Transcripts:: FOXK1:ENST00000328914.5:c.747-5656C>G:p.(=)

Pathogenicity Data:: Best Score: 0.025683641; CADD: 0.026 (0.113)

Frequency Data:: TOPMed: 0.0016%; gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr7:g.4706036G>* [-/1]

Variant score: 0.000

Transcripts:: FOXK1:ENST00000328914.5:c.560+23168G>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

CD99

Exomiser Score: 0.003

Phenotype Score: 0.512

Variant Score: 0.235

Phenotype matches:

Proximity score 0.512 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.512

Variant Score: 0.235

Variants contributing to score:

INTERGENIC_VARIANT chr23:g.2749147C>T [0|1] rs867301377 (variation viewer)

Variant score: 0.313 CONTRIBUTING VARIANT

Transcripts:: CD99:ENST00000381192.10::

Pathogenicity Data:: Best Score: 0.32391703; CADD: 0.324 (1.700)

Frequency Data:: gnomAD_G_AFR: 0.0254%; gnomAD_G_NFE: 0.0278%; gnomAD_G_OTH: 0.2183%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.2720620CT>C [-/1] rs71281938 (variation viewer)

Variant score: 0.158 CONTRIBUTING VARIANT

Transcripts:: CD99:ENST00000381184.6:c.262+197del:p.(=); CD99:ENST00000381187.8:c.214+197del:p.(=); CD99:ENST00000381192.10:c.262+197del:p.(=); CD99:ENST00000482405.7:c.262+197del:p.(=); CD99:ENST00000611428.5:c.262+197del:p.(=); CD99:ENST00000624481.4:c.262+197del:p.(=)

Pathogenicity Data:: Best Score: 0.15763563; CADD: 0.158 (0.745)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.512

Variant Score: 0.178

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.2709203A>ACATGCATGCACACTCATGCCATGCATATATG [1/1] rs776365919 (variation viewer)

Variant score: 0.178 CONTRIBUTING VARIANT

Transcripts:: CD99:ENST00000381184.6:c.68-5219_68-5218insCATGCATGCACACTCATGCCATGCATATATG:p.(=); CD99:ENST00000381187.8:c.68-5219_68-5218insCATGCATGCACACTCATGCCATGCATATATG:p.(=); CD99:ENST00000381192.10:c.68-5219_68-5218insCATGCATGCACACTCATGCCATGCATATATG:p.(=); CD99:ENST00000482405.7:c.68-5219_68-5218insCATGCATGCACACTCATGCCATGCATATATG:p.(=); CD99:ENST00000611428.5:c.68-5219_68-5218insCATGCATGCACACTCATGCCATGCATATATG:p.(=); CD99:ENST00000624481.4:c.68-5219_68-5218insCATGCATGCACACTCATGCCATGCATATATG:p.(=)

Pathogenicity Data:: Best Score: 0.17832512; CADD: 0.178 (0.853)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr23:g.2749155C>T [0|1] rs1216122323 (variation viewer)

Variant score: 0.131

Transcripts:: CD99:ENST00000381192.10::

Pathogenicity Data:: Best Score: 0.13183957; CADD: 0.132 (0.614)

Frequency Data:: gnomAD_G_AFR: 0.0431%; gnomAD_G_NFE: 0.0115%

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.2728200CTTTTTTTTTT>C [0/1] rs867514534 (variation viewer)

Variant score: 0.117

Transcripts:: CD99:ENST00000381184.6:c.526+858_526+867del:p.(=); CD99:ENST00000381187.8:c.427+1828_427+1837del:p.(=); CD99:ENST00000381192.10:c.475+1828_475+1837del:p.(=); CD99:ENST00000482405.7:c.475+1828_475+1837del:p.(=); CD99:ENST00000611428.5:c.475+1828_475+1837del:p.(=); CD99:ENST00000624481.4:c.475+1828_475+1837del:p.(=)

Pathogenicity Data:: Best Score: 0.13283849; CADD: 0.133 (0.619)

Frequency Data:: gnomAD_G_AFR: 0.2974%; gnomAD_G_AMR: 0.6211%; gnomAD_G_ASJ: 0.5682%; gnomAD_G_NFE: 0.5637%

INTERGENIC_VARIANT chr23:g.2749151C>G [0|1] rs1257828060 (variation viewer)

Variant score: 0.092

Transcripts:: CD99:ENST00000381192.10::

Pathogenicity Data:: Best Score: 0.09510124; CADD: 0.095 (0.434)

Frequency Data:: gnomAD_G_AFR: 0.0481%; gnomAD_G_NFE: 0.0127%; gnomAD_G_OTH: 0.1992%

INTERGENIC_VARIANT chr23:g.2677142C>CT [0/1] rs866476420 (variation viewer)

Variant score: 0.092

Transcripts:: CD99:ENST00000611428.5::; CD99:ENST00000435581.7::

Pathogenicity Data:: Best Score: 0.10133052; CADD: 0.101 (0.464)

Frequency Data:: gnomAD_G_AFR: 0.0480%; gnomAD_G_AMR: 0.5155%; gnomAD_G_FIN: 0.1586%; gnomAD_G_NFE: 0.0366%; gnomAD_G_OTH: 0.1266%

DOWNSTREAM_GENE_VARIANT chr23:g.2742640CTTTT>C [-/1] rs1158289378 (variation viewer)

Variant score: 0.092

Transcripts:: CD99:ENST00000381192.10::; CD99:ENST00000419513.7::

Pathogenicity Data:: Best Score: 0.091970444; CADD: 0.092 (0.419)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr23:g.2742640CTTTTT>C [-/1] rs1158289378 (variation viewer)

Variant score: 0.091

Transcripts:: CD99:ENST00000381192.10::; CD99:ENST00000419513.7::

Pathogenicity Data:: Best Score: 0.09050566; CADD: 0.091 (0.412)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr23:g.2745435C>CTGTGTGTGTGTGTGTGTGTGTG [0/1] rs770898451 (variation viewer)

Variant score: 0.045

Transcripts:: CD99:ENST00000381192.10::; CD99:ENST00000419513.7::

Pathogenicity Data:: Best Score: 0.044567525; CADD: 0.045 (0.198)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr23:g.2674282GGTT>* [-/1]

Variant score: 0.000

Transcripts:: CD99:ENST00000611428.5::; CD99:ENST00000435581.7::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr23:g.2674285T>* [-/1]

Variant score: 0.000

Transcripts:: CD99:ENST00000611428.5::; CD99:ENST00000435581.7::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

SEC24C

Exomiser Score: 0.003

Phenotype Score: 0.432

Variant Score: 0.317

Phenotype matches:

Phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.500 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases - observed variants incompatible with mode of inheritance:: ORPHA:567 22q11.2 deletion syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.432

Variant Score: 0.317

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr10:g.73771942T>C [0/1] rs144190215 (variation viewer)

Variant score: 0.529 CONTRIBUTING VARIANT

Transcripts:: SEC24C:ENST00000339365.2:c.*847T>C:p.(=); SEC24C:ENST00000345254.9:c.*847T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5752827; CADD: 0.575 (3.719)

Frequency Data:: 1000Genomes: 0.3195%; TOPMed: 0.3512%; UK10K: 0.4628%; gnomAD_G_AFR: 0.1604%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.3871%; gnomAD_G_OTH: 0.2037%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.73747389C>G [0/1] rs138176391 (variation viewer)

Variant score: 0.105 CONTRIBUTING VARIANT

Transcripts:: SEC24C:ENST00000339365.2:c.172+385C>G:p.(=); SEC24C:ENST00000345254.9:c.172+385C>G:p.(=)

Pathogenicity Data:: Best Score: 0.19739842; CADD: 0.197 (0.955)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.9111%; UK10K: 1.4017%; gnomAD_G_AFR: 0.2407%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 1.4986%; gnomAD_G_NFE: 1.2810%; gnomAD_G_OTH: 1.1224%

Other passed variants:

VCP

Exomiser Score: 0.003

Phenotype Score: 0.507

Variant Score: 0.232

Phenotype matches:

Phenotypic similarity 0.473 to Amyotrophic lateral sclerosis associated with VCP.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.507 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:167320 Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia 1 - autosomal dominant; OMIM:613954 Frontotemporal dementia and/or amyotrophic lateral sclerosis 6 - autosomal dominant; OMIM:616687 Charcot-Marie-Tooth disease, type 2Y - autosomal dominant; ORPHA:100070 Progressive non-fluent aphasia; ORPHA:275864 Behavioral variant of frontotemporal dementia; ORPHA:275872 Frontotemporal dementia with motor neuron disease; ORPHA:435387 Autosomal dominant Charcot-Marie-Tooth disease type 2Y; ORPHA:52430 Inclusion body myopathy with Paget disease of bone and frontotemporal dementia; ORPHA:803 Amyotrophic lateral sclerosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.507

Variant Score: 0.232

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.35069444CT>C [0/1] rs35498216 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: VCP:ENST00000358901.11:c.18-1083del:p.(=)

Pathogenicity Data:: Best Score: 0.23210824; CADD: 0.232 (1.147)

Frequency Data:: No frequency data

Other passed variants:

MAX

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.232

Phenotype matches:

Phenotypic similarity 0.430 to Hereditary pheochromocytoma-paraganglioma associated with MAX.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0025269, Panic attack

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:171300 Pheochromocytoma, susceptibility to (susceptibility); ORPHA:29072 Hereditary pheochromocytoma-paraganglioma

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.504

Variant Score: 0.232

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.65054203CT>C [0/1] rs963850318 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: MAX:ENST00000341653.6:c.171+39504del:p.(=); MAX:ENST00000549987.1:c.1170-371del:p.(=); MAX:ENST00000246166.3:c.1068-371del:p.(=)

Pathogenicity Data:: Best Score: 0.23228502; CADD: 0.232 (1.148)

Frequency Data:: TOPMed: 0.0024%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.199

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.65054203CT>C [0/1] rs963850318 (variation viewer)

Variant score: 0.232 CONTRIBUTING VARIANT

Transcripts:: MAX:ENST00000341653.6:c.171+39504del:p.(=); MAX:ENST00000549987.1:c.1170-371del:p.(=); MAX:ENST00000246166.3:c.1068-371del:p.(=)

Pathogenicity Data:: Best Score: 0.23228502; CADD: 0.232 (1.148)

Frequency Data:: TOPMed: 0.0024%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.65043828CAAA>C [0/1] rs749243788 (variation viewer)

Variant score: 0.165 CONTRIBUTING VARIANT

Transcripts:: MAX:ENST00000341653.6:c.172-37547_172-37545del:p.(=); MAX:ENST00000549987.1:c.925-482_925-480del:p.(=); MAX:ENST00000246166.3:c.823-482_823-480del:p.(=)

Pathogenicity Data:: Best Score: 0.16516626; CADD: 0.165 (0.784)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.65031643G>A [0/1] rs562707351 (variation viewer)

Variant score: 0.121

Transcripts:: MAX:ENST00000341653.6:c.172-25359C>T:p.(=); MAX:ENST00000549987.1:c.708-967G>A:p.(=); MAX:ENST00000246166.3:c.606-967G>A:p.(=)

Pathogenicity Data:: Best Score: 0.12279725; CADD: 0.123 (0.569)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0366%; gnomAD_G_AFR: 0.1032%; gnomAD_G_NFE: 0.0268%

NR2F1

Exomiser Score: 0.003

Phenotype Score: 0.252

Variant Score: 0.517

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:615722 Bosch-Boonstra-Schaaf optic atrophy syndrome - autosomal dominant; ORPHA:401777 Optic atrophy-intellectual disability syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.252

Variant Score: 0.517

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.93573836A>G [0/1] rs141834602 (variation viewer)

Variant score: 0.691 CONTRIBUTING VARIANT

Transcripts:: NR2F1:ENST00000327111.8::; NR2F1:ENST00000511220.1::

Pathogenicity Data:: Best Score: 0.95429116; CADD: 0.954 (13.400)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.5487%; UK10K: 1.1108%; gnomAD_G_AFR: 0.1031%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.8591%; gnomAD_G_NFE: 0.9932%; gnomAD_G_OTH: 0.3055%

UPSTREAM_GENE_VARIANT chr5:g.93578542C>A [0/1] rs541429345 (variation viewer)

Variant score: 0.343 CONTRIBUTING VARIANT

Transcripts:: NR2F1:ENST00000327111.8::; NR2F1:ENST00000511220.1::

Pathogenicity Data:: Best Score: 0.3538996; CADD: 0.354 (1.897)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1720%; gnomAD_G_NFE: 0.0868%; gnomAD_G_OTH: 0.2037%

Other passed variants:

INTERGENIC_VARIANT chr5:g.93564101CAAAAAAAAAAAAAAAAAAAAAA>C [1/1] rs60114975 (variation viewer)

Variant score: 0.384

Transcripts:: NR2F1:ENST00000327111.8::; NR2F1:ENST00000511220.1::

Pathogenicity Data:: Best Score: 0.3838308; CADD: 0.384 (2.103)

Frequency Data:: No frequency data

ASAH1

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.229

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:159950 Spinal muscular atrophy with progressive myoclonic epilepsy - autosomal recessive; OMIM:228000 Farber lipogranulomatosis - autosomal recessive; ORPHA:2590 Spinal muscular atrophy-progressive myoclonic epilepsy syndrome; ORPHA:333 Farber disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.229

Variants contributing to score:

REGULATORY_REGION_VARIANT chr8:g.18036285A>AAAAG [1|1] rs1554805440 (variation viewer)

Variant score: 0.229 CONTRIBUTING VARIANT

Transcripts:: ASAH1:ENST00000637790.2::

Pathogenicity Data:: Best Score: 0.22909653; CADD: 0.229 (1.130)

Frequency Data:: No frequency data

Other passed variants:

CYP17A1

Exomiser Score: 0.003

Phenotype Score: 0.503

Variant Score: 0.230

Phenotype matches:

Phenotypic similarity 0.428 to mouse mutant involving CYP17A1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:202110 17-alpha-hydroxylase/17,20-lyase deficiency - autosomal recessive; ORPHA:90793 Congenital adrenal hyperplasia due to 17-alpha-hydroxylase deficiency; ORPHA:90796 46,XY disorder of sex development due to isolated 17,20-lyase deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.117

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr10:g.102829164A>AAC [0|1] rs34005085 (variation viewer)

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: CYP17A1:ENST00000369887.4::; CYP17A1:ENST00000369889.5::

Pathogenicity Data:: Best Score: 0.11651331; CADD: 0.117 (0.538)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.003

Phenotype Score: 0.503

Variant Score: 0.230

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr10:g.102837987G>A [0/1] rs61752856 (variation viewer)

Variant score: 0.343 CONTRIBUTING VARIANT

Transcripts:: CYP17A1:ENST00000638971.1::; CYP17A1:ENST00000445829.1::

Pathogenicity Data:: Best Score: 0.54824805; CADD: 0.548 (3.451)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.5511%; UK10K: 0.8331%; gnomAD_G_AFR: 0.1148%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.6618%; gnomAD_G_OTH: 0.3061%

DOWNSTREAM_GENE_VARIANT chr10:g.102829164A>AAC [0|1] rs34005085 (variation viewer)

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: CYP17A1:ENST00000369887.4::; CYP17A1:ENST00000369889.5::

Pathogenicity Data:: Best Score: 0.11651331; CADD: 0.117 (0.538)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr10:g.102817978AC>A [0/1] rs1377076397 (variation viewer)

Variant score: 0.012

Transcripts:: CYP17A1:ENST00000369887.4::

Pathogenicity Data:: Best Score: 0.015308917; CADD: 0.015 (0.067)

Frequency Data:: gnomAD_G_AFR: 0.1290%; gnomAD_G_AMR: 0.2494%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 0.3028%; gnomAD_G_NFE: 0.8673%; gnomAD_G_OTH: 0.5241%

TNFRSF1A

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.228

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:142680 Periodic fever, familial - autosomal dominant; ORPHA:32960 Tumor necrosis factor receptor 1 associated periodic syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.505

Variant Score: 0.228

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr12:g.6343645C>CTGGGCTGCTAGAAATGCAGGCAGCTAGAAATTTCT [0/1] rs34822098 (variation viewer)

Variant score: 0.228 CONTRIBUTING VARIANT

Transcripts:: TNFRSF1A:ENST00000162749.7::; TNFRSF1A:ENST00000360168.7::

Pathogenicity Data:: Best Score: 0.227853; CADD: 0.228 (1.123)

Frequency Data:: No frequency data

Other passed variants:

NDUFS3

Exomiser Score: 0.003

Phenotype Score: 0.252

Variant Score: 0.510

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFS3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.505 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:618230 Mitochondrial complex I deficiency, nuclear type 8 - autosomal recessive; ORPHA:255241 Leigh syndrome with leukodystrophy; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.003

Phenotype Score: 0.252

Variant Score: 0.510

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.47579984G>GAC [-/1] rs36201718 (variation viewer)

Variant score: 0.510 CONTRIBUTING VARIANT

Transcripts:: NDUFS3:ENST00000263774.9:c.134-541_134-540insAC:p.(=); NDUFS3:ENST00000528192.5:c.134-541_134-540insAC:p.(=); NDUFS3:ENST00000534208.5:c.134-541_134-540insAC:p.(=); NDUFS3:ENST00000534716.2:c.134-541_134-540insAC:p.(=)

Pathogenicity Data:: Best Score: 0.5102212; CADD: 0.510 (3.100)

Frequency Data:: No frequency data

Other passed variants:

HYKK

Exomiser Score: 0.002

Phenotype Score: 0.501

Variant Score: 0.223

Phenotype matches:

Proximity score 0.501 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.501 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.501

Variant Score: 0.175

Variants contributing to score:

INTERGENIC_VARIANT chr15:g.78501804C>CAAAAAAAA [0/1] rs56318078 (variation viewer)

Variant score: 0.175 CONTRIBUTING VARIANT

Transcripts:: HYKK:ENST00000408962.6::

Pathogenicity Data:: Best Score: 0.17491251; CADD: 0.175 (0.835)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.501

Variant Score: 0.223

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr15:g.78504595G>GAA [1/1] rs71148530 (variation viewer)

Variant score: 0.223 CONTRIBUTING VARIANT

Transcripts:: HYKK:ENST00000408962.6::; HYKK:ENST00000258886.13::

Pathogenicity Data:: Best Score: 0.22321647; CADD: 0.223 (1.097)

Frequency Data:: No frequency data

Other passed variants:

COX5A

Exomiser Score: 0.002

Phenotype Score: 0.506

Variant Score: 0.215

Phenotype matches:

Proximity score 0.506 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.506

Variant Score: 0.215

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr15:g.74916019C>CAAA [0/1] rs71140113 (variation viewer)

Variant score: 0.215 CONTRIBUTING VARIANT

Transcripts:: COX5A:ENST00000322347.11::; COX5A:ENST00000357635.10::

Pathogenicity Data:: Best Score: 0.21548724; CADD: 0.215 (1.054)

Frequency Data:: No frequency data

Other passed variants:

KCNN4

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.219

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:616689 Dehydrated hereditary stomatocytosis 2 - autosomal dominant; ORPHA:3202 Dehydrated hereditary stomatocytosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.219

Variants contributing to score:

REGULATORY_REGION_VARIANT chr19:g.44736813CT>C [0/1] rs58455045 (variation viewer)

Variant score: 0.219 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.21891195; CADD: 0.219 (1.073)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.127

Variants contributing to score:

REGULATORY_REGION_VARIANT chr19:g.44736813CT>C [0/1] rs58455045 (variation viewer)

Variant score: 0.219 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.21891195; CADD: 0.219 (1.073)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr19:g.43764223T>A [0/1] rs111750400 (variation viewer)

Variant score: 0.035 CONTRIBUTING VARIANT

Transcripts:: KCNN4:ENST00000648319.1::; KCNN4:ENST00000601170.5::

Pathogenicity Data:: Best Score: 0.035727024; CADD: 0.036 (0.158)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1195%; UK10K: 0.1322%; gnomAD_G_AFR: 0.0688%; gnomAD_G_NFE: 0.1400%; gnomAD_G_OTH: 0.2041%

Other passed variants:

IL2RA

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.216

Phenotype matches:

Phenotypic similarity 0.454 to mouse mutant involving IL2RA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0020420, abnormal freezing behavior

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:601942 Diabetes, mellitus, insulin-dependent, susceptibility to, 10 (susceptibility); OMIM:606367 Immunodeficiency 41 with lymphoproliferation and autoimmunity - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.138

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.6051817C>CTATATATATATATATATATATATA [-/1] rs61008683 (variation viewer)

Variant score: 0.138 CONTRIBUTING VARIANT

Transcripts:: IL2RA:ENST00000256876.10:c.64+10270_64+10271insTATATATATATATATATATATATA:p.(=); IL2RA:ENST00000379954.5:c.64+10270_64+10271insTATATATATATATATATATATATA:p.(=); IL2RA:ENST00000379959.8:c.64+10270_64+10271insTATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.13761735; CADD: 0.138 (0.643)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.216

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.6017572AT>A [1/1] rs71390109 (variation viewer)

Variant score: 0.216 CONTRIBUTING VARIANT

Transcripts:: IL2RA:ENST00000256876.10:c.767+480del:p.(=); IL2RA:ENST00000379954.5:c.578+480del:p.(=); IL2RA:ENST00000379959.8:c.794+480del:p.(=)

Pathogenicity Data:: Best Score: 0.2156679; CADD: 0.216 (1.055)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.6051817C>CTATATATATATATATATATATATATATATA [-/1] rs61008683 (variation viewer)

Variant score: 0.123

Transcripts:: IL2RA:ENST00000256876.10:c.64+10270_64+10271insTATATATATATATATATATATATATATATA:p.(=); IL2RA:ENST00000379954.5:c.64+10270_64+10271insTATATATATATATATATATATATATATATA:p.(=); IL2RA:ENST00000379959.8:c.64+10270_64+10271insTATATATATATATATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.12259519; CADD: 0.123 (0.568)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.6020689C>A [0/1] rs41294683 (variation viewer)

Variant score: 0.014

Transcripts:: IL2RA:ENST00000256876.10:c.557-748G>T:p.(=); IL2RA:ENST00000379954.5:c.368-748G>T:p.(=); IL2RA:ENST00000379959.8:c.584-748G>T:p.(=)

Pathogenicity Data:: Best Score: 0.030829906; CADD: 0.031 (0.136)

Frequency Data:: 1000Genomes: 0.9185%; TOPMed: 1.0970%; UK10K: 1.6266%; gnomAD_G_AFR: 0.3101%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.5814%; gnomAD_G_NFE: 1.5965%; gnomAD_G_OTH: 1.3292%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.6051514TATA>* [-/1]

Variant score: 0.000

Transcripts:: IL2RA:ENST00000256876.10:c.64+10571_64+10574delTATAins:p.(=); IL2RA:ENST00000379954.5:c.64+10571_64+10574delTATAins:p.(=); IL2RA:ENST00000379959.8:c.64+10571_64+10574delTATAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DEGS1

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.213

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618404 Leukodystrophy, hypomyelinating, 18 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.256

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.224200528CAAAAAAAAAAAAA>C [0/1] rs71572888 (variation viewer)

Variant score: 0.256 CONTRIBUTING VARIANT

Transcripts:: DEGS1:ENST00000323699.9::

Pathogenicity Data:: Best Score: 0.25629622; CADD: 0.256 (1.286)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.213

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.224200528CAAAAAAAAAAAAA>C [0/1] rs71572888 (variation viewer)

Variant score: 0.256 CONTRIBUTING VARIANT

Transcripts:: DEGS1:ENST00000323699.9::

Pathogenicity Data:: Best Score: 0.25629622; CADD: 0.256 (1.286)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.224191590CT>C [0/1] rs748181749 (variation viewer)

Variant score: 0.170 CONTRIBUTING VARIANT

Transcripts:: DEGS1:ENST00000323699.9:c.826-741del:p.(=); DEGS1:ENST00000391877.3:c.826-741del:p.(=)

Pathogenicity Data:: Best Score: 0.1703403; CADD: 0.170 (0.811)

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr1:g.224196472C>CT [1/1] rs56243941 (variation viewer)

Variant score: 0.195

Transcripts:: DEGS1:ENST00000323699.9::; DEGS1:ENST00000469968.5::

Pathogenicity Data:: Best Score: 0.19462156; CADD: 0.195 (0.940)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr1:g.224193949A>ATT [0/1] rs71168330 (variation viewer)

Variant score: 0.151

Transcripts:: DEGS1:ENST00000323699.9::; DEGS1:ENST00000469968.5::

Pathogenicity Data:: Best Score: 0.15101504; CADD: 0.151 (0.711)

Frequency Data:: No frequency data

DHX9

Exomiser Score: 0.002

Phenotype Score: 0.511

Variant Score: 0.206

Phenotype matches:

Proximity score 0.511 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.511

Variant Score: 0.206

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.182846204A>G [0/1] rs548530404 (variation viewer)

Variant score: 0.206 CONTRIBUTING VARIANT

Transcripts:: DHX9:ENST00000367549.4:c.252+2770A>G:p.(=)

Pathogenicity Data:: Best Score: 0.20841056; CADD: 0.208 (1.015)

Frequency Data:: TOPMed: 0.0558%; gnomAD_G_AFR: 0.0807%; gnomAD_G_NFE: 0.0536%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.511

Variant Score: 0.171

Variants contributing to score:

INTERGENIC_VARIANT chr1:g.182898672CAAAAAAAAAAAAAAAAAAA>C [1/1] rs71127326 (variation viewer)

Variant score: 0.171 CONTRIBUTING VARIANT

Transcripts:: DHX9:ENST00000367549.4::

Pathogenicity Data:: Best Score: 0.17091322; CADD: 0.171 (0.814)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.182868520C>CTTTTTTTTTTTTTTT [0/1] rs59218081 (variation viewer)

Variant score: 0.122

Transcripts:: DHX9:ENST00000367549.4:c.1557+1477_1557+1478insTTTTTTTTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.12198889; CADD: 0.122 (0.565)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr1:g.182147338C>T [0/1] rs534735858 (variation viewer)

Variant score: 0.037

Transcripts:

Pathogenicity Data:: Best Score: 0.037501633; CADD: 0.038 (0.166)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0175%; gnomAD_G_AFR: 0.0573%; gnomAD_G_NFE: 0.0067%

UBQLN1

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.212

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.212

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.83662273TACACACACACACACACAC>T [0|1] rs370539805 (variation viewer)

Variant score: 0.212 CONTRIBUTING VARIANT

Transcripts:: UBQLN1:ENST00000257468.11:c.1534-352_1534-335del:p.(=); UBQLN1:ENST00000376395.9:c.1618-352_1618-335del:p.(=)

Pathogenicity Data:: Best Score: 0.21168464; CADD: 0.212 (1.033)

Frequency Data:: No frequency data

Other passed variants:

IL2RB

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.211

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618495 Immunodeficiency 63 with lymphoproliferation and autoimmunity - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.37137313TG>T [0/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: IL2RB:ENST00000216223.10:c.537+273del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.211

Variants contributing to score:

REGULATORY_REGION_VARIANT chr22:g.36884885C>A [0/1] rs549128459 (variation viewer)

Variant score: 0.422 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.42852134; CADD: 0.429 (2.430)

Frequency Data:: TOPMed: 0.0088%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1018%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.37137313TG>T [0/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: IL2RB:ENST00000216223.10:c.537+273del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

DOWNSTREAM_GENE_VARIANT chr22:g.37125516GGAGA>G [1/1] rs56998935 (variation viewer)

Variant score: 0.197

Transcripts:: IL2RB:ENST00000216223.10::; IL2RB:ENST00000406856.7::

Pathogenicity Data:: Best Score: 0.19684386; CADD: 0.197 (0.952)

Frequency Data:: No frequency data

SGPP1

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.207

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.207

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.63719016T>TA [0/1] rs868513976 (variation viewer)

Variant score: 0.207 CONTRIBUTING VARIANT

Transcripts:: SGPP1:ENST00000247225.7:c.684+8244_684+8245insT:p.(=)

Pathogenicity Data:: Best Score: 0.20786357; CADD: 0.208 (1.012)

Frequency Data:: gnomAD_G_NFE: 0.0458%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.505

Variant Score: 0.199

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.63719016T>TA [0/1] rs868513976 (variation viewer)

Variant score: 0.207 CONTRIBUTING VARIANT

Transcripts:: SGPP1:ENST00000247225.7:c.684+8244_684+8245insT:p.(=)

Pathogenicity Data:: Best Score: 0.20786357; CADD: 0.208 (1.012)

Frequency Data:: gnomAD_G_NFE: 0.0458%

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.63719015T>TA [0/1] rs1491285317 (variation viewer)

Variant score: 0.191 CONTRIBUTING VARIANT

Transcripts:: SGPP1:ENST00000247225.7:c.684+8245_684+8246insT:p.(=)

Pathogenicity Data:: Best Score: 0.20090204; CADD: 0.201 (0.974)

Frequency Data:: gnomAD_G_AFR: 0.0796%; gnomAD_G_NFE: 0.3044%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.63688273G>A [0|1] rs971814005 (variation viewer)

Variant score: 0.100

Transcripts:: SGPP1:ENST00000247225.7:c.775-1617C>T:p.(=)

Pathogenicity Data:: Best Score: 0.100295246; CADD: 0.100 (0.459)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.63712064CAAAT>C [0/1] rs200870124 (variation viewer)

Variant score: 0.026

Transcripts:: SGPP1:ENST00000247225.7:c.685-13410_685-13407del:p.(=)

Pathogenicity Data:: Best Score: 0.17529237; CADD: 0.175 (0.837)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 1.0990%; gnomAD_G_AFR: 0.2087%; gnomAD_G_AMR: 0.6329%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2792%; gnomAD_G_NFE: 1.9884%; gnomAD_G_OTH: 1.8750%

ENTPD3

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.207

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.133

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.40388585GAC>G [-/1] rs55657804 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: ENTPD3:ENST00000301825.8:c.40+489_40+490del:p.(=); ENTPD3:ENST00000445129.1:c.40+489_40+490del:p.(=); ENTPD3:ENST00000456402.5:c.40+489_40+490del:p.(=)

Pathogenicity Data:: Best Score: 0.13323772; CADD: 0.133 (0.621)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.207

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.40426562C>T [0/1] rs115544984 (variation viewer)

Variant score: 0.280 CONTRIBUTING VARIANT

Transcripts:: ENTPD3:ENST00000301825.8:c.1354-710C>T:p.(=); ENTPD3:ENST00000456402.5:c.1354-710C>T:p.(=)

Pathogenicity Data:: Best Score: 0.88027084; CADD: 0.880 (9.218)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 1.2540%; UK10K: 1.7985%; gnomAD_G_AFR: 0.3557%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2017%; gnomAD_G_NFE: 1.6940%; gnomAD_G_OTH: 1.3320%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.40388585GAC>G [-/1] rs55657804 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: ENTPD3:ENST00000301825.8:c.40+489_40+490del:p.(=); ENTPD3:ENST00000445129.1:c.40+489_40+490del:p.(=); ENTPD3:ENST00000456402.5:c.40+489_40+490del:p.(=)

Pathogenicity Data:: Best Score: 0.13323772; CADD: 0.133 (0.621)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.40402123C>CTTTTTTT [1/1] rs58000344 (variation viewer)

Variant score: 0.162

Transcripts:: ENTPD3:ENST00000301825.8:c.286+1112_286+1113insTTTTTTT:p.(=); ENTPD3:ENST00000445129.1:c.286+1112_286+1113insTTTTTTT:p.(=); ENTPD3:ENST00000456402.5:c.286+1112_286+1113insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.16227782; CADD: 0.162 (0.769)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr3:g.40448094G>A [0/1] rs150315344 (variation viewer)

Variant score: 0.090

Transcripts:: ENTPD3:ENST00000301825.8::; ENTPD3:ENST00000338970.10::

Pathogenicity Data:: Best Score: 0.3028921; CADD: 0.303 (1.567)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 1.2570%; UK10K: 1.8249%; gnomAD_G_AFR: 0.3553%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 0.2291%; gnomAD_G_NFE: 1.6995%; gnomAD_G_OTH: 1.3238%

INTERGENIC_VARIANT chr3:g.40434817AAAAAT>A [0/1] rs71094604 (variation viewer)

Variant score: 0.065

Transcripts:: ENTPD3:ENST00000301825.8::; ENTPD3:ENST00000338970.10::

Pathogenicity Data:: Best Score: 0.07679105; CADD: 0.077 (0.347)

Frequency Data:: gnomAD_G_AFR: 0.1595%; gnomAD_G_AMR: 0.4854%; gnomAD_G_ASJ: 0.7692%; gnomAD_G_EAS: 0.5988%; gnomAD_G_NFE: 0.1766%

INTERGENIC_VARIANT chr3:g.40443564G>A [0/1] rs144251252 (variation viewer)

Variant score: 0.057

Transcripts:: ENTPD3:ENST00000301825.8::; ENTPD3:ENST00000338970.10::

Pathogenicity Data:: Best Score: 0.19369382; CADD: 0.194 (0.935)

Frequency Data:: 1000Genomes: 0.7188%; TOPMed: 1.2600%; UK10K: 1.8249%; gnomAD_G_AFR: 0.3425%; gnomAD_G_AMR: 0.3989%; gnomAD_G_ASJ: 1.0067%; gnomAD_G_FIN: 0.0359%; gnomAD_G_NFE: 1.4464%; gnomAD_G_OTH: 0.8949%

DOWNSTREAM_GENE_VARIANT chr3:g.40432451C>T [0/1] rs192335460 (variation viewer)

Variant score: 0.053

Transcripts:: ENTPD3:ENST00000301825.8::; ENTPD3:ENST00000338970.10::

Pathogenicity Data:: Best Score: 0.062222064; CADD: 0.062 (0.279)

Frequency Data:: 1000Genomes: 0.2396%; TOPMed: 0.4938%; UK10K: 0.7273%; gnomAD_G_AFR: 0.1606%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.6398%; gnomAD_G_OTH: 0.3055%

INTERGENIC_VARIANT chr3:g.40434790CA>C [0/1] rs563366319 (variation viewer)

Variant score: 0.010

Transcripts:: ENTPD3:ENST00000301825.8::; ENTPD3:ENST00000338970.10::

Pathogenicity Data:: Best Score: 0.0150821805; CADD: 0.015 (0.066)

Frequency Data:: gnomAD_G_AFR: 0.1942%; gnomAD_G_ASJ: 1.2500%; gnomAD_G_NFE: 0.4736%

CHRNE

Exomiser Score: 0.002

Phenotype Score: 0.519

Variant Score: 0.186

Phenotype matches:

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:605809 Myasthenic syndrome, congenital, 4A, slow-channel - autosomal dominant/recessive; OMIM:608931 Myasthenic syndrome, congenital, 4C, associated with acetylcholine receptor deficiency - autosomal recessive; OMIM:616324 Myasthenic syndrome, congenital, 4B, fast-channel - autosomal recessive; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.519

Variant Score: 0.186

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.4921932C>CAA [1/1] rs34371210 (variation viewer)

Variant score: 0.186 CONTRIBUTING VARIANT

Transcripts:: CHRNE:ENST00000649830.1:c.-888+12409_-888+12410insTT:p.(=)

Pathogenicity Data:: Best Score: 0.18585831; CADD: 0.186 (0.893)

Frequency Data:: No frequency data

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr17:g.4912459C>CA [1/1] rs796911266 (variation viewer)

Variant score: 0.134

Transcripts:: CHRNE:ENST00000649830.1:c.-887-9697_-887-9696insT:p.(=)

Pathogenicity Data:: Best Score: 0.13383627; CADD: 0.134 (0.624)

Frequency Data:: No frequency data

AURKB

Exomiser Score: 0.002

Phenotype Score: 0.510

Variant Score: 0.195

Phenotype matches:

Proximity score 0.510 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.510

Variant Score: 0.195

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr17:g.8201910AAAG>A [0/1] rs1333101434 (variation viewer)

Variant score: 0.195 CONTRIBUTING VARIANT

Transcripts:: AURKB:ENST00000316199.10::

Pathogenicity Data:: Best Score: 0.194807; CADD: 0.195 (0.941)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.510

Variant Score: 0.144

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr17:g.8201910AAAG>A [0/1] rs1333101434 (variation viewer)

Variant score: 0.195 CONTRIBUTING VARIANT

Transcripts:: AURKB:ENST00000316199.10::

Pathogenicity Data:: Best Score: 0.194807; CADD: 0.195 (0.941)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr17:g.8216086AAAG>A [0|1] rs1309271950 (variation viewer)

Variant score: 0.093 CONTRIBUTING VARIANT

Transcripts:: AURKB:ENST00000316199.10::

Pathogenicity Data:: Best Score: 0.09572607; CADD: 0.096 (0.437)

Frequency Data:: gnomAD_G_AFR: 0.1377%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 0.0289%; gnomAD_G_NFE: 0.1873%; gnomAD_G_OTH: 0.1031%

Other passed variants:

UPSTREAM_GENE_VARIANT chr17:g.8214607T>TATATATATATACACACACAC [0/1] rs759941024 (variation viewer)

Variant score: 0.082

Transcripts:: AURKB:ENST00000316199.10::; AURKB:ENST00000651323.1::

Pathogenicity Data:: Best Score: 0.08230156; CADD: 0.082 (0.373)

Frequency Data:: No frequency data

OXA1L

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.201

Phenotype matches:

Proximity score 0.504 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.201

Variants contributing to score:

REGULATORY_REGION_VARIANT chr14:g.22590191G>GTT [0/1] rs5807180 (variation viewer)

Variant score: 0.201 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.20090204; CADD: 0.201 (0.974)

Frequency Data:: No frequency data

Other passed variants:

ELOC

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.200

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.200

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr8:g.73937606G>C [0/1] rs908063935 (variation viewer)

Variant score: 0.233 CONTRIBUTING VARIANT

Transcripts:: ELOC:ENST00000602840.5::; ELOC:ENST00000460864.4::

Pathogenicity Data:: Best Score: 0.2363401; CADD: 0.236 (1.171)

Frequency Data:: TOPMed: 0.0143%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.73943733C>A [0/1] rs1029488780 (variation viewer)

Variant score: 0.168 CONTRIBUTING VARIANT

Transcripts:: ELOC:ENST00000602840.5:c.149-2128G>T:p.(=)

Pathogenicity Data:: Best Score: 0.1703403; CADD: 0.170 (0.811)

Frequency Data:: TOPMed: 0.0143%; gnomAD_G_OTH: 0.1020%

Other passed variants:

BABAM1

Exomiser Score: 0.002

Phenotype Score: 0.520

Variant Score: 0.176

Phenotype matches:

Proximity score 0.520 in interactome to SLC25A13 and phenotypic similarity 0.683 to Citrullinemia type II associated with SLC25A13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0100754, Mania

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.520

Variant Score: 0.176

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.17273564G>GTTTTTTT [1/1] rs754203595 (variation viewer)

Variant score: 0.176 CONTRIBUTING VARIANT

Transcripts:: BABAM1:ENST00000359435.8:c.345-340_345-339insTTTTTTT:p.(=); BABAM1:ENST00000447614.6:c.344+1909_344+1910insTTTTTTT:p.(=); BABAM1:ENST00000595632.5:c.344+1909_344+1910insTTTTTTT:p.(=); BABAM1:ENST00000598188.6:c.345-340_345-339insTTTTTTT:p.(=); BABAM1:ENST00000601043.5:c.345-340_345-339insTTTTTTT:p.(=); BABAM1:ENST00000596542.1:c.286-340_286-339insTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.17624134; CADD: 0.176 (0.842)

Frequency Data:: No frequency data

Other passed variants:

AK4

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.194

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.170

Variants contributing to score:

REGULATORY_REGION_VARIANT chr1:g.65084099CA>C [0/1] rs34395027 (variation viewer)

Variant score: 0.170 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.16976696; CADD: 0.170 (0.808)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.194

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.65215993G>A [0/1] rs530874515 (variation viewer)

Variant score: 0.218 CONTRIBUTING VARIANT

Transcripts:: AK4:ENST00000327299.8:c.266-2761G>A:p.(=); AK4:ENST00000395334.6:c.266-2761G>A:p.(=); AK4:ENST00000545314.5:c.266-2761G>A:p.(=); AK4:ENST00000546702.5:c.110-2761G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5114602; CADD: 0.511 (3.111)

Frequency Data:: 1000Genomes: 0.6190%; TOPMed: 0.0749%; UK10K: 0.1455%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.0200%; gnomAD_G_OTH: 0.4073%

REGULATORY_REGION_VARIANT chr1:g.65084099CA>C [0/1] rs34395027 (variation viewer)

Variant score: 0.170 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.16976696; CADD: 0.170 (0.808)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr1:g.65247414C>CAAAAA [1/1] rs373799252 (variation viewer)

Variant score: 0.078

Transcripts:: AK4:ENST00000327299.8::

Pathogenicity Data:: Best Score: 0.078065634; CADD: 0.078 (0.353)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr1:g.65229511G>C [0/1] rs566762065 (variation viewer)

Variant score: 0.053

Transcripts:: AK4:ENST00000327299.8:c.*3334G>C:p.(=); AK4:ENST00000395334.6:c.*3334G>C:p.(=); AK4:ENST00000545314.5:c.*3334G>C:p.(=)

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: 1000Genomes: 0.6589%; TOPMed: 0.0749%; UK10K: 0.1455%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_NFE: 0.0203%; gnomAD_G_OTH: 0.4167%

DOWNSTREAM_GENE_VARIANT chr1:g.65232856C>CTTTT [1/1] rs71056086 (variation viewer)

Variant score: 0.045

Transcripts:: AK4:ENST00000327299.8::; AK4:ENST00000263441.11::

Pathogenicity Data:: Best Score: 0.04544711; CADD: 0.045 (0.202)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.65172063GTA>G [-/1] rs3051712 (variation viewer)

Variant score: 0.040

Transcripts:: AK4:ENST00000327299.8:c.146-18646_146-18645del:p.(=); AK4:ENST00000395334.6:c.146-18646_146-18645del:p.(=); AK4:ENST00000545314.5:c.146-18646_146-18645del:p.(=); AK4:ENST00000546702.5:c.-11-18646_-11-18645del:p.(=)

Pathogenicity Data:: Best Score: 0.03971535; CADD: 0.040 (0.176)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.65172063G>GTATATATATATATATATA [-/1] rs3051712 (variation viewer)

Variant score: 0.037

Transcripts:: AK4:ENST00000327299.8:c.146-18647_146-18646insTATATATATATATATATA:p.(=); AK4:ENST00000395334.6:c.146-18647_146-18646insTATATATATATATATATA:p.(=); AK4:ENST00000545314.5:c.146-18647_146-18646insTATATATATATATATATA:p.(=); AK4:ENST00000546702.5:c.-11-18647_-11-18646insTATATATATATATATATA:p.(=)

Pathogenicity Data:: Best Score: 0.037058294; CADD: 0.037 (0.164)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.65174278GT>G [0/1] rs566496059 (variation viewer)

Variant score: 0.001

Transcripts:: AK4:ENST00000327299.8:c.146-16431del:p.(=); AK4:ENST00000395334.6:c.146-16431del:p.(=); AK4:ENST00000545314.5:c.146-16431del:p.(=); AK4:ENST00000546702.5:c.-11-16431del:p.(=)

Pathogenicity Data:: Best Score: 0.0013806224; CADD: 0.001 (0.006)

Frequency Data:: gnomAD_G_AFR: 0.0474%; gnomAD_G_AMR: 0.1362%; gnomAD_G_EAS: 0.0626%; gnomAD_G_FIN: 0.1097%

MCM3

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.194

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.194

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.52270346G>A [0/1] rs78529404 (variation viewer)

Variant score: 0.194 CONTRIBUTING VARIANT

Transcripts:: MCM3:ENST00000229854.12:c.1858-1120C>T:p.(=); MCM3:ENST00000419835.8:c.1690-1120C>T:p.(=); MCM3:ENST00000596288.7:c.1828-1120C>T:p.(=); MCM3:ENST00000616552.4:c.1963-1120C>T:p.(=)

Pathogenicity Data:: Best Score: 0.19443607; CADD: 0.194 (0.939)

Frequency Data:: No frequency data

Other passed variants:

HTR2A

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.193

Phenotype matches:

Phenotypic similarity 0.471 to Obsessive-compulsive disorder, susceptibility to associated with HTR2A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Phenotypic similarity 0.454 to mouse mutant involving HTR2A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001362, abnormal anxiety-related response

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases:: OMIM:103780 Alcohol dependence, susceptibility to (susceptibility); OMIM:164230 Obsessive-compulsive disorder, susceptibility to (susceptibility); OMIM:181500 Schizophrenia, susceptibility to (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.193

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.46876405T>TA [0/1] rs1491555525 (variation viewer)

Variant score: 0.193 CONTRIBUTING VARIANT

Transcripts:: HTR2A:ENST00000378688.8:c.613+15984_613+15985insT:p.(=); HTR2A:ENST00000542664.3:c.613+15984_613+15985insT:p.(=); HTR2A:ENST00000543956.4:c.361+15984_361+15985insT:p.(=)

Pathogenicity Data:: Best Score: 0.19295079; CADD: 0.193 (0.931)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.184

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.46876405T>TA [0/1] rs1491555525 (variation viewer)

Variant score: 0.193 CONTRIBUTING VARIANT

Transcripts:: HTR2A:ENST00000378688.8:c.613+15984_613+15985insT:p.(=); HTR2A:ENST00000542664.3:c.613+15984_613+15985insT:p.(=); HTR2A:ENST00000543956.4:c.361+15984_361+15985insT:p.(=)

Pathogenicity Data:: Best Score: 0.19295079; CADD: 0.193 (0.931)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.46876406T>TATATATA [0/1]

Variant score: 0.175 CONTRIBUTING VARIANT

Transcripts:: HTR2A:ENST00000378688.8:c.613+15983_613+15984insTATATAT:p.(=); HTR2A:ENST00000542664.3:c.613+15983_613+15984insTATATAT:p.(=); HTR2A:ENST00000543956.4:c.361+15983_361+15984insTATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.1773786; CADD: 0.177 (0.848)

Frequency Data:: gnomAD_G_AFR: 0.0259%; gnomAD_G_NFE: 0.0754%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.46863657A>AAAAAAG [1/1] rs768058932 (variation viewer)

Variant score: 0.020

Transcripts:: HTR2A:ENST00000378688.8:c.614-28019_614-28018insCTTTTT:p.(=); HTR2A:ENST00000542664.3:c.614-28019_614-28018insCTTTTT:p.(=); HTR2A:ENST00000543956.4:c.362-28019_362-28018insCTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.0710336; CADD: 0.071 (0.320)

Frequency Data:: gnomAD_G_AFR: 1.8408%; gnomAD_G_AMR: 0.7009%; gnomAD_G_FIN: 0.4839%; gnomAD_G_NFE: 0.2284%; gnomAD_G_OTH: 0.1736%

AR

Exomiser Score: 0.002

Phenotype Score: 0.514

Variant Score: 0.180

Phenotype matches:

Proximity score 0.514 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:176807 Prostate cancer, susceptibility to (susceptibility); OMIM:300068 Androgen insensitivity - X-linked recessive; OMIM:300633 Hypospadias 1, X-linked - X-linked recessive; OMIM:312300 Androgen insensitivity, partial, with or without breast cancer - X-linked recessive; OMIM:313200 Spinal and bulbar muscular atrophy of Kennedy - X-linked recessive; ORPHA:481 Kennedy disease; ORPHA:90797 Partial androgen insensitivity syndrome; ORPHA:99429 Complete androgen insensitivity syndrome

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.514

Variant Score: 0.180

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.67654941C>T [1/1]

Variant score: 0.180 CONTRIBUTING VARIANT

Transcripts:: AR:ENST00000374690.9:c.1768+11534C>T:p.(=); AR:ENST00000396043.2:c.172+11534C>T:p.(=); AR:ENST00000396044.8:c.1768+11534C>T:p.(=); AR:ENST00000504326.5:c.1768+11534C>T:p.(=); AR:ENST00000612010.4:c.1768+11534C>T:p.(=); AR:ENST00000612452.4:c.1198+11534C>T:p.(=); AR:ENST00000613054.2:c.1617-31000C>T:p.(=)

Pathogenicity Data:: Best Score: 0.18002617; CADD: 0.180 (0.862)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.257

Variant Score: 0.180

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.67654941C>T [1/1]

Variant score: 0.180 CONTRIBUTING VARIANT

Transcripts:: AR:ENST00000374690.9:c.1768+11534C>T:p.(=); AR:ENST00000396043.2:c.172+11534C>T:p.(=); AR:ENST00000396044.8:c.1768+11534C>T:p.(=); AR:ENST00000504326.5:c.1768+11534C>T:p.(=); AR:ENST00000612010.4:c.1768+11534C>T:p.(=); AR:ENST00000612452.4:c.1198+11534C>T:p.(=); AR:ENST00000613054.2:c.1617-31000C>T:p.(=)

Pathogenicity Data:: Best Score: 0.18002617; CADD: 0.180 (0.862)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.67575776TC>T [1/1] rs1257105594 (variation viewer)

Variant score: 0.000

Transcripts:: AR:ENST00000374690.9:c.1616+29015del:p.(=); AR:ENST00000396043.2:c.20+6755del:p.(=); AR:ENST00000396044.8:c.1616+29015del:p.(=); AR:ENST00000504326.5:c.1616+29015del:p.(=); AR:ENST00000612010.4:c.1616+29015del:p.(=); AR:ENST00000612452.4:c.1046+29015del:p.(=); AR:ENST00000613054.2:c.1616+29015del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: TOPMed: 0.0024%

PDZD7

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.189

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 2 associated with PDZD7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.502 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.502 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:276901 Retinal disease in Usher syndrome type IIA, modifier of (susceptibility); OMIM:605472 Usher syndrome, type IIC, GPR98/PDZD7 digenic - autosomal recessive; OMIM:618003 Deafness, autosomal recessive 57 - autosomal recessive; ORPHA:231178 Usher syndrome type 2; ORPHA:231178 Usher syndrome type 2

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.502

Variant Score: 0.189

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.101025755G>T [0|1] rs1010679549 (variation viewer)

Variant score: 0.226 CONTRIBUTING VARIANT

Transcripts:: PDZD7:ENST00000370215.7:c.227-1687C>A:p.(=); PDZD7:ENST00000619208.6:c.227-1687C>A:p.(=); PDZD7:ENST00000644782.1:c.227-1687C>A:p.(=); PDZD7:ENST00000645349.1:c.227-1687C>A:p.(=)

Pathogenicity Data:: Best Score: 0.23862255; CADD: 0.239 (1.184)

Frequency Data:: TOPMed: 0.0255%; gnomAD_G_AFR: 0.0117%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1022%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.101025754G>A [0|1] rs536348123 (variation viewer)

Variant score: 0.152 CONTRIBUTING VARIANT

Transcripts:: PDZD7:ENST00000370215.7:c.227-1686C>T:p.(=); PDZD7:ENST00000619208.6:c.227-1686C>T:p.(=); PDZD7:ENST00000644782.1:c.227-1686C>T:p.(=); PDZD7:ENST00000645349.1:c.227-1686C>T:p.(=)

Pathogenicity Data:: Best Score: 0.17415226; CADD: 0.174 (0.831)

Frequency Data:: 1000Genomes: 0.2596%; TOPMed: 0.2572%; gnomAD_G_AFR: 0.6580%; gnomAD_G_ASJ: 0.3333%; gnomAD_G_EAS: 0.1233%; gnomAD_G_NFE: 0.0469%; gnomAD_G_OTH: 0.2049%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.101009599C>CT [1/1] rs142806278 (variation viewer)

Variant score: 0.128

Transcripts:: PDZD7:ENST00000619208.6:c.2618-250_2618-249insA:p.(=)

Pathogenicity Data:: Best Score: 0.1280331; CADD: 0.128 (0.595)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.101020011C>T [0/1] rs141375120 (variation viewer)

Variant score: 0.075

Transcripts:: PDZD7:ENST00000370215.7:c.928+607G>A:p.(=); PDZD7:ENST00000619208.6:c.928+607G>A:p.(=); PDZD7:ENST00000644782.1:c.928+607G>A:p.(=); PDZD7:ENST00000645349.1:c.928+607G>A:p.(=)

Pathogenicity Data:: Best Score: 0.31561577; CADD: 0.316 (1.647)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 1.3590%; UK10K: 1.8910%; gnomAD_G_AFR: 0.4497%; gnomAD_G_AMR: 0.9685%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.4717%; gnomAD_G_NFE: 1.8332%; gnomAD_G_OTH: 1.2270%

HLA-B

Exomiser Score: 0.002

Phenotype Score: 0.252

Variant Score: 0.471

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:106300 Spondyloarthropathy, susceptibility to, 1 (susceptibility); ORPHA:117 Behçet disease; ORPHA:3287 Takayasu arteritis; ORPHA:36426 Stevens-Johnson syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.125

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31307251CAAAAAAAAAA>C [0|1] rs9279102 (variation viewer)

Variant score: 0.125 CONTRIBUTING VARIANT

Transcripts:: HLA-B:ENST00000640615.1:c.206-37736_206-37727del:p.(=)

Pathogenicity Data:: Best Score: 0.12501621; CADD: 0.125 (0.580)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.252

Variant Score: 0.471

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31346356G>C [0/1] rs115110387 (variation viewer)

Variant score: 0.500 CONTRIBUTING VARIANT

Transcripts:: HLA-B:ENST00000640615.1:c.205+8751C>G:p.(=)

Pathogenicity Data:: Best Score: 0.75984037; CADD: 0.760 (6.195)

Frequency Data:: 1000Genomes: 1.1980%; TOPMed: 0.6650%; UK10K: 0.1587%; gnomAD_G_AFR: 1.2597%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.2597%; gnomAD_G_OTH: 0.5112%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31334053C>T [0/1] rs28793963 (variation viewer)

Variant score: 0.441 CONTRIBUTING VARIANT

Transcripts:: HLA-B:ENST00000640615.1:c.205+21054G>A:p.(=)

Pathogenicity Data:: Best Score: 0.6703903; CADD: 0.670 (4.820)

Frequency Data:: 1000Genomes: 1.2180%; TOPMed: 0.6650%; UK10K: 0.1851%; gnomAD_G_AFR: 1.2606%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.2601%; gnomAD_G_OTH: 0.5102%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31307619G>A [0/1] rs145080427 (variation viewer)

Variant score: 0.360

Transcripts:: HLA-B:ENST00000640615.1:c.206-38094C>T:p.(=)

Pathogenicity Data:: Best Score: 0.6239029; CADD: 0.624 (4.247)

Frequency Data:: 1000Genomes: 1.4180%; TOPMed: 1.4180%; gnomAD_G_AFR: 1.1588%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.2674%; gnomAD_G_OTH: 0.6135%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31272325C>T [0/1] rs281860308 (variation viewer)

Variant score: 0.136

Transcripts:: HLA-B:ENST00000640615.1:c.206-2800G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5722401; CADD: 0.572 (3.688)

Frequency Data:: 1000Genomes: 1.3180%; TOPMed: 1.3180%; gnomAD_G_AFR: 1.8922%; gnomAD_G_AMR: 0.7177%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0860%; gnomAD_G_NFE: 0.2668%; gnomAD_G_OTH: 0.4073%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31310950A>AATAT [1/1] rs572243496 (variation viewer)

Variant score: 0.108

Transcripts:: HLA-B:ENST00000640615.1:c.206-41426_206-41425insATAT:p.(=)

Pathogenicity Data:: Best Score: 0.13821286; CADD: 0.138 (0.646)

Frequency Data:: gnomAD_G_AFR: 0.3373%; gnomAD_G_EAS: 0.3546%; gnomAD_G_NFE: 0.9610%; gnomAD_G_OTH: 0.8065%

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.31282058T>TG [0/1] rs34072090 (variation viewer)

Variant score: 0.101

Transcripts:: HLA-B:ENST00000640615.1:c.206-12534_206-12533insC:p.(=)

Pathogenicity Data:: Best Score: 0.15995991; CADD: 0.160 (0.757)

Frequency Data:: 1000Genomes: 1.0780%; TOPMed: 1.0780%; gnomAD_G_AFR: 1.3164%; gnomAD_G_AMR: 0.6394%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 0.0341%; gnomAD_G_NFE: 0.2784%; gnomAD_G_OTH: 0.5411%

PRKAR1A

Exomiser Score: 0.002

Phenotype Score: 0.507

Variant Score: 0.179

Phenotype matches:

Phenotypic similarity 0.471 to Pigmented nodular adrenocortical disease, primary, 1 associated with PRKAR1A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:101800 Acrodysostosis 1, with or without hormone resistance - autosomal dominant; OMIM:160980 Carney complex, type 1 - autosomal dominant; OMIM:255960 Myxoma, intracardiac - autosomal dominant; OMIM:610489 Pigmented nodular adrenocortical disease, primary, 1 - autosomal dominant; ORPHA:1359 Carney complex; ORPHA:189439 Primary pigmented nodular adrenocortical disease; ORPHA:280651 Acrodysostosis with multiple hormone resistance; ORPHA:520 Acute promyelocytic leukemia; ORPHA:615 Familial atrial myxoma; ORPHA:950 Acrodysostosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.507

Variant Score: 0.179

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.68496818C>CTTTT [0/1] rs372918487 (variation viewer)

Variant score: 0.179 CONTRIBUTING VARIANT

Transcripts:: PRKAR1A:ENST00000358598.6::

Pathogenicity Data:: Best Score: 0.17927057; CADD: 0.179 (0.858)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.155

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.68496818C>CTTTT [0/1] rs372918487 (variation viewer)

Variant score: 0.179 CONTRIBUTING VARIANT

Transcripts:: PRKAR1A:ENST00000358598.6::

Pathogenicity Data:: Best Score: 0.17927057; CADD: 0.179 (0.858)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.68520039G>A [0/1] rs142052251 (variation viewer)

Variant score: 0.130 CONTRIBUTING VARIANT

Transcripts:: PRKAR1A:ENST00000358598.6:c.178-2717G>A:p.(=); PRKAR1A:ENST00000392711.5:c.178-2717G>A:p.(=); PRKAR1A:ENST00000536854.6:c.178-2717G>A:p.(=); PRKAR1A:ENST00000586397.5:c.178-2717G>A:p.(=); PRKAR1A:ENST00000588188.6:c.178-2717G>A:p.(=); PRKAR1A:ENST00000589228.5:c.178-2717G>A:p.(=)

Pathogenicity Data:: Best Score: 0.44817674; CADD: 0.448 (2.582)

Frequency Data:: 1000Genomes: 0.4792%; TOPMed: 0.7422%; UK10K: 1.2034%; gnomAD_G_AFR: 0.2177%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.8317%; gnomAD_G_NFE: 1.2257%; gnomAD_G_OTH: 1.5275%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.68534881A>AC [0/1] rs529670992 (variation viewer)

Variant score: 0.095

Transcripts:: PRKAR1A:ENST00000588188.6:c.973+4880_973+4881insC:p.(=)

Pathogenicity Data:: Best Score: 0.23949862; CADD: 0.239 (1.189)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.6666%; UK10K: 1.1505%; gnomAD_G_AFR: 0.2063%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.6983%; gnomAD_G_NFE: 1.0607%; gnomAD_G_OTH: 1.2245%

NME2

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.181

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.181

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr17:g.51176422A>T [1/1] rs373300910 (variation viewer)

Variant score: 0.181 CONTRIBUTING VARIANT

Transcripts:: NME2:ENST00000512737.5::

Pathogenicity Data:: Best Score: 0.18134671; CADD: 0.181 (0.869)

Frequency Data:: No frequency data

Other passed variants:

MRE11

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.180

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:604391 Ataxia-telangiectasia-like disorder 1 - autosomal recessive; ORPHA:145 Hereditary breast and ovarian cancer syndrome; ORPHA:251347 Ataxia-telangiectasia-like disorder

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.133

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr11:g.94419465G>GGAGAGAGA [0/1] rs201800515 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: MRE11:ENST00000323929.7:c.*652_*659dup:p.(=)

Pathogenicity Data:: Best Score: 0.13323772; CADD: 0.133 (0.621)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.180

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr11:g.94453109A>G [0/1] rs189664156 (variation viewer)

Variant score: 0.226 CONTRIBUTING VARIANT

Transcripts:: MRE11:ENST00000323929.7:c.1563+3167T>C:p.(=); MRE11:ENST00000323977.7:c.1563+3167T>C:p.(=); MRE11:ENST00000393241.8:c.1563+3167T>C:p.(=); MRE11:ENST00000407439.7:c.1572+3167T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5391071; CADD: 0.539 (3.364)

Frequency Data:: 1000Genomes: 0.1997%; TOPMed: 0.5272%; UK10K: 0.8728%; gnomAD_G_AFR: 0.2083%; gnomAD_G_AMR: 0.3614%; gnomAD_G_ASJ: 1.6667%; gnomAD_G_FIN: 0.6520%; gnomAD_G_NFE: 0.9045%; gnomAD_G_OTH: 0.8403%

THREE_PRIME_UTR_EXON_VARIANT chr11:g.94419465G>GGAGAGAGA [0/1] rs201800515 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: MRE11:ENST00000323929.7:c.*652_*659dup:p.(=)

Pathogenicity Data:: Best Score: 0.13323772; CADD: 0.133 (0.621)

Frequency Data:: No frequency data

Other passed variants:

KLKB1

Exomiser Score: 0.002

Phenotype Score: 0.508

Variant Score: 0.172

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612423 Fletcher factor (prekallikrein) deficiency - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.254

Variant Score: 0.342

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186242928G>A [0|1] rs1459982608 (variation viewer)

Variant score: 0.342 CONTRIBUTING VARIANT

Transcripts:: KLKB1:ENST00000264690.11:c.598+4563G>A:p.(=); KLKB1:ENST00000513864.2:c.484+4563G>A:p.(=)

Pathogenicity Data:: Best Score: 0.34219068; CADD: 0.342 (1.819)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.508

Variant Score: 0.172

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186242928G>A [0|1] rs1459982608 (variation viewer)

Variant score: 0.342 CONTRIBUTING VARIANT

Transcripts:: KLKB1:ENST00000264690.11:c.598+4563G>A:p.(=); KLKB1:ENST00000513864.2:c.484+4563G>A:p.(=)

Pathogenicity Data:: Best Score: 0.34219068; CADD: 0.342 (1.819)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.186238425C>T [0/1] rs146737970 (variation viewer)

Variant score: 0.002 CONTRIBUTING VARIANT

Transcripts:: KLKB1:ENST00000264690.11:c.598+60C>T:p.(=); KLKB1:ENST00000513864.2:c.484+60C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0032184124; CADD: 0.003 (0.014)

Frequency Data:: 1000Genomes: 0.1797%; TOPMed: 0.4762%; gnomAD_G_AFR: 1.1687%; gnomAD_G_AMR: 0.2392%; gnomAD_G_OTH: 0.1018%

Other passed variants:

SAR1A

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.175

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.70154511C>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: SAR1A:ENST00000373238.5:c.349-542G>:p.(=); SAR1A:ENST00000373241.9:c.349-542G>:p.(=); SAR1A:ENST00000373242.6:c.349-542G>:p.(=); SAR1A:ENST00000431664.6:c.349-542G>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.175

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr10:g.70151259CAAAAAA>C [1|1] rs201493587 (variation viewer)

Variant score: 0.175 CONTRIBUTING VARIANT

Transcripts:: SAR1A:ENST00000373238.5:c.*1211_*1216del:p.(=); SAR1A:ENST00000373241.9:c.*1211_*1216del:p.(=); SAR1A:ENST00000373242.6:c.*1211_*1216del:p.(=); SAR1A:ENST00000431664.6:c.*1171_*1176del:p.(=)

Pathogenicity Data:: Best Score: 0.17491251; CADD: 0.175 (0.835)

Frequency Data:: No frequency data

Other passed variants:

VDAC1

Exomiser Score: 0.002

Phenotype Score: 0.516

Variant Score: 0.160

Phenotype matches:

Proximity score 0.516 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.002

Phenotype Score: 0.516

Variant Score: 0.160

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.133979424C>CT [-/1] rs71581380 (variation viewer)

Variant score: 0.160 CONTRIBUTING VARIANT

Transcripts:: VDAC1:ENST00000265333.8:c.551+1304_551+1305insA:p.(=); VDAC1:ENST00000395044.7:c.551+1304_551+1305insA:p.(=); VDAC1:ENST00000395047.6:c.551+1304_551+1305insA:p.(=)

Pathogenicity Data:: Best Score: 0.16015333; CADD: 0.160 (0.758)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.516

Variant Score: 0.155

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.133979424C>CT [-/1] rs71581380 (variation viewer)

Variant score: 0.160 CONTRIBUTING VARIANT

Transcripts:: VDAC1:ENST00000265333.8:c.551+1304_551+1305insA:p.(=); VDAC1:ENST00000395044.7:c.551+1304_551+1305insA:p.(=); VDAC1:ENST00000395047.6:c.551+1304_551+1305insA:p.(=)

Pathogenicity Data:: Best Score: 0.16015333; CADD: 0.160 (0.758)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.133979424C>CTTTT [-/1] rs71581380 (variation viewer)

Variant score: 0.151 CONTRIBUTING VARIANT

Transcripts:: VDAC1:ENST00000265333.8:c.551+1304_551+1305insAAAA:p.(=); VDAC1:ENST00000395044.7:c.551+1304_551+1305insAAAA:p.(=); VDAC1:ENST00000395047.6:c.551+1304_551+1305insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.15062398; CADD: 0.151 (0.709)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr5:g.133980670C>T [0/1] rs149459850 (variation viewer)

Variant score: 0.115

Transcripts:: VDAC1:ENST00000265333.8:c.551+59G>A:p.(=); VDAC1:ENST00000395044.7:c.551+59G>A:p.(=); VDAC1:ENST00000395047.6:c.551+59G>A:p.(=)

Pathogenicity Data:: Best Score: 0.39018232; CADD: 0.390 (2.148)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.3794%; gnomAD_G_AFR: 0.0809%; gnomAD_G_AMR: 0.9685%; gnomAD_G_ASJ: 1.6667%; gnomAD_G_FIN: 1.8268%; gnomAD_G_NFE: 0.9916%; gnomAD_G_OTH: 0.8386%

WHRN

Exomiser Score: 0.002

Phenotype Score: 0.513

Variant Score: 0.161

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 2 associated with WHRN.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.513 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:607084 Deafness, autosomal recessive 31 - autosomal recessive; OMIM:611383 Usher syndrome, type 2D - autosomal recessive; ORPHA:231178 Usher syndrome type 2

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.257

Variant Score: 0.317

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.114472596C>A [0/1]

Variant score: 0.317 CONTRIBUTING VARIANT

Transcripts:: WHRN:ENST00000362057.4:c.837+5957G>T:p.(=); WHRN:ENST00000265134.10:c.-313+5957G>T:p.(=)

Pathogenicity Data:: Best Score: 0.31687528; CADD: 0.317 (1.655)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.513

Variant Score: 0.161

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.114472596C>A [0/1]

Variant score: 0.317 CONTRIBUTING VARIANT

Transcripts:: WHRN:ENST00000362057.4:c.837+5957G>T:p.(=); WHRN:ENST00000265134.10:c.-313+5957G>T:p.(=)

Pathogenicity Data:: Best Score: 0.31687528; CADD: 0.317 (1.655)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr9:g.114495384C>T [0/1] rs564078685 (variation viewer)

Variant score: 0.005 CONTRIBUTING VARIANT

Transcripts:: WHRN:ENST00000362057.4:c.618+8800G>A:p.(=); WHRN:ENST00000374057.3:c.618+8800G>A:p.(=); WHRN:ENST00000265134.10:c.-532+7723G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0045945644; CADD: 0.005 (0.020)

Frequency Data:: 1000Genomes: 0.0200%

Other passed variants:

ACLY

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.171

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.503

Variant Score: 0.171

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.41889524C>CAAAAAAAA [1/1] rs533387140 (variation viewer)

Variant score: 0.171 CONTRIBUTING VARIANT

Transcripts:: ACLY:ENST00000352035.7:c.1771-1822_1771-1821insTTTTTTTT:p.(=); ACLY:ENST00000353196.5:c.1741-1822_1741-1821insTTTTTTTT:p.(=); ACLY:ENST00000393896.6:c.1741-1822_1741-1821insTTTTTTTT:p.(=); ACLY:ENST00000537919.5:c.958-1822_958-1821insTTTTTTTT:p.(=); ACLY:ENST00000590151.5:c.1771-1822_1771-1821insTTTTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.17129493; CADD: 0.171 (0.816)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.41879647CAAAAAAAAA>C [1/1] rs558056100 (variation viewer)

Variant score: 0.161

Transcripts:: ACLY:ENST00000352035.7:c.2266-732_2266-724del:p.(=); ACLY:ENST00000353196.5:c.2236-732_2236-724del:p.(=); ACLY:ENST00000393896.6:c.2236-732_2236-724del:p.(=); ACLY:ENST00000537919.5:c.1453-732_1453-724del:p.(=); ACLY:ENST00000590151.5:c.2266-732_2266-724del:p.(=)

Pathogenicity Data:: Best Score: 0.1611197; CADD: 0.161 (0.763)

Frequency Data:: No frequency data

PNPT1

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.171

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:614932 Combined oxidative phosphorylation deficiency 13 - autosomal recessive; OMIM:614934 Deafness, autosomal recessive 70 - autosomal recessive; ORPHA:319514 Combined oxidative phosphorylation defect type 13

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.002

Phenotype Score: 0.504

Variant Score: 0.171

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.55661091CT>C [1/1] rs1171064705 (variation viewer)

Variant score: 0.171 CONTRIBUTING VARIANT

Transcripts:: PNPT1:ENST00000447944.7:c.1247+864del:p.(=)

Pathogenicity Data:: Best Score: 0.1707223; CADD: 0.171 (0.813)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.55676262C>CA [1/1] rs11400030 (variation viewer)

Variant score: 0.109

Transcripts:: PNPT1:ENST00000447944.7:c.680-3184_680-3183insT:p.(=)

Pathogenicity Data:: Best Score: 0.10936451; CADD: 0.109 (0.503)

Frequency Data:: No frequency data

NEDD8

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.168

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.106

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.24226424T>C [0/1] rs1208930534 (variation viewer)

Variant score: 0.106 CONTRIBUTING VARIANT

Transcripts:: NEDD8:ENST00000250495.10:c.18+5826A>G:p.(=); NEDD8:ENST00000524927.1:c.18+5826A>G:p.(=); NEDD8:ENST00000534348.5:c.18+5826A>G:p.(=)

Pathogenicity Data:: Best Score: 0.105665445; CADD: 0.106 (0.485)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.168

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.24223085C>CA [1/1] rs71426836 (variation viewer)

Variant score: 0.168 CONTRIBUTING VARIANT

Transcripts:: NEDD8:ENST00000250495.10:c.19-4655_19-4654insT:p.(=); NEDD8:ENST00000524927.1:c.19-4655_19-4654insT:p.(=); NEDD8:ENST00000534348.5:c.19-4655_19-4654insT:p.(=)

Pathogenicity Data:: Best Score: 0.1684277; CADD: 0.168 (0.801)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.24219475CA>C [1/1] rs59964484 (variation viewer)

Variant score: 0.030

Transcripts:: NEDD8:ENST00000250495.10:c.19-1045del:p.(=); NEDD8:ENST00000524927.1:c.19-1045del:p.(=); NEDD8:ENST00000534348.5:c.19-1045del:p.(=)

Pathogenicity Data:: Best Score: 0.030160189; CADD: 0.030 (0.133)

Frequency Data:: No frequency data

B3GALNT1

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.167

Phenotype matches:

Proximity score 0.502 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.167

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.161092763C>CTT [0/1] rs33946641 (variation viewer)

Variant score: 0.167 CONTRIBUTING VARIANT

Transcripts:: B3GALNT1:ENST00000320474.10:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000392779.6:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000392781.7:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000417187.2:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000473285.5:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000476999.6:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000488170.5:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000494173.7:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000494818.6:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000650695.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000650733.1:c.-137-2702_-137-2701insAA:p.(=); B3GALNT1:ENST00000651117.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651147.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651178.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651254.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651282.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651292.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651305.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651379.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651380.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651430.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651509.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651686.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651689.1:c.-137-2702_-137-2701insAA:p.(=); B3GALNT1:ENST00000651791.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651801.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000651916.1:c.-157-2698_-157-2697insAA:p.(=); B3GALNT1:ENST00000651953.1:c.-153-2702_-153-2701insAA:p.(=); B3GALNT1:ENST00000651972.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652032.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652059.1:c.-137-2702_-137-2701insAA:p.(=); B3GALNT1:ENST00000652111.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652143.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652377.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652593.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652669.1:c.-34-5976_-34-5975insAA:p.(=); B3GALNT1:ENST00000652730.1:c.-34-5976_-34-5975insAA:p.(=)

Pathogenicity Data:: Best Score: 0.16651076; CADD: 0.167 (0.791)

Frequency Data:: No frequency data

Other passed variants:

COPZ2

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.162

Phenotype matches:

Proximity score 0.505 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.162

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.48044403C>CTTTT [0/1] rs3048654 (variation viewer)

Variant score: 0.162 CONTRIBUTING VARIANT

Transcripts:: COPZ2:ENST00000621465.5::

Pathogenicity Data:: Best Score: 0.161892; CADD: 0.162 (0.767)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.109

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr17:g.48021719T>C [1|1] rs1469467198 (variation viewer)

Variant score: 0.109 CONTRIBUTING VARIANT

Transcripts:: COPZ2:ENST00000621465.5::; COPZ2:ENST00000338399.9::

Pathogenicity Data:: Best Score: 0.15530485; CADD: 0.155 (0.733)

Frequency Data:: gnomAD_G_AFR: 0.1450%; gnomAD_G_AMR: 1.1628%; gnomAD_G_EAS: 0.0685%; gnomAD_G_FIN: 0.7384%; gnomAD_G_NFE: 0.9995%; gnomAD_G_OTH: 0.1718%

Other passed variants:

COX8A

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.161

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:619059 ?Mitochondrial complex IV deficiency, nuclear type 15 (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.109

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.63966198A>ATCTAATCT [-/1] rs140893687 (variation viewer)

Variant score: 0.109 CONTRIBUTING VARIANT

Transcripts:: COX8A:ENST00000314133.4::

Pathogenicity Data:: Best Score: 0.10874909; CADD: 0.109 (0.500)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.161

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.63967742C>CAAAA [1/1] rs71039693 (variation viewer)

Variant score: 0.161 CONTRIBUTING VARIANT

Transcripts:: COX8A:ENST00000314133.4::

Pathogenicity Data:: Best Score: 0.1611197; CADD: 0.161 (0.763)

Frequency Data:: No frequency data

Other passed variants:

UPSTREAM_GENE_VARIANT chr11:g.63972810A>T [0|1]

Variant score: 0.022

Transcripts:: COX8A:ENST00000314133.4::; COX8A:ENST00000377793.9::

Pathogenicity Data:: Best Score: 0.022087514; CADD: 0.022 (0.097)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr11:g.63966198AATCT>* [-/1]

Variant score: 0.000

Transcripts:: COX8A:ENST00000314133.4::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

COX7C

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.159

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.070

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.86633907G>A [0/1] rs1048758497 (variation viewer)

Variant score: 0.070 CONTRIBUTING VARIANT

Transcripts:: COX7C:ENST00000247655.4::; COX7C:ENST00000486625.1::

Pathogenicity Data:: Best Score: 0.070391655; CADD: 0.070 (0.317)

Frequency Data:: TOPMed: 0.0016%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.159

Variants contributing to score:

INTERGENIC_VARIANT chr5:g.86630737A>AAGAGAG [1/1] rs70993369 (variation viewer)

Variant score: 0.159 CONTRIBUTING VARIANT

Transcripts:: COX7C:ENST00000247655.4::; COX7C:ENST00000486625.1::

Pathogenicity Data:: Best Score: 0.15899223; CADD: 0.159 (0.752)

Frequency Data:: No frequency data

Other passed variants:

REGULATORY_REGION_VARIANT chr5:g.86358640CTTTT>C [1|1] rs71610472 (variation viewer)

Variant score: 0.070

Transcripts:

Pathogenicity Data:: Best Score: 0.070177615; CADD: 0.070 (0.316)

Frequency Data:: No frequency data

TGFB1

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.162

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:131300 Camurati-Engelmann disease - autosomal dominant; OMIM:219700 Cystic fibrosis lung disease, modifier of (susceptibility); OMIM:618213 Inflammatory bowel disease, immunodeficiency, and encephalopathy - autosomal recessive; ORPHA:1328 Camurati-Engelmann disease; ORPHA:586 Cystic fibrosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.133

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr19:g.41328870G>T [0/1]

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: TGFB1:ENST00000221930.6::; TGFB1:ENST00000269967.4::

Pathogenicity Data:: Best Score: 0.13283849; CADD: 0.133 (0.619)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.162

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.41341466C>CAAAAA [1/1] rs770264069 (variation viewer)

Variant score: 0.162 CONTRIBUTING VARIANT

Transcripts:: TGFB1:ENST00000221930.6:c.860+416_860+417insTTTTT:p.(=)

Pathogenicity Data:: Best Score: 0.16227782; CADD: 0.162 (0.769)

Frequency Data:: No frequency data

Other passed variants:

POLD1

Exomiser Score: 0.001

Phenotype Score: 0.517

Variant Score: 0.144

Phenotype matches:

Proximity score 0.517 in interactome to POLG and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:612591 Colorectal cancer, susceptibility to, 10 (susceptibility); OMIM:615381 Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome - autosomal dominant; ORPHA:447877 Polymerase proofreading-related adenomatous polyposis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.517

Variant Score: 0.144

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr19:g.50397933C>T [0/1] rs544605025 (variation viewer)

Variant score: 0.144 CONTRIBUTING VARIANT

Transcripts:: POLD1:ENST00000440232.6:c.-1-918C>T:p.(=); POLD1:ENST00000595904.6:c.-1-918C>T:p.(=); POLD1:ENST00000599857.7:c.-4-915C>T:p.(=); POLD1:ENST00000601098.6:c.-1-918C>T:p.(=); POLD1:ENST00000613923.6:c.-4-915C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14434242; CADD: 0.144 (0.677)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0175%; UK10K: 0.0132%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.0133%

Other passed variants:

RNF41

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.156

Phenotype matches:

Proximity score 0.506 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.156

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr12:g.56200421C>CA [1/1] rs57768926 (variation viewer)

Variant score: 0.156 CONTRIBUTING VARIANT

Transcripts:: RNF41:ENST00000345093.9::; RNF41:ENST00000394023.7::

Pathogenicity Data:: Best Score: 0.15569377; CADD: 0.156 (0.735)

Frequency Data:: No frequency data

Other passed variants:

ENTPD5

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.157

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.157

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr14:g.74001666CAAAAAAAAAAAA>C [1/1] rs541623960 (variation viewer)

Variant score: 0.157 CONTRIBUTING VARIANT

Transcripts:: ENTPD5:ENST00000334696.10:c.-71+9413_-71+9424del:p.(=); ENTPD5:ENST00000556242.5:c.-71+9413_-71+9424del:p.(=); ENTPD5:ENST00000557325.5:c.-71+6018_-71+6029del:p.(=)

Pathogenicity Data:: Best Score: 0.15705353; CADD: 0.157 (0.742)

Frequency Data:: No frequency data

Other passed variants:

PANK2

Exomiser Score: 0.001

Phenotype Score: 0.530

Variant Score: 0.124

Phenotype matches:

Phenotypic similarity 0.479 to Neurodegeneration with brain iron accumulation 1 associated with PANK2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.530 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:234200 Neurodegeneration with brain iron accumulation 1 - autosomal recessive; OMIM:607236 HARP syndrome - autosomal recessive; ORPHA:216866 Classic pantothenate kinase-associated neurodegeneration; ORPHA:216873 Atypical pantothenate kinase-associated neurodegeneration

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.265

Variant Score: 0.264

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.3912930CA>C [-/1] rs71331078 (variation viewer)

Variant score: 0.264 CONTRIBUTING VARIANT

Transcripts:: PANK2:ENST00000316562.8:c.1412+297del:p.(=); PANK2:ENST00000497424.5:c.539+297del:p.(=); PANK2:ENST00000610179.5:c.1043+297del:p.(=); PANK2:ENST00000621507.1:c.539+297del:p.(=)

Pathogenicity Data:: Best Score: 0.26362336; CADD: 0.264 (1.329)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.530

Variant Score: 0.124

Variants contributing to score:

INTERGENIC_VARIANT chr20:g.3876361G>GT [1/1] rs386393138 (variation viewer)

Variant score: 0.124 CONTRIBUTING VARIANT

Transcripts:: PANK2:ENST00000497424.5::

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: No frequency data

Other passed variants:

TFDP3

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.154

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.154

Variants contributing to score:

REGULATORY_REGION_VARIANT chr23:g.133987408A>G [1/1]

Variant score: 0.154 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.1543318; CADD: 0.154 (0.728)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.154

Variants contributing to score:

REGULATORY_REGION_VARIANT chr23:g.133987408A>G [1/1]

Variant score: 0.154 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.1543318; CADD: 0.154 (0.728)

Frequency Data:: No frequency data

Other passed variants:

CBX4

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.151

Phenotype matches:

Proximity score 0.503 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.151

Variants contributing to score:

INTERGENIC_VARIANT chr17:g.79823232A>AT [0/1] rs1003061495 (variation viewer)

Variant score: 0.260 CONTRIBUTING VARIANT

Transcripts:: CBX4:ENST00000269397.9::

Pathogenicity Data:: Best Score: 0.58149564; CADD: 0.581 (3.783)

Frequency Data:: gnomAD_G_AFR: 0.1289%; gnomAD_G_AMR: 0.5181%; gnomAD_G_ASJ: 0.7042%; gnomAD_G_EAS: 0.1880%; gnomAD_G_FIN: 0.5417%; gnomAD_G_NFE: 0.7681%; gnomAD_G_OTH: 1.6269%

DOWNSTREAM_GENE_VARIANT chr17:g.79828530A>T [0/1] rs868812406 (variation viewer)

Variant score: 0.043 CONTRIBUTING VARIANT

Transcripts:: CBX4:ENST00000269397.9::; CBX4:ENST00000269385.9::

Pathogenicity Data:: Best Score: 0.06502497; CADD: 0.065 (0.292)

Frequency Data:: gnomAD_G_AFR: 0.2272%; gnomAD_G_AMR: 0.9063%; gnomAD_G_ASJ: 0.3846%; gnomAD_G_EAS: 1.2650%; gnomAD_G_FIN: 0.5062%; gnomAD_G_NFE: 0.8759%; gnomAD_G_OTH: 0.7481%

Other passed variants:

REGULATORY_REGION_VARIANT chr17:g.80161459CTTTTTT>C [1/1] rs568182873 (variation viewer)

Variant score: 0.105

Transcripts:

Pathogenicity Data:: Best Score: 0.10484135; CADD: 0.105 (0.481)

Frequency Data:: No frequency data

EGF

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.148

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:611718 Hypomagnesemia 4, renal - autosomal recessive; ORPHA:34527 Familial primary hypomagnesemia with normocalciuria and normocalcemia

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.179

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109986456C>T [0/1] rs989591864 (variation viewer)

Variant score: 0.179 CONTRIBUTING VARIANT

Transcripts:: EGF:ENST00000265171.10:c.2492-1288C>T:p.(=); EGF:ENST00000503392.1:c.2492-1288C>T:p.(=); EGF:ENST00000509793.5:c.2366-1288C>T:p.(=); EGF:ENST00000652245.1:c.2365+2915C>T:p.(=)

Pathogenicity Data:: Best Score: 0.17945957; CADD: 0.179 (0.859)

Frequency Data:: gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.148

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109986456C>T [0/1] rs989591864 (variation viewer)

Variant score: 0.179 CONTRIBUTING VARIANT

Transcripts:: EGF:ENST00000265171.10:c.2492-1288C>T:p.(=); EGF:ENST00000503392.1:c.2492-1288C>T:p.(=); EGF:ENST00000509793.5:c.2366-1288C>T:p.(=); EGF:ENST00000652245.1:c.2365+2915C>T:p.(=)

Pathogenicity Data:: Best Score: 0.17945957; CADD: 0.179 (0.859)

Frequency Data:: gnomAD_G_NFE: 0.0067%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.110004215TACACACACAC>T [0/1] rs772189572 (variation viewer)

Variant score: 0.116 CONTRIBUTING VARIANT

Transcripts:: EGF:ENST00000265171.10:c.3174-289_3174-280del:p.(=); EGF:ENST00000503392.1:c.3051-289_3051-280del:p.(=); EGF:ENST00000509793.5:c.3048-289_3048-280del:p.(=); EGF:ENST00000652245.1:c.2805-289_2805-280del:p.(=)

Pathogenicity Data:: Best Score: 0.11630988; CADD: 0.116 (0.537)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.109932360C>CATATATATATATATATATATATATATAT [0/1] rs57424246 (variation viewer)

Variant score: 0.026

Transcripts:: EGF:ENST00000265171.10:c.128-8586_128-8585insATATATATATATATATATATATATATAT:p.(=); EGF:ENST00000503392.1:c.128-8586_128-8585insATATATATATATATATATATATATATAT:p.(=); EGF:ENST00000509793.5:c.128-8586_128-8585insATATATATATATATATATATATATATAT:p.(=); EGF:ENST00000652245.1:c.128-8586_128-8585insATATATATATATATATATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.026356459; CADD: 0.026 (0.116)

Frequency Data:: No frequency data

RNF128

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.148

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.148

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.106749447C>G [1/1] rs751754851 (variation viewer)

Variant score: 0.148 CONTRIBUTING VARIANT

Transcripts:: RNF128:ENST00000255499.3:c.484+22050C>G:p.(=); RNF128:ENST00000324342.7:c.407-23466C>G:p.(=)

Pathogenicity Data:: Best Score: 0.15257746; CADD: 0.153 (0.719)

Frequency Data:: TOPMed: 0.0788%; UK10K: 0.0758%; gnomAD_G_AFR: 0.0336%; gnomAD_G_AMR: 0.1621%; gnomAD_G_FIN: 0.0770%; gnomAD_G_NFE: 0.1896%; gnomAD_G_OTH: 0.1381%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr23:g.106780355C>T [1/1] rs192022367 (variation viewer)

Variant score: 0.026

Transcripts:: RNF128:ENST00000255499.3:c.733-4710C>T:p.(=); RNF128:ENST00000324342.7:c.655-4710C>T:p.(=)

Pathogenicity Data:: Best Score: 0.02702874; CADD: 0.027 (0.119)

Frequency Data:: 1000Genomes: 0.0265%; TOPMed: 0.0828%; UK10K: 0.0758%; gnomAD_G_AFR: 0.0368%; gnomAD_G_AMR: 0.1653%; gnomAD_G_FIN: 0.0765%; gnomAD_G_NFE: 0.1607%; gnomAD_G_OTH: 0.1368%

FOXO1

Exomiser Score: 0.001

Phenotype Score: 0.255

Variant Score: 0.429

Phenotype matches:

Proximity score 0.511 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:268220 Rhabdomyosarcoma, alveolar - somatic

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.255

Variant Score: 0.332

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40637443CA>C [0/1] rs894457880 (variation viewer)

Variant score: 0.332 CONTRIBUTING VARIANT

Transcripts:: FOXO1:ENST00000379561.6:c.630+28139del:p.(=)

Pathogenicity Data:: Best Score: 0.33211762; CADD: 0.332 (1.753)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.255

Variant Score: 0.429

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40630373A>AG [0/1] rs544797925 (variation viewer)

Variant score: 0.526 CONTRIBUTING VARIANT

Transcripts:: FOXO1:ENST00000379561.6:c.630+35209_630+35210insC:p.(=)

Pathogenicity Data:: Best Score: 0.6829703; CADD: 0.683 (4.989)

Frequency Data:: 1000Genomes: 0.0998%; TOPMed: 0.0788%; gnomAD_G_AFR: 0.0115%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_NFE: 0.0600%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40637443CA>C [0/1] rs894457880 (variation viewer)

Variant score: 0.332 CONTRIBUTING VARIANT

Transcripts:: FOXO1:ENST00000379561.6:c.630+28139del:p.(=)

Pathogenicity Data:: Best Score: 0.33211762; CADD: 0.332 (1.753)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40619176C>A [0/1] rs146982053 (variation viewer)

Variant score: 0.135

Transcripts:: FOXO1:ENST00000379561.6:c.630+46407G>T:p.(=); FOXO1:ENST00000339626.5:n.262-148C>A:

Pathogenicity Data:: Best Score: 0.41088516; CADD: 0.411 (2.298)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.8904%; UK10K: 1.7852%; gnomAD_G_AFR: 0.2751%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.3434%; gnomAD_G_NFE: 1.4725%; gnomAD_G_OTH: 0.7143%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40585343G>GCGCGCA [-/1] rs10623475 (variation viewer)

Variant score: 0.098

Transcripts:: FOXO1:ENST00000379561.6:c.631-24484_631-24483insTGCGCG:p.(=)

Pathogenicity Data:: Best Score: 0.09801358; CADD: 0.098 (0.448)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40595248G>A [0/1] rs118159920 (variation viewer)

Variant score: 0.092

Transcripts:: FOXO1:ENST00000379561.6:c.631-34388C>T:p.(=)

Pathogenicity Data:: Best Score: 0.27154958; CADD: 0.272 (1.376)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 0.8896%; UK10K: 1.7720%; gnomAD_G_AFR: 0.2750%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.3438%; gnomAD_G_NFE: 1.4790%; gnomAD_G_OTH: 0.7143%

CODING_TRANSCRIPT_INTRON_VARIANT chr13:g.40606716T>C [0/1] rs189083824 (variation viewer)

Variant score: 0.005

Transcripts:: FOXO1:ENST00000379561.6:c.631-45856A>G:p.(=)

Pathogenicity Data:: Best Score: 0.006655276; CADD: 0.007 (0.029)

Frequency Data:: 1000Genomes: 0.5192%; TOPMed: 0.4603%; UK10K: 0.7670%; gnomAD_G_AFR: 0.1722%; gnomAD_G_AMR: 0.2387%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_EAS: 0.0619%; gnomAD_G_FIN: 0.0860%; gnomAD_G_NFE: 0.5943%; gnomAD_G_OTH: 0.3061%

JUND

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.148

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.148

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr19:g.18276307CAAAAAAAAAAAAAAA>C [-/1] rs758706644 (variation viewer)

Variant score: 0.148 CONTRIBUTING VARIANT

Transcripts:: JUND:ENST00000252818.5::

Pathogenicity Data:: Best Score: 0.14807767; CADD: 0.148 (0.696)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.147

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr19:g.18276307CAAAAAAAAAAAAAAA>C [-/1] rs758706644 (variation viewer)

Variant score: 0.148 CONTRIBUTING VARIANT

Transcripts:: JUND:ENST00000252818.5::

Pathogenicity Data:: Best Score: 0.14807767; CADD: 0.148 (0.696)

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr19:g.18276307CAAAAAAAAAAAAAAAA>C [-/1] rs758706644 (variation viewer)

Variant score: 0.146 CONTRIBUTING VARIANT

Transcripts:: JUND:ENST00000252818.5::

Pathogenicity Data:: Best Score: 0.14552373; CADD: 0.146 (0.683)

Frequency Data:: No frequency data

Other passed variants:

CHRNB1

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.128

Phenotype matches:

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:616313 Myasthenic syndrome, congenital, 2A, slow-channel - autosomal dominant; OMIM:616314 ?Myasthenic syndrome, congenital, 2C, associated with acetylcholine receptor deficiency (unconfirmed); ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.093

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.7451274C>CT [0/1] rs34769424 (variation viewer)

Variant score: 0.093 CONTRIBUTING VARIANT

Transcripts:: CHRNB1:ENST00000306071.7:c.820+2486_820+2487insT:p.(=); CHRNB1:ENST00000536404.6:c.604+2486_604+2487insT:p.(=); CHRNB1:ENST00000576360.1:c.604+2486_604+2487insT:p.(=)

Pathogenicity Data:: Best Score: 0.092597425; CADD: 0.093 (0.422)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.128

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.7452141C>T [0/1] rs113286297 (variation viewer)

Variant score: 0.164 CONTRIBUTING VARIANT

Transcripts:: CHRNB1:ENST00000306071.7:c.821-2156C>T:p.(=); CHRNB1:ENST00000536404.6:c.605-2156C>T:p.(=); CHRNB1:ENST00000576360.1:c.605-2303C>T:p.(=)

Pathogenicity Data:: Best Score: 0.26430124; CADD: 0.264 (1.333)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.8028%; UK10K: 1.2034%; gnomAD_G_AFR: 0.1504%; gnomAD_G_AMR: 0.5995%; gnomAD_G_ASJ: 1.3333%; gnomAD_G_FIN: 0.1481%; gnomAD_G_NFE: 0.8285%; gnomAD_G_OTH: 0.5285%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.7451274C>CT [0/1] rs34769424 (variation viewer)

Variant score: 0.093 CONTRIBUTING VARIANT

Transcripts:: CHRNB1:ENST00000306071.7:c.820+2486_820+2487insT:p.(=); CHRNB1:ENST00000536404.6:c.604+2486_604+2487insT:p.(=); CHRNB1:ENST00000576360.1:c.604+2486_604+2487insT:p.(=)

Pathogenicity Data:: Best Score: 0.092597425; CADD: 0.093 (0.422)

Frequency Data:: No frequency data

Other passed variants:

VDAC2

Exomiser Score: 0.001

Phenotype Score: 0.516

Variant Score: 0.131

Phenotype matches:

Proximity score 0.516 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.516

Variant Score: 0.131

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.75226451GT>G [1/1] rs147954706 (variation viewer)

Variant score: 0.131 CONTRIBUTING VARIANT

Transcripts:: VDAC2:ENST00000313132.8:c.781-3192del:p.(=); VDAC2:ENST00000332211.10:c.736-3192del:p.(=); VDAC2:ENST00000543351.5:c.736-3192del:p.(=)

Pathogenicity Data:: Best Score: 0.13123965; CADD: 0.131 (0.611)

Frequency Data:: No frequency data

Other passed variants:

ORMDL3

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.140

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.116

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr17:g.39930632C>T [0/1] rs1469166110 (variation viewer)

Variant score: 0.116 CONTRIBUTING VARIANT

Transcripts:: ORMDL3:ENST00000304046.7::; ORMDL3:ENST00000377924.5::

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: gnomAD_G_AFR: 0.0120%; gnomAD_G_NFE: 0.0840%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.140

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr17:g.39930203G>A [0/1] rs558201673 (variation viewer)

Variant score: 0.164 CONTRIBUTING VARIANT

Transcripts:: ORMDL3:ENST00000304046.7::; ORMDL3:ENST00000377924.5::

Pathogenicity Data:: Best Score: 0.27003843; CADD: 0.270 (1.367)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0773%; UK10K: 0.0264%; gnomAD_G_AFR: 0.0243%; gnomAD_G_AMR: 0.1247%; gnomAD_G_ASJ: 1.3605%; gnomAD_G_NFE: 0.0289%; gnomAD_G_OTH: 0.3472%

UPSTREAM_GENE_VARIANT chr17:g.39930632C>T [0/1] rs1469166110 (variation viewer)

Variant score: 0.116 CONTRIBUTING VARIANT

Transcripts:: ORMDL3:ENST00000304046.7::; ORMDL3:ENST00000377924.5::

Pathogenicity Data:: Best Score: 0.11732668; CADD: 0.117 (0.542)

Frequency Data:: gnomAD_G_AFR: 0.0120%; gnomAD_G_NFE: 0.0840%

Other passed variants:

TYMS

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.144

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.144

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.670503G>A [0/1] rs375299193 (variation viewer)

Variant score: 0.144 CONTRIBUTING VARIANT

Transcripts:: TYMS:ENST00000323224.7:c.455-189G>A:p.(=); TYMS:ENST00000323250.9:c.308-189G>A:p.(=); TYMS:ENST00000323274.15:c.557-189G>A:p.(=); TYMS:ENST00000383578.7:c.*2718C>T:p.(=); TYMS:ENST00000647584.2:c.*3802C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14473641; CADD: 0.145 (0.679)

Frequency Data:: TOPMed: 0.0279%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0200%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.129

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.670503G>A [0/1] rs375299193 (variation viewer)

Variant score: 0.144 CONTRIBUTING VARIANT

Transcripts:: TYMS:ENST00000323224.7:c.455-189G>A:p.(=); TYMS:ENST00000323250.9:c.308-189G>A:p.(=); TYMS:ENST00000323274.15:c.557-189G>A:p.(=); TYMS:ENST00000383578.7:c.*2718C>T:p.(=); TYMS:ENST00000647584.2:c.*3802C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14473641; CADD: 0.145 (0.679)

Frequency Data:: TOPMed: 0.0279%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr18:g.660302TC>T [0/1] rs553825542 (variation viewer)

Variant score: 0.115 CONTRIBUTING VARIANT

Transcripts:: TYMS:ENST00000323224.7:c.279+589del:p.(=); TYMS:ENST00000323250.9:c.205+2356del:p.(=); TYMS:ENST00000323274.15:c.279+589del:p.(=)

Pathogenicity Data:: Best Score: 0.12843454; CADD: 0.128 (0.597)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.2811%; UK10K: 0.5819%; gnomAD_G_AFR: 0.0917%; gnomAD_G_FIN: 0.1145%; gnomAD_G_NFE: 0.5199%; gnomAD_G_OTH: 0.2045%

Other passed variants:

CHMP4B

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.141

Phenotype matches:

Proximity score 0.506 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:605387 Cataract 31, multiple types - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.141

Variants contributing to score:

INTERGENIC_VARIANT chr20:g.33861325C>T [0/1] rs182975291 (variation viewer)

Variant score: 0.141 CONTRIBUTING VARIANT

Transcripts:: CHMP4B:ENST00000217402.3::; CHMP4B:ENST00000397772.2::

Pathogenicity Data:: Best Score: 0.14217246; CADD: 0.142 (0.666)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0319%; gnomAD_G_EAS: 0.0617%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.0267%

Other passed variants:

CMPK1

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.142

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.142

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr1:g.47380250GTTTT>G [0|1] rs770909160 (variation viewer)

Variant score: 0.142 CONTRIBUTING VARIANT

Transcripts:: CMPK1:ENST00000371873.9::; CMPK1:ENST00000335071.4::

Pathogenicity Data:: Best Score: 0.14177728; CADD: 0.142 (0.664)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.134

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr1:g.47380250GTTTT>G [0|1] rs770909160 (variation viewer)

Variant score: 0.142 CONTRIBUTING VARIANT

Transcripts:: CMPK1:ENST00000371873.9::; CMPK1:ENST00000335071.4::

Pathogenicity Data:: Best Score: 0.14177728; CADD: 0.142 (0.664)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.47346798C>T [0|1] rs545763450 (variation viewer)

Variant score: 0.126 CONTRIBUTING VARIANT

Transcripts:: CMPK1:ENST00000371873.9:c.171+12682C>T:p.(=); CMPK1:ENST00000450808.2:c.171+12682C>T:p.(=); CMPK1:ENST00000471289.2:c.172-11500C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14296216; CADD: 0.143 (0.670)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.3018%; UK10K: 0.6348%; gnomAD_G_AFR: 0.2297%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.0574%; gnomAD_G_NFE: 0.3282%; gnomAD_G_OTH: 0.2045%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.47335849C>T [0/1] rs571229115 (variation viewer)

Variant score: 0.035

Transcripts:: CMPK1:ENST00000371873.9:c.171+1733C>T:p.(=); CMPK1:ENST00000450808.2:c.171+1733C>T:p.(=); CMPK1:ENST00000471289.2:c.171+1733C>T:p.(=)

Pathogenicity Data:: Best Score: 0.06567061; CADD: 0.066 (0.295)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.2931%; UK10K: 0.2248%; gnomAD_G_AFR: 0.1610%; gnomAD_G_FIN: 1.4808%; gnomAD_G_NFE: 0.5036%; gnomAD_G_OTH: 1.0288%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.47365633C>CAAAAAAAAAA [-/1] rs10623948 (variation viewer)

Variant score: 0.025

Transcripts:: CMPK1:ENST00000371873.9:c.172-2836_172-2835insAAAAAAAAAA:p.(=); CMPK1:ENST00000450808.2:c.172-7322_172-7321insAAAAAAAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.025010347; CADD: 0.025 (0.110)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.47346744TTGCCTGC>T [0|1]

Variant score: 0.000

Transcripts:: CMPK1:ENST00000371873.9:c.171+12629_171+12635del:p.(=); CMPK1:ENST00000450808.2:c.171+12629_171+12635del:p.(=); CMPK1:ENST00000471289.2:c.172-11553_172-11547del:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DOWNSTREAM_GENE_VARIANT chr1:g.47380253T>* [-/1]

Variant score: 0.000

Transcripts:: CMPK1:ENST00000371873.9::; CMPK1:ENST00000335071.4::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

TLE2

Exomiser Score: 0.001

Phenotype Score: 0.514

Variant Score: 0.129

Phenotype matches:

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 1.000 to DiGeorge syndrome associated with TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.514 in interactome to TBX1 and phenotypic similarity 0.383 to mouse mutant of TBX1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002797, increased thigmotaxis

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.514

Variant Score: 0.129

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.3041013ATTTTT>A [1/1] rs1168699418 (variation viewer)

Variant score: 0.129 CONTRIBUTING VARIANT

Transcripts:: TLE2:ENST00000426948.6:c.63+4708_63+4712del:p.(=); TLE2:ENST00000591529.5:c.63+4708_63+4712del:p.(=)

Pathogenicity Data:: Best Score: 0.12943739; CADD: 0.129 (0.602)

Frequency Data:: No frequency data

Other passed variants:

NDUFB9

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.140

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618245 ?Mitochondrial complex I deficiency, nuclear type 24 (unconfirmed); ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.243

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.124564691T>TCACACACACACACACA [0/1] rs56708127 (variation viewer)

Variant score: 0.243 CONTRIBUTING VARIANT

Transcripts:: NDUFB9:ENST00000606244.2:c.409-14887_409-14886insCACACACACACACACA:p.(=); NDUFB9:ENST00000325064.9:c.836+970_836+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000378017.7:c.824+970_824+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000431961.6:c.224+970_224+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000518547.5:c.824+970_824+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000524090.5:c.494+970_494+971insTGTGTGTGTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.24334133; CADD: 0.243 (1.211)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.140

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.124564691T>TCACACACACACACACA [0/1] rs56708127 (variation viewer)

Variant score: 0.243 CONTRIBUTING VARIANT

Transcripts:: NDUFB9:ENST00000606244.2:c.409-14887_409-14886insCACACACACACACACA:p.(=); NDUFB9:ENST00000325064.9:c.836+970_836+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000378017.7:c.824+970_824+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000431961.6:c.224+970_224+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000518547.5:c.824+970_824+971insTGTGTGTGTGTGTGTG:p.(=); NDUFB9:ENST00000524090.5:c.494+970_494+971insTGTGTGTGTGTGTGTG:p.(=)

Pathogenicity Data:: Best Score: 0.24334133; CADD: 0.243 (1.211)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr8:g.124542807CT>C [-/1] rs58685573 (variation viewer)

Variant score: 0.037 CONTRIBUTING VARIANT

Transcripts:: NDUFB9:ENST00000276689.8:c.102-279del:p.(=); NDUFB9:ENST00000517367.1:c.102-312del:p.(=); NDUFB9:ENST00000518008.5:c.102-279del:p.(=); NDUFB9:ENST00000606244.2:c.102-279del:p.(=)

Pathogenicity Data:: Best Score: 0.037058294; CADD: 0.037 (0.164)

Frequency Data:: No frequency data

Other passed variants:

RBBP4

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.139

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.048

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32675033G>A [0/1] rs182710932 (variation viewer)

Variant score: 0.048 CONTRIBUTING VARIANT

Transcripts:: RBBP4:ENST00000373485.5:c.1212+2132G>A:p.(=); RBBP4:ENST00000373493.10:c.1212+2132G>A:p.(=); RBBP4:ENST00000414241.7:c.1209+2132G>A:p.(=); RBBP4:ENST00000458695.6:c.1107+2132G>A:p.(=)

Pathogenicity Data:: Best Score: 0.0487383; CADD: 0.049 (0.217)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0414%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0134%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.139

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32661301C>CTT [1|1] rs370489912 (variation viewer)

Variant score: 0.139 CONTRIBUTING VARIANT

Transcripts:: RBBP4:ENST00000373485.5:c.310+3729_310+3730insTT:p.(=); RBBP4:ENST00000373493.10:c.310+3729_310+3730insTT:p.(=); RBBP4:ENST00000414241.7:c.307+3729_307+3730insTT:p.(=); RBBP4:ENST00000458695.6:c.205+3729_205+3730insTT:p.(=)

Pathogenicity Data:: Best Score: 0.13940269; CADD: 0.139 (0.652)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32653663TTTG>* [-/1]

Variant score: 0.000

Transcripts:: RBBP4:ENST00000373485.5:c.164+1602_164+1605delTTTGins*:p.(=); RBBP4:ENST00000373493.10:c.164+1602_164+1605delTTTGins*:p.(=); RBBP4:ENST00000414241.7:c.161+1602_161+1605delTTTGins*:p.(=); RBBP4:ENST00000458695.6:c.59+1602_59+1605delTTTGins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NAGA

Exomiser Score: 0.001

Phenotype Score: 0.529

Variant Score: 0.109

Phenotype matches:

Proximity score 0.529 in interactome to FA2H and phenotypic similarity 0.864 to Fatty acid hydroxylase-associated neurodegeneration associated with FA2H.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:609241 Schindler disease, type I - autosomal recessive; OMIM:609242 Kanzaki disease - autosomal recessive; ORPHA:79279 Alpha-N-acetylgalactosaminidase deficiency type 1; ORPHA:79280 Alpha-N-acetylgalactosaminidase deficiency type 2; ORPHA:79281 Alpha-N-acetylgalactosaminidase deficiency type 3

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.529

Variant Score: 0.109

Variants contributing to score:

REGULATORY_REGION_VARIANT chr22:g.42132027C>T [1|1] rs139702605 (variation viewer)

Variant score: 0.109 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.10915941; CADD: 0.109 (0.502)

Frequency Data:: No frequency data

Other passed variants:

NUMBL

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.133

Phenotype matches:

Proximity score 0.507 in interactome to ARVCF and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with ARVCF.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.133

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr19:g.40661344CT>C [0/1] rs56368294 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: NUMBL:ENST00000252891.8::; NUMBL:ENST00000204005.13::

Pathogenicity Data:: Best Score: 0.13343728; CADD: 0.133 (0.622)

Frequency Data:: No frequency data

Other passed variants:

SPATA5L1

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.134

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.134

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.45419997CAA>C [0/1] rs1179876194 (variation viewer)

Variant score: 0.134 CONTRIBUTING VARIANT

Transcripts:: SPATA5L1:ENST00000305560.11:c.2095-1045_2095-1044del:p.(=)

Pathogenicity Data:: Best Score: 0.13363677; CADD: 0.134 (0.623)

Frequency Data:: No frequency data

Other passed variants:

COX10

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.134

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:619046 Mitochondrial complex IV deficiency, nuclear type 3 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.135

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.14141529CA>C [-/1] rs71147842 (variation viewer)

Variant score: 0.135 CONTRIBUTING VARIANT

Transcripts:: COX10:ENST00000261643.8:c.625-18347del:p.(=)

Pathogenicity Data:: Best Score: 0.13483292; CADD: 0.135 (0.629)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.134

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.14141529CA>C [-/1] rs71147842 (variation viewer)

Variant score: 0.135 CONTRIBUTING VARIANT

Transcripts:: COX10:ENST00000261643.8:c.625-18347del:p.(=)

Pathogenicity Data:: Best Score: 0.13483292; CADD: 0.135 (0.629)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.14141529CAA>C [-/1] rs71147842 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: COX10:ENST00000261643.8:c.625-18347_625-18346del:p.(=)

Pathogenicity Data:: Best Score: 0.13263875; CADD: 0.133 (0.618)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.14166785CT>C [0/1] rs57127092 (variation viewer)

Variant score: 0.070

Transcripts:: COX10:ENST00000261643.8:c.695+6839del:p.(=)

Pathogenicity Data:: Best Score: 0.070177615; CADD: 0.070 (0.316)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.14204160A>G [0/1] rs1224275527 (variation viewer)

Variant score: 0.046

Transcripts:: COX10:ENST00000261643.8:c.929-2650A>G:p.(=)

Pathogenicity Data:: Best Score: 0.046984434; CADD: 0.047 (0.209)

Frequency Data:: TOPMed: 0.0072%; gnomAD_G_NFE: 0.0067%; gnomAD_G_OTH: 0.1020%

REGULATORY_REGION_VARIANT chr17:g.14748318T>TAAAAAAAAAAAAAAAA [1/1] rs55775289 (variation viewer)

Variant score: 0.021

Transcripts:

Pathogenicity Data:: Best Score: 0.021411717; CADD: 0.021 (0.094)

Frequency Data:: No frequency data

GALC

Exomiser Score: 0.001

Phenotype Score: 0.253

Variant Score: 0.419

Phenotype matches:

Proximity score 0.505 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:245200 Krabbe disease - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.253

Variant Score: 0.419

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.87935255A>T [0/1] rs1023414917 (variation viewer)

Variant score: 0.419 CONTRIBUTING VARIANT

Transcripts:: GALC:ENST00000261304.7:c.1912-377T>A:p.(=); GALC:ENST00000393568.8:c.1843-377T>A:p.(=); GALC:ENST00000393569.6:c.1834-377T>A:p.(=); GALC:ENST00000544807.6:c.1744-1256T>A:p.(=)

Pathogenicity Data:: Best Score: 0.41936928; CADD: 0.419 (2.361)

Frequency Data:: TOPMed: 0.0032%

Other passed variants:

AMTN

Exomiser Score: 0.001

Phenotype Score: 0.510

Variant Score: 0.127

Phenotype matches:

Proximity score 0.510 in interactome to CLCN4 and phenotypic similarity 0.864 to Raynaud-Claes syndrome associated with CLCN4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617607 ?Amelogenesis imperfecta, type IIIB (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.510

Variant Score: 0.127

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.70521640CTTTTTTT>C [0/1] rs763143860 (variation viewer)

Variant score: 0.127 CONTRIBUTING VARIANT

Transcripts:: AMTN:ENST00000339336.9:c.55-1114_55-1108del:p.(=); AMTN:ENST00000504451.1:c.55-1117_55-1111del:p.(=)

Pathogenicity Data:: Best Score: 0.12702864; CADD: 0.127 (0.590)

Frequency Data:: No frequency data

Other passed variants:

SVIP

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.132

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.132

Variants contributing to score:

INTERGENIC_VARIANT chr11:g.22838645GATCT>G [-/1] rs60022030 (variation viewer)

Variant score: 0.132 CONTRIBUTING VARIANT

Transcripts:: SVIP:ENST00000354193.5::; SVIP:ENST00000532798.3::

Pathogenicity Data:: Best Score: 0.13223928; CADD: 0.132 (0.616)

Frequency Data:: No frequency data

Other passed variants:

SIN3B

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.115

Phenotype matches:

Proximity score 0.519 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.046

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.16862707G>A [0/1] rs767836465 (variation viewer)

Variant score: 0.046 CONTRIBUTING VARIANT

Transcripts:: SIN3B:ENST00000248054.9:c.1266+148G>A:p.(=); SIN3B:ENST00000379803.5:c.1266+148G>A:p.(=)

Pathogenicity Data:: Best Score: 0.046545446; CADD: 0.047 (0.207)

Frequency Data:: TOPMed: 0.0120%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0458%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.115

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.16835793A>G [0/1] rs139491489 (variation viewer)

Variant score: 0.138 CONTRIBUTING VARIANT

Transcripts:: SIN3B:ENST00000248054.9:c.381+4146A>G:p.(=); SIN3B:ENST00000379803.5:c.381+4146A>G:p.(=); SIN3B:ENST00000596802.5:c.381+4146A>G:p.(=)

Pathogenicity Data:: Best Score: 0.43284732; CADD: 0.433 (2.463)

Frequency Data:: 1000Genomes: 0.4992%; TOPMed: 1.0370%; UK10K: 1.7985%; gnomAD_G_AFR: 0.2064%; gnomAD_G_AMR: 0.5967%; gnomAD_G_ASJ: 0.9934%; gnomAD_G_FIN: 1.1448%; gnomAD_G_NFE: 1.6673%; gnomAD_G_OTH: 1.2220%

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.16830251C>A [0/1] rs143896944 (variation viewer)

Variant score: 0.092 CONTRIBUTING VARIANT

Transcripts:: SIN3B:ENST00000248054.9:c.227+354C>A:p.(=); SIN3B:ENST00000379803.5:c.227+354C>A:p.(=); SIN3B:ENST00000596802.5:c.227+354C>A:p.(=)

Pathogenicity Data:: Best Score: 0.6462471; CADD: 0.646 (4.513)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.6188%; UK10K: 0.0661%; gnomAD_G_AFR: 1.9936%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0400%; gnomAD_G_OTH: 0.3055%

Other passed variants:

ALDH3B2

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.126

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.126

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr11:g.67672042CAT>C [-/1] rs57997475 (variation viewer)

Variant score: 0.126 CONTRIBUTING VARIANT

Transcripts:: ALDH3B2:ENST00000349015.7:c.-245+2393_-245+2394del:p.(=); ALDH3B2:ENST00000530069.6:c.-244-4409_-244-4408del:p.(=); ALDH3B2:ENST00000673966.1:c.-245+2392_-245+2393del:p.(=)

Pathogenicity Data:: Best Score: 0.12562042; CADD: 0.126 (0.583)

Frequency Data:: No frequency data

Other passed variants:

PPIF

Exomiser Score: 0.001

Phenotype Score: 0.517

Variant Score: 0.110

Phenotype matches:

Proximity score 0.517 in interactome to SLC25A4 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with SLC25A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.517

Variant Score: 0.110

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr10:g.79358076CAAAAAAAAA>C [1/1] rs529376988 (variation viewer)

Variant score: 0.110 CONTRIBUTING VARIANT

Transcripts:: PPIF:ENST00000225174.8::; PPIF:ENST00000372336.4::

Pathogenicity Data:: Best Score: 0.10956955; CADD: 0.110 (0.504)

Frequency Data:: No frequency data

Other passed variants:

CHRNA5

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.106

Phenotype matches:

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.519

Variant Score: 0.106

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.78570424A>AT [0/1] rs71148540 (variation viewer)

Variant score: 0.106 CONTRIBUTING VARIANT

Transcripts:: CHRNA5:ENST00000299565.9:c.106+4599_106+4600insT:p.(=); CHRNA5:ENST00000559554.5:c.106+4599_106+4600insT:p.(=)

Pathogenicity Data:: Best Score: 0.106077254; CADD: 0.106 (0.487)

Frequency Data:: No frequency data

Other passed variants:

STN1

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.124

Phenotype matches:

Proximity score 0.503 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:617341 Cerebroretinal microangiopathy with calcifications and cysts 2 - autosomal recessive; ORPHA:2032 Idiopathic pulmonary fibrosis

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.076

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.103892393G>A [0/1] rs974684601 (variation viewer)

Variant score: 0.076 CONTRIBUTING VARIANT

Transcripts:: STN1:ENST00000224950.8:c.754-141C>T:p.(=); STN1:ENST00000369764.1:c.754-141C>T:p.(=)

Pathogenicity Data:: Best Score: 0.07594037; CADD: 0.076 (0.343)

Frequency Data:: TOPMed: 0.0056%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.124

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr10:g.103875859G>GTCTCTCTCTCTCTCTCTCTCTCTC [1|1] rs556502190 (variation viewer)

Variant score: 0.124 CONTRIBUTING VARIANT

Transcripts:: STN1:ENST00000224950.8::; STN1:ENST00000369774.8::

Pathogenicity Data:: Best Score: 0.1240083; CADD: 0.124 (0.575)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.103914367TATATATA>T [-/1] rs560044235 (variation viewer)

Variant score: 0.057

Transcripts:: STN1:ENST00000224950.8:c.133+3088_133+3094del:p.(=); STN1:ENST00000369764.1:c.133+3088_133+3094del:p.(=)

Pathogenicity Data:: Best Score: 0.060493052; CADD: 0.060 (0.271)

Frequency Data:: gnomAD_G_AFR: 0.3574%; gnomAD_G_EAS: 0.1764%; gnomAD_G_NFE: 0.2869%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.103909376A>ATGTATATATATGTATATATATATGTATATATGTATGTATATATATGTATATG [0|1] rs866423216 (variation viewer)

Variant score: 0.000

Transcripts:: STN1:ENST00000224950.8:c.229+1150_229+1151insCATATACATATATATACATACATATATACATATATATATACATATATATACA:p.(=); STN1:ENST00000369764.1:c.229+1150_229+1151insCATATACATATATATACATACATATATACATATATATATACATATATATACA:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: gnomAD_G_AFR: 0.0847%; gnomAD_G_AMR: 0.4348%; gnomAD_G_ASJ: 1.7442%; gnomAD_G_EAS: 0.1634%; gnomAD_G_FIN: 0.5155%; gnomAD_G_NFE: 1.8257%; gnomAD_G_OTH: 2.0000%

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.103914367TATATATA>* [-/1]

Variant score: 0.000

Transcripts:: STN1:ENST00000224950.8:c.133+3088_133+3095delTATATATAins:p.(=); STN1:ENST00000369764.1:c.133+3088_133+3095delTATATATAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

MARS1

Exomiser Score: 0.001

Phenotype Score: 0.515

Variant Score: 0.109

Phenotype matches:

Proximity score 0.515 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:615486 Interstitial lung and liver disease - autosomal recessive; OMIM:616280 Charcot-Marie-Tooth disease, axonal, type 2U - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.515

Variant Score: 0.109

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.57508699A>AGGTAGAGGTAGAGGGTAGAG [-/1] rs71280717 (variation viewer)

Variant score: 0.109 CONTRIBUTING VARIANT

Transcripts:: MARS1:ENST00000262027.10:c.1369-2999_1369-2998insGGTAGAGGTAGAGGGTAGAG:p.(=); MARS1:ENST00000628866.2:c.*870-2999_*870-2998insGGTAGAGGTAGAGGGTAGAG:p.(=)

Pathogenicity Data:: Best Score: 0.10915941; CADD: 0.109 (0.502)

Frequency Data:: No frequency data

Other passed variants:

NR0B1

Exomiser Score: 0.001

Phenotype Score: 0.511

Variant Score: 0.111

Phenotype matches:

Proximity score 0.511 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:300018 46XY sex reversal 2, dosage-sensitive - X-linked; OMIM:300200 Adrenal hypoplasia, congenital - X-linked recessive; ORPHA:242 46,XY complete gonadal dysgenesis; ORPHA:251510 46,XY partial gonadal dysgenesis; ORPHA:393 46,XX testicular disorder of sex development

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.511

Variant Score: 0.111

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr23:g.30312940C>T [1/1] rs145534945 (variation viewer)

Variant score: 0.111 CONTRIBUTING VARIANT

Transcripts:: NR0B1:ENST00000378970.5::; NR0B1:ENST00000378962.4::

Pathogenicity Data:: Best Score: 0.7519153; CADD: 0.752 (6.054)

Frequency Data:: 1000Genomes: 0.7152%; TOPMed: 1.2190%; UK10K: 1.9554%; gnomAD_G_AFR: 0.2911%; gnomAD_G_AMR: 0.3344%; gnomAD_G_ASJ: 1.0638%; gnomAD_G_FIN: 1.7401%; gnomAD_G_NFE: 1.9873%; gnomAD_G_OTH: 1.5299%

X_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.511

Variant Score: 0.083

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr23:g.30301001G>GGAGAGAGAGAGAGAGA [1/1] rs572432890 (variation viewer)

Variant score: 0.083 CONTRIBUTING VARIANT

Transcripts:: NR0B1:ENST00000378970.5::; NR0B1:ENST00000622094.1::

Pathogenicity Data:: Best Score: 0.082512856; CADD: 0.083 (0.374)

Frequency Data:: No frequency data

Other passed variants:

RAF1

Exomiser Score: 0.001

Phenotype Score: 0.508

Variant Score: 0.112

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:611553 Noonan syndrome 5 - autosomal dominant; OMIM:611554 LEOPARD syndrome 2 - autosomal dominant; OMIM:615916 Cardiomyopathy, dilated, 1NN - autosomal dominant; ORPHA:154 Familial isolated dilated cardiomyopathy; ORPHA:500 Noonan syndrome with multiple lentigines; ORPHA:648 Noonan syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.508

Variant Score: 0.112

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.12605250A>ATGTGTGTGTGTGTGTG [0/1] rs139616156 (variation viewer)

Variant score: 0.112 CONTRIBUTING VARIANT

Transcripts:: RAF1:ENST00000251849.8:c.680+950_680+951insCACACACACACACACA:p.(=); RAF1:ENST00000442415.7:c.680+950_680+951insCACACACACACACACA:p.(=)

Pathogenicity Data:: Best Score: 0.11182201; CADD: 0.112 (0.515)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.254

Variant Score: 0.343

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.12598111T>C [0/1] rs138074044 (variation viewer)

Variant score: 0.518 CONTRIBUTING VARIANT

Transcripts:: RAF1:ENST00000251849.8:c.1108+1580A>G:p.(=); RAF1:ENST00000442415.7:c.1168+1580A>G:p.(=)

Pathogenicity Data:: Best Score: 0.74834824; CADD: 0.748 (5.992)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.8187%; UK10K: 1.1769%; gnomAD_G_AFR: 0.2314%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.2884%; gnomAD_G_NFE: 1.1858%; gnomAD_G_OTH: 0.8247%

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.12651341T>C [0/1] rs538663572 (variation viewer)

Variant score: 0.168 CONTRIBUTING VARIANT

Transcripts:: RAF1:ENST00000251849.8:c.-27+12472A>G:p.(=); RAF1:ENST00000442415.7:c.-27+12472A>G:p.(=)

Pathogenicity Data:: Best Score: 0.17167646; CADD: 0.172 (0.818)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0852%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0229%; gnomAD_G_AMR: 0.1199%; gnomAD_G_FIN: 0.0287%; gnomAD_G_NFE: 0.1600%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.12598725CA>C [1/1] rs59472802 (variation viewer)

Variant score: 0.043

Transcripts:: RAF1:ENST00000251849.8:c.1108+965del:p.(=); RAF1:ENST00000442415.7:c.1168+965del:p.(=)

Pathogenicity Data:: Best Score: 0.043246627; CADD: 0.043 (0.192)

Frequency Data:: No frequency data

KLRB1

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.113

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.9606757TATA>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: KLRB1:ENST00000229402.4:c.85+995_85+998delTATAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.113

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.9607355C>CTTCCTTTCTTTCTTTCTTT [1/1] rs1555097796 (variation viewer)

Variant score: 0.113 CONTRIBUTING VARIANT

Transcripts:: KLRB1:ENST00000229402.4:c.85+399_85+400insAAAGAAAGAAAGAAAGGAA:p.(=)

Pathogenicity Data:: Best Score: 0.112639666; CADD: 0.113 (0.519)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.9606760A>* [-/1]

Variant score: 0.000

Transcripts:: KLRB1:ENST00000229402.4:c.85+995T>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

ENAM

Exomiser Score: 0.001

Phenotype Score: 0.513

Variant Score: 0.101

Phenotype matches:

Proximity score 0.513 in interactome to CLCN4 and phenotypic similarity 0.864 to Raynaud-Claes syndrome associated with CLCN4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:104500 Amelogenesis imperfecta, type IB - autosomal dominant; OMIM:204650 Amelogenesis imperfecta, type IC - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.513

Variant Score: 0.101

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.70652803G>GA [0/1] rs567048349 (variation viewer)

Variant score: 0.101 CONTRIBUTING VARIANT

Transcripts:: ENAM:ENST00000396073.3::

Pathogenicity Data:: Best Score: 0.10050243; CADD: 0.101 (0.460)

Frequency Data:: No frequency data

Other passed variants:

NDUFB3

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.110

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:618246 Mitochondrial complex I deficiency, nuclear type 25 - autosomal recessive; ORPHA:2609 Isolated complex I deficiency

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.110

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.201098899G>C [0/1] rs35560638 (variation viewer)

Variant score: 0.153 CONTRIBUTING VARIANT

Transcripts:: NDUFB3:ENST00000454214.1::

Pathogenicity Data:: Best Score: 0.38919866; CADD: 0.389 (2.141)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.2196%; UK10K: 1.3621%; gnomAD_G_AFR: 0.2683%; gnomAD_G_AMR: 0.2457%; gnomAD_G_ASJ: 0.6711%; gnomAD_G_FIN: 1.7029%; gnomAD_G_NFE: 1.5740%; gnomAD_G_OTH: 1.6598%

FIVE_PRIME_UTR_INTRON_VARIANT chr2:g.201076869G>A [0/1] rs148157524 (variation viewer)

Variant score: 0.068 CONTRIBUTING VARIANT

Transcripts:: NDUFB3:ENST00000237889.9:c.-2-2012G>A:p.(=); NDUFB3:ENST00000433898.5:c.-2-2012G>A:p.(=); NDUFB3:ENST00000454214.1:c.-2-2012G>A:p.(=)

Pathogenicity Data:: Best Score: 0.3044954; CADD: 0.304 (1.577)

Frequency Data:: 1000Genomes: 0.8786%; TOPMed: 1.1250%; UK10K: 1.4546%; gnomAD_G_AFR: 0.3436%; gnomAD_G_AMR: 1.9093%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.4582%; gnomAD_G_NFE: 1.5323%; gnomAD_G_OTH: 0.9165%

Other passed variants:

ASPSCR1

Exomiser Score: 0.001

Phenotype Score: 0.252

Variant Score: 0.395

Phenotype matches:

Phenotypic similarity 0.454 to mouse mutant involving ASPSCR1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0020420, abnormal freezing behavior

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:606243 Alveolar soft-part sarcoma - somatic

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.252

Variant Score: 0.395

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.82015849C>T [0/1] rs541097378 (variation viewer)

Variant score: 0.557 CONTRIBUTING VARIANT

Transcripts:: ASPSCR1:ENST00000306729.11:c.1635+493C>T:p.(=); ASPSCR1:ENST00000306739.9:c.1354-627C>T:p.(=); ASPSCR1:ENST00000580534.5:c.1198-627C>T:p.(=)

Pathogenicity Data:: Best Score: 0.637757; CADD: 0.638 (4.410)

Frequency Data:: 1000Genomes: 0.0399%; TOPMed: 0.0661%; gnomAD_G_AFR: 0.0229%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_NFE: 0.0467%

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.81992602G>A [0/1] rs374772892 (variation viewer)

Variant score: 0.233 CONTRIBUTING VARIANT

Transcripts:: ASPSCR1:ENST00000306729.11:c.375-2219G>A:p.(=); ASPSCR1:ENST00000306739.9:c.375-2219G>A:p.(=); ASPSCR1:ENST00000580534.5:c.144-2219G>A:p.(=); ASPSCR1:ENST00000581647.5:c.375-2219G>A:p.(=)

Pathogenicity Data:: Best Score: 0.5457447; CADD: 0.546 (3.427)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.1027%; UK10K: 0.0529%; gnomAD_G_AFR: 0.0917%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_EAS: 0.3699%; gnomAD_G_NFE: 0.0467%

Other passed variants:

YARS1

Exomiser Score: 0.001

Phenotype Score: 0.516

Variant Score: 0.094

Phenotype matches:

Proximity score 0.516 in interactome to POLG2 and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with POLG2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:608323 Charcot-Marie-Tooth disease, dominant intermediate C - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.516

Variant Score: 0.094

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32806004C>T [0/1] rs540721340 (variation viewer)

Variant score: 0.094 CONTRIBUTING VARIANT

Transcripts:: YARS1:ENST00000373477.8:c.510+478G>A:p.(=); YARS1:ENST00000616261.1:c.510+478G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09468442; CADD: 0.095 (0.432)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0032%; UK10K: 0.0132%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.258

Variant Score: 0.206

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32796684C>T [0/1] rs180919482 (variation viewer)

Variant score: 0.318 CONTRIBUTING VARIANT

Transcripts:: YARS1:ENST00000373477.8:c.591+1079G>A:p.(=); YARS1:ENST00000616261.1:c.591+1079G>A:p.(=)

Pathogenicity Data:: Best Score: 0.35775608; CADD: 0.358 (1.923)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.2596%; UK10K: 0.3306%; gnomAD_G_AFR: 0.0345%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.0581%; gnomAD_G_NFE: 0.2162%; gnomAD_G_OTH: 0.1029%

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32806004C>T [0/1] rs540721340 (variation viewer)

Variant score: 0.094 CONTRIBUTING VARIANT

Transcripts:: YARS1:ENST00000373477.8:c.510+478G>A:p.(=); YARS1:ENST00000616261.1:c.510+478G>A:p.(=)

Pathogenicity Data:: Best Score: 0.09468442; CADD: 0.095 (0.432)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0032%; UK10K: 0.0132%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr1:g.32792897A>AAAAT [1/1] rs1050520656 (variation viewer)

Variant score: 0.143

Transcripts:: YARS1:ENST00000373477.8:c.592-1644_592-1643insATTT:p.(=); YARS1:ENST00000616261.1:c.592-1644_592-1643insATTT:p.(=)

Pathogenicity Data:: Best Score: 0.14846992; CADD: 0.148 (0.698)

Frequency Data:: gnomAD_G_AMR: 0.2500%; gnomAD_G_NFE: 0.0202%

SYVN1

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.103

Phenotype matches:

Proximity score 0.506 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.506

Variant Score: 0.103

Variants contributing to score:

REGULATORY_REGION_VARIANT chr11:g.65149269GTTTTTTTTTTTTTTTTTTT>G [0/1] rs752895594 (variation viewer)

Variant score: 0.103 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.10339737; CADD: 0.103 (0.474)

Frequency Data:: No frequency data

Other passed variants:

CLRN1

Exomiser Score: 0.001

Phenotype Score: 0.511

Variant Score: 0.090

Phenotype matches:

Phenotypic similarity 0.471 to Usher syndrome type 3 associated with CLRN1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.511 in interactome to CDH23 and phenotypic similarity 0.864 to Cushing disease associated with CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.511 in interactome to CDH23 and phenotypic similarity 0.514 to mouse mutant of CDH23.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0005357, novel environmental response-related retropulsion

Known diseases:: OMIM:276902 Usher syndrome, type 3A - autosomal recessive; OMIM:614180 Retinitis pigmentosa 61 - autosomal recessive; ORPHA:231183 Usher syndrome type 3; ORPHA:791 Retinitis pigmentosa

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.256

Variant Score: 0.120

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.150946704CT>C [0/1] rs34471891 (variation viewer)

Variant score: 0.120 CONTRIBUTING VARIANT

Transcripts:: CLRN1:ENST00000327047.5:c.254-4944del:p.(=); CLRN1:ENST00000328863.8:c.254-4944del:p.(=)

Pathogenicity Data:: Best Score: 0.11955953; CADD: 0.120 (0.553)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.511

Variant Score: 0.090

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.150946704CT>C [0/1] rs34471891 (variation viewer)

Variant score: 0.120 CONTRIBUTING VARIANT

Transcripts:: CLRN1:ENST00000327047.5:c.254-4944del:p.(=); CLRN1:ENST00000328863.8:c.254-4944del:p.(=)

Pathogenicity Data:: Best Score: 0.11955953; CADD: 0.120 (0.553)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.150934837G>A [0/1]

Variant score: 0.060 CONTRIBUTING VARIANT

Transcripts:: CLRN1:ENST00000295911.6:c.206-6636C>T:p.(=); CLRN1:ENST00000327047.5:c.434-6636C>T:p.(=); CLRN1:ENST00000328863.8:c.472+5644C>T:p.(=); CLRN1:ENST00000569170.5:c.162+6745C>T:p.(=)

Pathogenicity Data:: Best Score: 0.05984384; CADD: 0.060 (0.268)

Frequency Data:: No frequency data

Other passed variants:

ENTPD8

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.097

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.039

Variants contributing to score:

INTERGENIC_VARIANT chr9:g.137447006C>T [0/1] rs556153601 (variation viewer)

Variant score: 0.039 CONTRIBUTING VARIANT

Transcripts:: ENTPD8:ENST00000371506.6::

Pathogenicity Data:: Best Score: 0.039494157; CADD: 0.039 (0.175)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0231%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0333%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.097

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr9:g.137445726A>C [0/1] rs148879432 (variation viewer)

Variant score: 0.154 CONTRIBUTING VARIANT

Transcripts:: ENTPD8:ENST00000371506.6::; ENTPD8:ENST00000371473.7::

Pathogenicity Data:: Best Score: 0.36041242; CADD: 0.360 (1.941)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.8545%; UK10K: 0.8463%; gnomAD_G_AFR: 0.1950%; gnomAD_G_AMR: 1.0766%; gnomAD_G_ASJ: 1.6556%; gnomAD_G_FIN: 0.4296%; gnomAD_G_NFE: 1.2563%; gnomAD_G_OTH: 0.7143%

INTERGENIC_VARIANT chr9:g.137447006C>T [0/1] rs556153601 (variation viewer)

Variant score: 0.039 CONTRIBUTING VARIANT

Transcripts:: ENTPD8:ENST00000371506.6::

Pathogenicity Data:: Best Score: 0.039494157; CADD: 0.039 (0.175)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0231%; UK10K: 0.0397%; gnomAD_G_NFE: 0.0333%

Other passed variants:

NPTX2

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.097

Phenotype matches:

Proximity score 0.503 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.503

Variant Score: 0.000

Variants contributing to score:

INTERGENIC_VARIANT chr7:g.98599025TAAA>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NPTX2:ENST00000265634.4::; NPTX2:ENST00000441836.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.503

Variant Score: 0.097

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr7:g.98632848G>T [0/1] rs73145404 (variation viewer)

Variant score: 0.194 CONTRIBUTING VARIANT

Transcripts:: NPTX2:ENST00000265634.4::; NPTX2:ENST00000416379.6::

Pathogenicity Data:: Best Score: 0.95812064; CADD: 0.958 (13.780)

Frequency Data:: 1000Genomes: 0.3994%; TOPMed: 1.0480%; UK10K: 1.9307%; gnomAD_G_AFR: 0.4465%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.7159%; gnomAD_G_NFE: 1.8849%; gnomAD_G_OTH: 0.8147%

INTERGENIC_VARIANT chr7:g.98599025TAAA>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NPTX2:ENST00000265634.4::; NPTX2:ENST00000441836.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr7:g.98599025TAAA>T [-/1]

Variant score: 0.000

Transcripts:: NPTX2:ENST00000265634.4::; NPTX2:ENST00000441836.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr7:g.98599029TA>T [0|1]

Variant score: 0.000

Transcripts:: NPTX2:ENST00000265634.4::; NPTX2:ENST00000441836.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

F12

Exomiser Score: 0.001

Phenotype Score: 0.508

Variant Score: 0.087

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:234000 Factor XII deficiency - autosomal recessive; OMIM:610618 Angioedema, hereditary, type III - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.508

Variant Score: 0.087

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr5:g.177411658C>T [0/1] rs918715049 (variation viewer)

Variant score: 0.087 CONTRIBUTING VARIANT

Transcripts:: F12:ENST00000253496.3::; F12:ENST00000355472.10::

Pathogenicity Data:: Best Score: 0.087148786; CADD: 0.087 (0.396)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_NFE: 0.0074%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.508

Variant Score: 0.071

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr5:g.177411658C>T [0/1] rs918715049 (variation viewer)

Variant score: 0.087 CONTRIBUTING VARIANT

Transcripts:: F12:ENST00000253496.3::; F12:ENST00000355472.10::

Pathogenicity Data:: Best Score: 0.087148786; CADD: 0.087 (0.396)

Frequency Data:: TOPMed: 0.0064%; gnomAD_G_NFE: 0.0074%

INTERGENIC_VARIANT chr5:g.177416717C>T [0/1] rs72815108 (variation viewer)

Variant score: 0.055 CONTRIBUTING VARIANT

Transcripts:: F12:ENST00000253496.3::; F12:ENST00000355472.10::

Pathogenicity Data:: Best Score: 0.055504262; CADD: 0.056 (0.248)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0454%; UK10K: 0.1058%; gnomAD_G_AFR: 0.0115%; gnomAD_G_EAS: 0.0617%; gnomAD_G_NFE: 0.0400%

Other passed variants:

B2M

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.089

Phenotype matches:

Proximity score 0.504 in interactome to SEC24C and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with SEC24C.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:105200 ?Amyloidosis, familial visceral (unconfirmed); OMIM:241600 Immunodeficiency 43 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.089

Variants contributing to score:

INTERGENIC_VARIANT chr15:g.44725255C>CTATCTATCTATCTATCTATTTATCTATG [-/1] rs71111880 (variation viewer)

Variant score: 0.089 CONTRIBUTING VARIANT

Transcripts:: B2M:ENST00000648006.2::

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.083

Variants contributing to score:

INTERGENIC_VARIANT chr15:g.44725255C>CTATCTATCTATCTATCTATTTATCTATG [-/1] rs71111880 (variation viewer)

Variant score: 0.089 CONTRIBUTING VARIANT

Transcripts:: B2M:ENST00000648006.2::

Pathogenicity Data:: Best Score: 0.08945799; CADD: 0.089 (0.407)

Frequency Data:: No frequency data

INTERGENIC_VARIANT chr15:g.44725255C>CTATCTATCTATCTATCTATCTATCTATTTATCTATG [-/1] rs71111880 (variation viewer)

Variant score: 0.076 CONTRIBUTING VARIANT

Transcripts:: B2M:ENST00000648006.2::

Pathogenicity Data:: Best Score: 0.0761531; CADD: 0.076 (0.344)

Frequency Data:: No frequency data

Other passed variants:

SGMS2

Exomiser Score: 0.001

Phenotype Score: 0.501

Variant Score: 0.088

Phenotype matches:

Proximity score 0.501 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:126550 Calvarial doughnut lesions with bone fragility with or without spondylometaphyseal dysplasia - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.501

Variant Score: 0.088

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.107877913CT>C [0/1] rs774442653 (variation viewer)

Variant score: 0.088 CONTRIBUTING VARIANT

Transcripts:: SGMS2:ENST00000394684.8:c.-244-17396del:p.(=)

Pathogenicity Data:: Best Score: 0.088409066; CADD: 0.088 (0.402)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.100

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.107818543C>T [0/1] rs144671970 (variation viewer)

Variant score: 0.111 CONTRIBUTING VARIANT

Transcripts:: SGMS2:ENST00000394684.8::

Pathogenicity Data:: Best Score: 0.12420994; CADD: 0.124 (0.576)

Frequency Data:: 1000Genomes: 0.3395%; TOPMed: 0.3799%; UK10K: 0.5819%; gnomAD_G_AFR: 0.1603%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_FIN: 0.0859%; gnomAD_G_NFE: 0.4197%

FIVE_PRIME_UTR_INTRON_VARIANT chr4:g.107877913CT>C [0/1] rs774442653 (variation viewer)

Variant score: 0.088 CONTRIBUTING VARIANT

Transcripts:: SGMS2:ENST00000394684.8:c.-244-17396del:p.(=)

Pathogenicity Data:: Best Score: 0.088409066; CADD: 0.088 (0.402)

Frequency Data:: No frequency data

Other passed variants:

STAMBP

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.082

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:614261 Microcephaly-capillary malformation syndrome - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.164

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.73835682C>T [0/1] rs907906319 (variation viewer)

Variant score: 0.164 CONTRIBUTING VARIANT

Transcripts:: STAMBP:ENST00000339566.7:c.203+4623C>T:p.(=); STAMBP:ENST00000394070.7:c.203+4623C>T:p.(=); STAMBP:ENST00000394073.5:c.203+4623C>T:p.(=); STAMBP:ENST00000409707.5:c.203+4623C>T:p.(=); STAMBP:ENST00000536064.1:c.203+4623C>T:p.(=)

Pathogenicity Data:: Best Score: 0.16478169; CADD: 0.165 (0.782)

Frequency Data:: TOPMed: 0.0183%; gnomAD_G_NFE: 0.0267%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.082

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.73835682C>T [0/1] rs907906319 (variation viewer)

Variant score: 0.164 CONTRIBUTING VARIANT

Transcripts:: STAMBP:ENST00000339566.7:c.203+4623C>T:p.(=); STAMBP:ENST00000394070.7:c.203+4623C>T:p.(=); STAMBP:ENST00000394073.5:c.203+4623C>T:p.(=); STAMBP:ENST00000409707.5:c.203+4623C>T:p.(=); STAMBP:ENST00000536064.1:c.203+4623C>T:p.(=)

Pathogenicity Data:: Best Score: 0.16478169; CADD: 0.165 (0.782)

Frequency Data:: TOPMed: 0.0183%; gnomAD_G_NFE: 0.0267%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.73834237AT>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: STAMBP:ENST00000339566.7:c.203+3178_203+3179delATins*:p.(=); STAMBP:ENST00000394070.7:c.203+3178_203+3179delATins*:p.(=); STAMBP:ENST00000394073.5:c.203+3178_203+3179delATins*:p.(=); STAMBP:ENST00000409707.5:c.203+3178_203+3179delATins*:p.(=); STAMBP:ENST00000536064.1:c.203+3178_203+3179delATins*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

SEL1L

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.083

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.083

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr14:g.81510514C>CTCTCTATATATA [0/1] rs35474067 (variation viewer)

Variant score: 0.083 CONTRIBUTING VARIANT

Transcripts:: SEL1L:ENST00000336735.9:c.341-4274_341-4273insTATATATAGAGA:p.(=); SEL1L:ENST00000555824.5:c.341-4274_341-4273insTATATATAGAGA:p.(=)

Pathogenicity Data:: Best Score: 0.082724094; CADD: 0.083 (0.375)

Frequency Data:: No frequency data

Other passed variants:

SUV39H1

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.081

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

X_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.081

Variants contributing to score:

INTERGENIC_VARIANT chr23:g.48714266A>AGCTAGATGGACG [1/1] rs112232518 (variation viewer)

Variant score: 0.081 CONTRIBUTING VARIANT

Transcripts:: SUV39H1:ENST00000376687.3::; SUV39H1:ENST00000303227.11::

Pathogenicity Data:: Best Score: 0.081455946; CADD: 0.081 (0.369)

Frequency Data:: No frequency data

X_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.081

Variants contributing to score:

INTERGENIC_VARIANT chr23:g.48714266A>AGCTAGATGGACG [1/1] rs112232518 (variation viewer)

Variant score: 0.081 CONTRIBUTING VARIANT

Transcripts:: SUV39H1:ENST00000376687.3::; SUV39H1:ENST00000303227.11::

Pathogenicity Data:: Best Score: 0.081455946; CADD: 0.081 (0.369)

Frequency Data:: No frequency data

Other passed variants:

SMO

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.080

Phenotype matches:

Phenotypic similarity 0.479 to Meningioma associated with SMO.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:241800 Pallister-Hall-like syndrome - autosomal recessive; OMIM:601707 Curry-Jones syndrome, somatic mosaic - somatic; OMIM:605462 Basal cell carcinoma, somatic - unknown; ORPHA:1553 Curry-Jones syndrome; ORPHA:2495 Meningioma

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.000

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr7:g.129214702T>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: SMO:ENST00000249373.8::; SMO:ENST00000325006.7::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.080

Variants contributing to score:

INTERGENIC_VARIANT chr7:g.129174367C>CA [1/1] rs34036553 (variation viewer)

Variant score: 0.080 CONTRIBUTING VARIANT

Transcripts:: SMO:ENST00000249373.8::

Pathogenicity Data:: Best Score: 0.08018601; CADD: 0.080 (0.363)

Frequency Data:: No frequency data

Other passed variants:

INTERGENIC_VARIANT chr7:g.129177847C>T [0/1] rs185107657 (variation viewer)

Variant score: 0.047

Transcripts:: SMO:ENST00000249373.8::; SMO:ENST00000486685.3::

Pathogenicity Data:: Best Score: 0.057676554; CADD: 0.058 (0.258)

Frequency Data:: 1000Genomes: 0.1597%; TOPMed: 0.4046%; UK10K: 0.8728%; gnomAD_G_AFR: 0.2644%; gnomAD_G_NFE: 0.5489%; gnomAD_G_OTH: 0.1027%

INTERGENIC_VARIANT chr7:g.129175719GA>G [0/1] rs56239457 (variation viewer)

Variant score: 0.040

Transcripts:: SMO:ENST00000249373.8::; SMO:ENST00000486685.3::

Pathogenicity Data:: Best Score: 0.17681015; CADD: 0.177 (0.845)

Frequency Data:: gnomAD_G_AFR: 1.6936%; gnomAD_G_AMR: 0.9563%; gnomAD_G_EAS: 0.2558%; gnomAD_G_FIN: 1.0714%; gnomAD_G_NFE: 1.9031%; gnomAD_G_OTH: 1.5625%

ATCAY

Exomiser Score: 0.001

Phenotype Score: 0.501

Variant Score: 0.083

Phenotype matches:

Proximity score 0.501 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:601238 Ataxia, cerebellar, Cayman type - autosomal recessive; ORPHA:94122 Cerebellar ataxia, Cayman type

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.501

Variant Score: 0.083

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr19:g.3927284G>A [0/1] rs117794052 (variation viewer)

ClinVar: LIKELY_BENIGN (criteria_provided,_single_submitter)

Variant score: 0.152 CONTRIBUTING VARIANT

Transcripts:: ATCAY:ENST00000450849.7:c.*2692G>A:p.(=)

Pathogenicity Data:: Best Score: 0.2772302; CADD: 0.277 (1.410)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.8983%; UK10K: 1.2960%; gnomAD_G_AFR: 0.1489%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 0.7441%; gnomAD_G_NFE: 1.4671%; gnomAD_G_OTH: 0.8147%

INTERGENIC_VARIANT chr19:g.3872835C>T [0/1] rs181389175 (variation viewer)

Variant score: 0.013 CONTRIBUTING VARIANT

Transcripts:: ATCAY:ENST00000450849.7::

Pathogenicity Data:: Best Score: 0.018252075; CADD: 0.018 (0.080)

Frequency Data:: 1000Genomes: 0.3794%; TOPMed: 0.7064%; gnomAD_G_AFR: 0.1493%; gnomAD_G_AMR: 0.3580%; gnomAD_G_ASJ: 0.6667%; gnomAD_G_FIN: 0.1433%; gnomAD_G_NFE: 1.0976%; gnomAD_G_OTH: 0.3067%

Other passed variants:

COX6A2

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.077

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.077

Variants contributing to score:

REGULATORY_REGION_VARIANT chr16:g.31353277G>A [0/1] rs1044541962 (variation viewer)

Variant score: 0.077 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.07742858; CADD: 0.077 (0.350)

Frequency Data:: gnomAD_G_AFR: 0.0115%; gnomAD_G_EAS: 0.0619%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CMPK2

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.069

Phenotype matches:

Phenotypic similarity 0.428 to mouse mutant involving CMPK2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001363, increased anxiety-related response

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.004

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.6849625G>A [0/1] rs987755445 (variation viewer)

Variant score: 0.004 CONTRIBUTING VARIANT

Transcripts:: CMPK2:ENST00000458098.5:c.993-8947C>T:p.(=); CMPK2:ENST00000256722.9:c.*225C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0036773682; CADD: 0.004 (0.016)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.069

Variants contributing to score:

REGULATORY_REGION_VARIANT chr2:g.8572803G>T [0/1] rs115148688 (variation viewer)

Variant score: 0.134 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.9045007; CADD: 0.905 (10.200)

Frequency Data:: 1000Genomes: 0.4593%; TOPMed: 0.7438%; UK10K: 1.1240%; gnomAD_G_AFR: 0.1719%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 1.9868%; gnomAD_G_FIN: 0.2862%; gnomAD_G_NFE: 0.7537%; gnomAD_G_OTH: 0.7157%

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.6849625G>A [0/1] rs987755445 (variation viewer)

Variant score: 0.004 CONTRIBUTING VARIANT

Transcripts:: CMPK2:ENST00000458098.5:c.993-8947C>T:p.(=); CMPK2:ENST00000256722.9:c.*225C>T:p.(=)

Pathogenicity Data:: Best Score: 0.0036773682; CADD: 0.004 (0.016)

Frequency Data:: No frequency data

Other passed variants:

REGULATORY_REGION_VARIANT chr2:g.8627059TGTGAGAGAGGGA>* [-/1]

Variant score: 0.000

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

HRC

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.064

Phenotype matches:

Proximity score 0.507 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.507

Variant Score: 0.064

Variants contributing to score:

REGULATORY_REGION_VARIANT chr19:g.49329622CT>C [0/1] rs71180620 (variation viewer)

Variant score: 0.064 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.063516796; CADD: 0.064 (0.285)

Frequency Data:: No frequency data

Other passed variants:

USP28

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.063

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.063

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr11:g.113798066G>GT [-/1] rs528048657 (variation viewer)

Variant score: 0.063 CONTRIBUTING VARIANT

Transcripts:: USP28:ENST00000003302.8:c.*1173dup:p.(=)

Pathogenicity Data:: Best Score: 0.06286967; CADD: 0.063 (0.282)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.061

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr11:g.113798066G>GT [-/1] rs528048657 (variation viewer)

Variant score: 0.063 CONTRIBUTING VARIANT

Transcripts:: USP28:ENST00000003302.8:c.*1173dup:p.(=)

Pathogenicity Data:: Best Score: 0.06286967; CADD: 0.063 (0.282)

Frequency Data:: No frequency data

THREE_PRIME_UTR_EXON_VARIANT chr11:g.113798066G>GTTT [-/1] rs528048657 (variation viewer)

Variant score: 0.060 CONTRIBUTING VARIANT

Transcripts:: USP28:ENST00000003302.8:c.*1171_*1173dup:p.(=)

Pathogenicity Data:: Best Score: 0.05984384; CADD: 0.060 (0.268)

Frequency Data:: No frequency data

Other passed variants:

OTUD4

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.065

Phenotype matches:

Proximity score 0.502 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.502

Variant Score: 0.065

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr4:g.145131511GGTT>G [0/1] rs542838169 (variation viewer)

Variant score: 0.069 CONTRIBUTING VARIANT

Transcripts:: OTUD4:ENST00000454497.6::

Pathogenicity Data:: Best Score: 0.07572758; CADD: 0.076 (0.342)

Frequency Data:: 1000Genomes: 0.1198%; TOPMed: 0.3201%; UK10K: 0.5025%; gnomAD_G_AFR: 0.1146%; gnomAD_G_AMR: 0.2387%; gnomAD_G_FIN: 0.2003%; gnomAD_G_NFE: 0.2533%; gnomAD_G_OTH: 0.5102%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.145158255G>A [0/1] rs190460838 (variation viewer)

Variant score: 0.061 CONTRIBUTING VARIANT

Transcripts:: OTUD4:ENST00000447906.8:c.629+1248C>T:p.(=); OTUD4:ENST00000454497.6:c.434+1248C>T:p.(=)

Pathogenicity Data:: Best Score: 0.1496455; CADD: 0.150 (0.704)

Frequency Data:: 1000Genomes: 0.6989%; TOPMed: 1.1080%; UK10K: 1.6794%; gnomAD_G_AFR: 0.3098%; gnomAD_G_AMR: 1.3158%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.6351%; gnomAD_G_NFE: 1.2358%; gnomAD_G_OTH: 1.5400%

Other passed variants:

NSFL1C

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.050

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.000

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr20:g.1437190CCTCT>C [0/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NSFL1C:ENST00000353088.6::; NSFL1C:ENST00000618612.4::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.050

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr20:g.1456277G>A [0/1] rs117825776 (variation viewer)

Variant score: 0.101 CONTRIBUTING VARIANT

Transcripts:: NSFL1C:ENST00000216879.8:c.279-1145C>T:p.(=); NSFL1C:ENST00000353088.6:c.279-1145C>T:p.(=); NSFL1C:ENST00000476071.5:c.279-558C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14611381; CADD: 0.146 (0.686)

Frequency Data:: 1000Genomes: 0.2995%; TOPMed: 0.7056%; UK10K: 1.1637%; gnomAD_G_AFR: 0.2978%; gnomAD_G_AMR: 0.7160%; gnomAD_G_FIN: 0.3148%; gnomAD_G_NFE: 1.1922%; gnomAD_G_OTH: 0.3055%

DOWNSTREAM_GENE_VARIANT chr20:g.1437190CCTCT>C [0/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NSFL1C:ENST00000353088.6::; NSFL1C:ENST00000618612.4::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

NDUFB7

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.049

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.504

Variant Score: 0.049

Variants contributing to score:

INTERGENIC_VARIANT chr19:g.14579953CT>C [1/1] rs68028720 (variation viewer)

Variant score: 0.049 CONTRIBUTING VARIANT

Transcripts:: NDUFB7:ENST00000215565.3::

Pathogenicity Data:: Best Score: 0.049395204; CADD: 0.049 (0.220)

Frequency Data:: No frequency data

Other passed variants:

UGT2B7

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.049

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.001

Phenotype Score: 0.505

Variant Score: 0.049

Variants contributing to score:

INTERGENIC_VARIANT chr4:g.69123848CAA>C [1/1] rs61317832 (variation viewer)

Variant score: 0.049 CONTRIBUTING VARIANT

Transcripts:: UGT2B7:ENST00000305231.12::

Pathogenicity Data:: Best Score: 0.048519254; CADD: 0.049 (0.216)

Frequency Data:: No frequency data

Other passed variants:

GGT1

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.049

Phenotype matches:

Proximity score 0.501 in interactome to TWNK and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with TWNK.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:231950 ?Glutathioninuria (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.501

Variant Score: 0.049

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.24601323T>C [0|1] rs79959377 (variation viewer)

Variant score: 0.063 CONTRIBUTING VARIANT

Transcripts:: GGT1:ENST00000248923.9:c.-428-6631T>C:p.(=)

Pathogenicity Data:: Best Score: 0.16343439; CADD: 0.163 (0.775)

Frequency Data:: gnomAD_G_AFR: 0.4276%; gnomAD_G_AMR: 1.0989%; gnomAD_G_ASJ: 0.8130%; gnomAD_G_EAS: 1.7137%; gnomAD_G_FIN: 1.0879%; gnomAD_G_NFE: 0.6306%; gnomAD_G_OTH: 0.6983%

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.24601328C>A [0|1] rs74888287 (variation viewer)

Variant score: 0.034 CONTRIBUTING VARIANT

Transcripts:: GGT1:ENST00000248923.9:c.-428-6626C>A:p.(=)

Pathogenicity Data:: Best Score: 0.053326964; CADD: 0.053 (0.238)

Frequency Data:: gnomAD_G_AFR: 0.3513%; gnomAD_G_AMR: 0.8961%; gnomAD_G_ASJ: 0.3968%; gnomAD_G_EAS: 1.2846%; gnomAD_G_FIN: 1.0305%; gnomAD_G_NFE: 0.5075%; gnomAD_G_OTH: 0.4087%

Other passed variants:

FIVE_PRIME_UTR_INTRON_VARIANT chr22:g.24601333T>C [0|1] rs78467758 (variation viewer)

Variant score: 0.013

Transcripts:: GGT1:ENST00000248923.9:c.-428-6621T>C:p.(=)

Pathogenicity Data:: Best Score: 0.015535653; CADD: 0.016 (0.068)

Frequency Data:: gnomAD_G_AFR: 0.3812%; gnomAD_G_AMR: 0.5300%; gnomAD_G_ASJ: 0.4065%; gnomAD_G_EAS: 0.7937%; gnomAD_G_FIN: 0.7494%; gnomAD_G_NFE: 0.4567%; gnomAD_G_OTH: 0.2833%

VPS4A

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.039

Phenotype matches:

Proximity score 0.505 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.039

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr16:g.69324485C>T [0/1] rs865828638 (variation viewer)

Variant score: 0.039 CONTRIBUTING VARIANT

Transcripts:: VPS4A:ENST00000254950.13:c.*176C>T:p.(=)

Pathogenicity Data:: Best Score: 0.03905177; CADD: 0.039 (0.173)

Frequency Data:: TOPMed: 0.0088%

Other passed variants:

SOS1

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.321

Phenotype matches:

Proximity score 0.504 in interactome to SMPD1 and phenotypic similarity 0.913 to Niemann-Pick disease type B associated with SMPD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:135300 ?Fibromatosis, gingival, 1 (unconfirmed); OMIM:610733 Noonan syndrome 4 - autosomal dominant; ORPHA:2024 Hereditary gingival fibromatosis; ORPHA:648 Noonan syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.321

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.39079511T>TTTG [1/1] rs201987472 (variation viewer)

Variant score: 0.321 CONTRIBUTING VARIANT

Transcripts:: SOS1:ENST00000395038.6:c.88-11759_88-11758insCAA:p.(=); SOS1:ENST00000402219.7:c.88-11759_88-11758insCAA:p.(=)

Pathogenicity Data:: Best Score: 0.32142168; CADD: 0.321 (1.684)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.39102530C>CA [1/1] rs70954782 (variation viewer)

Variant score: 0.263

Transcripts:: SOS1:ENST00000395038.6:c.87+17805_87+17806insT:p.(=); SOS1:ENST00000402219.7:c.87+17805_87+17806insT:p.(=)

Pathogenicity Data:: Best Score: 0.26277512; CADD: 0.263 (1.324)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.39045273A>AGTGTGT [1/1] rs60673777 (variation viewer)

Variant score: 0.132

Transcripts:: SOS1:ENST00000395038.6:c.864+5870_864+5871insACACAC:p.(=); SOS1:ENST00000402219.7:c.864+5870_864+5871insACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.13203943; CADD: 0.132 (0.615)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.39064742A>ATTTT [1/1] rs4015841 (variation viewer)

Variant score: 0.126

Transcripts:: SOS1:ENST00000395038.6:c.213+2885_213+2886insAAAA:p.(=); SOS1:ENST00000402219.7:c.213+2885_213+2886insAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.126023; CADD: 0.126 (0.585)

Frequency Data:: No frequency data

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.39079154A>ACAGTAATGCTTAAAAAGCAAAACTTGTAAACAACCAGAATGTCCATCAACATTAGAATGGAC [1/1] rs70954781 (variation viewer)

Variant score: 0.000

Transcripts:: SOS1:ENST00000395038.6:c.88-11402_88-11401insGTCCATTCTAATGTTGATGGACATTCTGGTTGTTTACAAGTTTTGCTTTTTAAGCATTACTG:p.(=); SOS1:ENST00000402219.7:c.88-11402_88-11401insGTCCATTCTAATGTTGATGGACATTCTGGTTGTTTACAAGTTTTGCTTTTTAAGCATTACTG:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

DNMT1

Exomiser Score: 0.000

Phenotype Score: 0.517

Variant Score: 0.021

Phenotype matches:

Phenotypic similarity 0.479 to Autosomal dominant cerebellar ataxia-deafness-narcolepsy syndrome associated with DNMT1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Proximity score 0.517 in interactome to MECP2 and phenotypic similarity 0.909 to X-linked intellectual disability-psychosis-macroorchidism syndrome associated with MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.517 in interactome to MECP2 and phenotypic similarity 0.458 to mouse mutant of MECP2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Known diseases:: OMIM:604121 Cerebellar ataxia, deafness, and narcolepsy, autosomal dominant - autosomal dominant; OMIM:614116 Neuropathy, hereditary sensory, type IE - autosomal dominant; ORPHA:314404 Autosomal dominant cerebellar ataxia-deafness-narcolepsy syndrome

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.517

Variant Score: 0.021

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.10160198G>A [0/1] rs567804391 (variation viewer)

Variant score: 0.021 CONTRIBUTING VARIANT

Transcripts:: DNMT1:ENST00000340748.8:c.996-135C>T:p.(=); DNMT1:ENST00000359526.9:c.1044-135C>T:p.(=)

Pathogenicity Data:: Best Score: 0.020735502; CADD: 0.021 (0.091)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0056%; gnomAD_G_NFE: 0.0266%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.259

Variant Score: 0.240

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.10186838CA>C [1/1] rs35238334 (variation viewer)

Variant score: 0.240 CONTRIBUTING VARIANT

Transcripts:: DNMT1:ENST00000340748.8:c.81-4762del:p.(=); DNMT1:ENST00000359526.9:c.81-4762del:p.(=)

Pathogenicity Data:: Best Score: 0.24002379; CADD: 0.240 (1.192)

Frequency Data:: No frequency data

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.10180732G>A [0/1] rs150891761 (variation viewer)

Variant score: 0.078

Transcripts:: DNMT1:ENST00000340748.8:c.225+46C>T:p.(=); DNMT1:ENST00000359526.9:c.225+46C>T:p.(=)

Pathogenicity Data:: Best Score: 0.079550445; CADD: 0.080 (0.360)

Frequency Data:: 1000Genomes: 0.0599%; TOPMed: 0.0096%; ESP EA: 0.0116%; ESP All: 0.0077%; ExAC AFR: 0.0201%; ExAC NFE: 0.0064%; ExAC OTH: 0.1149%; gnomAD_E_AFR: 0.0200%; gnomAD_E_AMR: 0.0030%; gnomAD_E_NFE: 0.0064%; gnomAD_G_NFE: 0.0133%

CHRNB4

Exomiser Score: 0.000

Phenotype Score: 0.523

Variant Score: 0.000

Phenotype matches:

Proximity score 0.523 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.523 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.523

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.78626377TGTGTGTG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: CHRNB4:ENST00000261751.8:c.1339-1093_1339-1086delCACACACAins:p.(=); CHRNB4:ENST00000412074.6:c.360-1093_360-1086delCACACACAins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

CHRND

Exomiser Score: 0.000

Phenotype Score: 0.519

Variant Score: 0.000

Phenotype matches:

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 1.000 to 15q13.3 microdeletion syndrome associated with CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.519 in interactome to CHRNA7 and phenotypic similarity 0.436 to mouse mutant of CHRNA7.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Known diseases:: OMIM:253290 Multiple pterygium syndrome, lethal type - autosomal recessive; OMIM:616321 ?Myasthenic syndrome, congenital, 3A, slow-channel (unconfirmed); OMIM:616322 Myasthenic syndrome, congenital, 3B, fast-channel - autosomal recessive; OMIM:616323 ?Myasthenic syndrome, congenital, 3C, associated with acetylcholine receptor deficiency (unconfirmed); ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes; ORPHA:98913 Postsynaptic congenital myasthenic syndromes

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.519

Variant Score: 0.000

Variants contributing to score:

REGULATORY_REGION_VARIANT chr2:g.231604701CAGG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.519

Variant Score: 0.000

Variants contributing to score:

REGULATORY_REGION_VARIANT chr2:g.231604701CAGG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr2:g.231604712CAGCA>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

KRT31

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.009

Phenotype matches:

Proximity score 0.504 in interactome to USP8 and phenotypic similarity 0.864 to Cushing disease associated with USP8.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.009

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr17:g.41401030A>G [0/1] rs761583103 (variation viewer)

Variant score: 0.009 CONTRIBUTING VARIANT

Transcripts:: KRT31:ENST00000251645.3::; KRT31:ENST00000393988.2::

Pathogenicity Data:: Best Score: 0.009168029; CADD: 0.009 (0.040)

Frequency Data:: TOPMed: 0.0120%; UK10K: 0.0132%; gnomAD_G_NFE: 0.0067%

Other passed variants:

DERL2

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.008

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.008

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5479496TA>T [1/1] rs11306765 (variation viewer)

Variant score: 0.008 CONTRIBUTING VARIANT

Transcripts:: DERL2:ENST00000158771.9:c.614+557del:p.(=); DERL2:ENST00000570848.5:c.*25+557del:p.(=); DERL2:ENST00000572834.5:c.*25+557del:p.(=)

Pathogenicity Data:: Best Score: 0.0080266595; CADD: 0.008 (0.035)

Frequency Data:: No frequency data

Other passed variants:

MAT1A

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.000

Phenotype matches:

Proximity score 0.505 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:250850 Methionine adenosyltransferase deficiency, autosomal recessive - autosomal dominant/recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.000

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr10:g.80266884A>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: MAT1A:ENST00000372213.8::; MAT1A:ENST00000441206.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

MAT2A

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.000

Phenotype matches:

Proximity score 0.505 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: ORPHA:91387 Familial thoracic aortic aneurysm and aortic dissection

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.505

Variant Score: 0.000

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.85526342TTG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: MAT2A:ENST00000306434.8::; MAT2A:ENST00000453567.1::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

CBX5

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr12:g.54232348G>GT [0/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: CBX5:ENST00000209875.9:c.*9406dup:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

NME3

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr16:g.1771793A>ACCCCGCCCCCCCCCCCCCCCCCCC [0/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: NME3:ENST00000219302.7::; NME3:ENST00000177742.7::

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

PKM

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Phenotype matches:

Proximity score 0.504 in interactome to RRM2B and phenotypic similarity 0.864 to Autosomal dominant progressive external ophthalmoplegia associated with RRM2B.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

No known disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.504

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.72209417ATATATATATATATATATATATATGTATATATATATATATATG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: PKM:ENST00000319622.10:c.565+214_565+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000335181.10:c.565+214_565+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000389093.7:c.343+214_343+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000449901.6:c.520+214_520+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000565154.5:c.565+214_565+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000565184.5:c.565+214_565+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000568459.5:c.565+214_565+256delCATATATATATATATATACATATATATATATATATATATATATins:p.(=); PKM:ENST00000568883.5:c.120-617_120-575delCATATATATATATATATACATATATATATATATATATATATATins:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

CCL11

Exomiser Score: 0.000

Phenotype Score: 0.502

Variant Score: 0.000

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases:: OMIM:600807 Asthma, susceptibility to (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.502

Variant Score: 0.000

Variants contributing to score:

THREE_PRIME_UTR_EXON_VARIANT chr17:g.34287828A>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: CCL11:ENST00000305869.4:c.*138A>*:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

AXIN1

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.283

Phenotype matches:

Proximity score 0.503 in interactome to MT-ND4 and phenotypic similarity 0.864 to MELAS associated with MT-ND4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:114550 Hepatocellular carcinoma, somatic - somatic; OMIM:607864 ?Caudal duplication anomaly (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.160

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.318525G>A [0/1] rs753997964 (variation viewer)

Variant score: 0.160 CONTRIBUTING VARIANT

Transcripts:: AXIN1:ENST00000262320.8:c.879-3842C>T:p.(=); AXIN1:ENST00000354866.7:c.879-3842C>T:p.(=)

Pathogenicity Data:: Best Score: 0.16053998; CADD: 0.161 (0.760)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.283

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.318174C>T [0/1] rs751548877 (variation viewer)

Variant score: 0.406 CONTRIBUTING VARIANT

Transcripts:: AXIN1:ENST00000262320.8:c.879-3491G>A:p.(=); AXIN1:ENST00000354866.7:c.879-3491G>A:p.(=)

Pathogenicity Data:: Best Score: 0.42838973; CADD: 0.428 (2.429)

Frequency Data:: TOPMed: 0.0558%; UK10K: 0.0397%; gnomAD_G_AMR: 0.1193%; gnomAD_G_ASJ: 0.3311%; gnomAD_G_NFE: 0.0200%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.318525G>A [0/1] rs753997964 (variation viewer)

Variant score: 0.160 CONTRIBUTING VARIANT

Transcripts:: AXIN1:ENST00000262320.8:c.879-3842C>T:p.(=); AXIN1:ENST00000354866.7:c.879-3842C>T:p.(=)

Pathogenicity Data:: Best Score: 0.16053998; CADD: 0.161 (0.760)

Frequency Data:: TOPMed: 0.0040%; UK10K: 0.0132%; gnomAD_G_AFR: 0.0115%; gnomAD_G_NFE: 0.0067%

Other passed variants:

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.296518C>T [0/1] rs560138260 (variation viewer)

Variant score: 0.013

Transcripts:: AXIN1:ENST00000262320.8:c.1955+538G>A:p.(=); AXIN1:ENST00000354866.7:c.1955+538G>A:p.(=)

Pathogenicity Data:: Best Score: 0.013720512; CADD: 0.014 (0.060)

Frequency Data:: 1000Genomes: 0.0200%; TOPMed: 0.0581%; UK10K: 0.0926%; gnomAD_G_AFR: 0.0344%; gnomAD_G_AMR: 0.1193%; gnomAD_G_NFE: 0.0934%

CODING_TRANSCRIPT_INTRON_VARIANT chr16:g.318897A>AGCCAGGGCCTTGGTGAGAGCGGCTCTGACCCCTGGCTGTGCGGAGAGAATGCG [0/1]

Variant score: 0.000

Transcripts:: AXIN1:ENST00000262320.8:c.879-4215_879-4214insCGCATTCTCTCCGCACAGCCAGGGGTCAGAGCCGCTCTCACCAAGGCCCTGGC:p.(=); AXIN1:ENST00000354866.7:c.879-4215_879-4214insCGCATTCTCTCCGCACAGCCAGGGGTCAGAGCCGCTCTCACCAAGGCCCTGGC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

EWSR1

Exomiser Score: 0.000

Phenotype Score: 0.256

Variant Score: 0.238

Phenotype matches:

Proximity score 0.512 in interactome to FLI1 and phenotypic similarity 1.000 to Jacobsen syndrome associated with FLI1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:612219 Neuroepithelioma - somatic

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.256

Variant Score: 0.238

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.29287933G>A [0/1] rs1036385975 (variation viewer)

Variant score: 0.238 CONTRIBUTING VARIANT

Transcripts:: EWSR1:ENST00000331029.11:c.794-673G>A:p.(=); EWSR1:ENST00000332035.10:c.626-673G>A:p.(=); EWSR1:ENST00000332050.10:c.793+799G>A:p.(=); EWSR1:ENST00000333395.10:c.794-673G>A:p.(=); EWSR1:ENST00000397938.6:c.794-673G>A:p.(=); EWSR1:ENST00000406548.5:c.794-673G>A:p.(=); EWSR1:ENST00000414183.6:c.812-673G>A:p.(=); EWSR1:ENST00000629659.2:c.796+799G>A:p.(=)

Pathogenicity Data:: Best Score: 0.23844725; CADD: 0.238 (1.183)

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.256

Variant Score: 0.223

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.29287933G>A [0/1] rs1036385975 (variation viewer)

Variant score: 0.238 CONTRIBUTING VARIANT

Transcripts:: EWSR1:ENST00000331029.11:c.794-673G>A:p.(=); EWSR1:ENST00000332035.10:c.626-673G>A:p.(=); EWSR1:ENST00000332050.10:c.793+799G>A:p.(=); EWSR1:ENST00000333395.10:c.794-673G>A:p.(=); EWSR1:ENST00000397938.6:c.794-673G>A:p.(=); EWSR1:ENST00000406548.5:c.794-673G>A:p.(=); EWSR1:ENST00000414183.6:c.812-673G>A:p.(=); EWSR1:ENST00000629659.2:c.796+799G>A:p.(=)

Pathogenicity Data:: Best Score: 0.23844725; CADD: 0.238 (1.183)

Frequency Data:: No frequency data

REGULATORY_REGION_VARIANT chr22:g.29195727G>A [0/1]

Variant score: 0.208 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.20841056; CADD: 0.208 (1.015)

Frequency Data:: No frequency data

Other passed variants:

UQCRQ

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.217

Phenotype matches:

Proximity score 0.506 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:615159 Mitochondrial complex III deficiency, nuclear type 4 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.217

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr5:g.132869132G>GTTTT [0/1] rs542381065 (variation viewer)

Variant score: 0.217 CONTRIBUTING VARIANT

Transcripts:: UQCRQ:ENST00000378670.8::

Pathogenicity Data:: Best Score: 0.21747178; CADD: 0.217 (1.065)

Frequency Data:: No frequency data

Other passed variants:

DRD3

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.211

Phenotype matches:

Phenotypic similarity 0.445 to mouse mutant involving DRD3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0020422, decreased freezing behavior

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.503 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:181500 Schizophrenia, susceptibility to (susceptibility); OMIM:190300 Essential tremor, hereditary, 1 (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.211

Variants contributing to score:

FIVE_PRIME_UTR_INTRON_VARIANT chr3:g.114193082A>G [0/1] rs189809316 (variation viewer)

Variant score: 0.293 CONTRIBUTING VARIANT

Transcripts:: DRD3:ENST00000460779.5:c.-156+6191T>C:p.(=)

Pathogenicity Data:: Best Score: 0.5191606; CADD: 0.519 (3.180)

Frequency Data:: 1000Genomes: 0.7788%; TOPMed: 1.1130%; gnomAD_G_AFR: 0.2752%; gnomAD_G_AMR: 0.7212%; gnomAD_G_ASJ: 1.0204%; gnomAD_G_FIN: 1.0602%; gnomAD_G_NFE: 1.4405%; gnomAD_G_OTH: 1.3347%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.114140017G>A [0/1] rs141446862 (variation viewer)

Variant score: 0.128 CONTRIBUTING VARIANT

Transcripts:: DRD3:ENST00000295881.9:c.527-321C>T:p.(=); DRD3:ENST00000383673.5:c.527-321C>T:p.(=); DRD3:ENST00000460779.5:c.527-321C>T:p.(=); DRD3:ENST00000467632.5:c.527-321C>T:p.(=)

Pathogenicity Data:: Best Score: 0.13483292; CADD: 0.135 (0.629)

Frequency Data:: 1000Genomes: 0.0799%; TOPMed: 0.1537%; UK10K: 0.1587%; gnomAD_G_AFR: 0.0573%; gnomAD_G_NFE: 0.2799%; gnomAD_G_OTH: 0.3061%

Other passed variants:

THREE_PRIME_UTR_EXON_VARIANT chr3:g.114127974C>T [0/1] rs78591315 (variation viewer)

Variant score: 0.111

Transcripts:: DRD3:ENST00000383673.5:c.*742G>A:p.(=)

Pathogenicity Data:: Best Score: 0.802303; CADD: 0.802 (7.040)

Frequency Data:: 1000Genomes: 0.7788%; TOPMed: 1.0550%; UK10K: 1.9968%; gnomAD_G_AFR: 0.2405%; gnomAD_G_AMR: 0.7160%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.0017%; gnomAD_G_NFE: 1.3118%; gnomAD_G_OTH: 1.3238%

REGULATORY_REGION_VARIANT chr3:g.115792788T>C [0/1] rs139374383 (variation viewer)

Variant score: 0.031

Transcripts:

Pathogenicity Data:: Best Score: 0.041041076; CADD: 0.041 (0.182)

Frequency Data:: 1000Genomes: 0.5391%; TOPMed: 0.1633%; UK10K: 0.2513%; gnomAD_G_AFR: 0.0458%; gnomAD_G_AMR: 0.1193%; gnomAD_G_FIN: 1.0303%; gnomAD_G_NFE: 0.3730%; gnomAD_G_OTH: 0.9165%

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.114133621A>AGAAAAGAAATAGGGAAAAATGGGTTTGGGATGAGTAGCCTCTGAGAATGGAAAACT [1/1] rs71146308 (variation viewer)

Variant score: 0.000

Transcripts:: DRD3:ENST00000295881.9:c.724-2222_724-2221insAGTTTTCCATTCTCAGAGGCTACTCATCCCAAACCCATTTTTCCCTATTTCTTTTC:p.(=); DRD3:ENST00000383673.5:c.724-2222_724-2221insAGTTTTCCATTCTCAGAGGCTACTCATCCCAAACCCATTTTTCCCTATTTCTTTTC:p.(=); DRD3:ENST00000460779.5:c.724-2222_724-2221insAGTTTTCCATTCTCAGAGGCTACTCATCCCAAACCCATTTTTCCCTATTTCTTTTC:p.(=); DRD3:ENST00000467632.5:c.724-2222_724-2221insAGTTTTCCATTCTCAGAGGCTACTCATCCCAAACCCATTTTTCCCTATTTCTTTTC:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

NFKBIA

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.184

Phenotype matches:

Proximity score 0.503 in interactome to MT-CO2 and phenotypic similarity 0.864 to MELAS associated with MT-CO2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:612132 Ectodermal dysplasia and immunodeficiency 2 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.184

Variants contributing to score:

DOWNSTREAM_GENE_VARIANT chr14:g.35399950CA>C [1/1] rs71121288 (variation viewer)

Variant score: 0.184 CONTRIBUTING VARIANT

Transcripts:: NFKBIA:ENST00000216797.9::; NFKBIA:ENST00000459899.1::

Pathogenicity Data:: Best Score: 0.18435723; CADD: 0.184 (0.885)

Frequency Data:: No frequency data

Other passed variants:

NDUFA12

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.157

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFA12.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:618244 ?Mitochondrial complex I deficiency, nuclear type 23 (unconfirmed); ORPHA:255241 Leigh syndrome with leukodystrophy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.157

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr12:g.94987791CA>C [0/1] rs61711763 (variation viewer)

Variant score: 0.157 CONTRIBUTING VARIANT

Transcripts:: NDUFA12:ENST00000327772.7:c.257+6378del:p.(=); NDUFA12:ENST00000547157.1:c.102+15014del:p.(=); NDUFA12:ENST00000547986.5:c.169+14947del:p.(=)

Pathogenicity Data:: Best Score: 0.15744162; CADD: 0.157 (0.744)

Frequency Data:: No frequency data

Other passed variants:

PRKACA

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.144

Phenotype matches:

Phenotypic similarity 0.479 to Cushing syndrome, ACTH-independent adrenal, somatic associated with PRKACA.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.507 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:615830 Cushing syndrome, ACTH-independent adrenal, somatic - autosomal dominant; ORPHA:189439 Primary pigmented nodular adrenocortical disease

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.144

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.14109999T>TACAC [1/1] rs764855462 (variation viewer)

Variant score: 0.144 CONTRIBUTING VARIANT

Transcripts:: PRKACA:ENST00000308677.9:c.47-2591_47-2590insGTGT:p.(=); PRKACA:ENST00000589994.5:c.23-2591_23-2590insGTGT:p.(=); PRKACA:ENST00000590853.5:c.47-2591_47-2590insGTGT:p.(=)

Pathogenicity Data:: Best Score: 0.14414537; CADD: 0.144 (0.676)

Frequency Data:: No frequency data

Other passed variants:

ITPR3

Exomiser Score: 0.000

Phenotype Score: 0.254

Variant Score: 0.137

Phenotype matches:

Phenotypic similarity 0.385 to Diabetes, type 1, susceptibility to associated with ITPR3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0002591, Polyphagia

Phenotypic similarity 0.436 to mouse mutant involving ITPR3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0001364, decreased anxiety-related response

Proximity score 0.508 in interactome to ATP2A2 and phenotypic similarity 1.000 to Darier disease associated with ATP2A2.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:222100 Diabetes, type 1, susceptibility to (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.254

Variant Score: 0.137

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr6:g.33661992GAAAAA>G [0/1] rs55958712 (variation viewer)

Variant score: 0.137 CONTRIBUTING VARIANT

Transcripts:: ITPR3:ENST00000374316.9:c.712-535_712-531del:p.(=); ITPR3:ENST00000605930.3:c.712-535_712-531del:p.(=)

Pathogenicity Data:: Best Score: 0.13741875; CADD: 0.137 (0.642)

Frequency Data:: No frequency data

Other passed variants:

SLC6A4

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.133

Phenotype matches:

Phenotypic similarity 0.471 to Obsessive-compulsive disorder associated with SLC6A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000716, Depressivity

Phenotypic similarity 0.461 to mouse mutant involving SLC6A4.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0002065, abnormal fear/anxiety-related behavior

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.504 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:164230 Obsessive-compulsive disorder (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.133

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.30206712C>CTTTTCT [1/1] rs61636654 (variation viewer)

Variant score: 0.133 CONTRIBUTING VARIANT

Transcripts:: SLC6A4:ENST00000261707.7:c.1650+1019_1650+1020insAGAAAA:p.(=); SLC6A4:ENST00000401766.6:c.1650+1019_1650+1020insAGAAAA:p.(=); SLC6A4:ENST00000650711.1:c.1650+1019_1650+1020insAGAAAA:p.(=)

Pathogenicity Data:: Best Score: 0.13283849; CADD: 0.133 (0.619)

Frequency Data:: No frequency data

Other passed variants:

VPS33B

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.132

Phenotype matches:

Proximity score 0.505 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:208085 Arthrogryposis, renal dysfunction, and cholestasis 1 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.132

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr15:g.91017367A>AATATATATATAT [-/1]

Variant score: 0.132 CONTRIBUTING VARIANT

Transcripts:: VPS33B:ENST00000333371.7:c.178-344_178-343insATATATATATAT:p.(=); VPS33B:ENST00000535906.1:c.97-344_97-343insATATATATATAT:p.(=); VPS33B:ENST00000643536.1:c.178-344_178-343insATATATATATAT:p.(=)

Pathogenicity Data:: Best Score: 0.13183957; CADD: 0.132 (0.614)

Frequency Data:: No frequency data

Other passed variants:

COX6B1

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.117

Phenotype matches:

Proximity score 0.505 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:619051 Mitochondrial complex IV deficiency, nuclear type 7 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.253

Variant Score: 0.117

Variants contributing to score:

UPSTREAM_GENE_VARIANT chr19:g.35647250GAAAAAAAAAA>G [0/1] rs55996729 (variation viewer)

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: COX6B1:ENST00000649813.2::; COX6B1:ENST00000621247.4::

Pathogenicity Data:: Best Score: 0.11651331; CADD: 0.117 (0.538)

Frequency Data:: No frequency data

Other passed variants:

NDUFB8

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.117

Phenotype matches:

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:618252 Mitochondrial complex I deficiency, nuclear type 32 - autosomal recessive; ORPHA:70474 Leigh syndrome with cardiomyopathy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.117

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr10:g.100525717C>CGTGTGTGTGTGTGT [-/1] rs71013460 (variation viewer)

Variant score: 0.117 CONTRIBUTING VARIANT

Transcripts:: NDUFB8:ENST00000299166.9:c.468+681_468+682insACACACACACACAC:p.(=); NDUFB8:ENST00000370320.4:c.468+681_468+682insACACACACACACAC:p.(=); NDUFB8:ENST00000370322.5:c.375+681_375+682insACACACACACACAC:p.(=); NDUFB8:ENST00000557395.5:c.468+681_468+682insACACACACACACAC:p.(=)

Pathogenicity Data:: Best Score: 0.11671674; CADD: 0.117 (0.539)

Frequency Data:: No frequency data

Other passed variants:

XRCC1

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.112

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:617633 ?Spinocerebellar ataxia, autosomal recessive 26 (unconfirmed)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.112

Variants contributing to score:

REGULATORY_REGION_VARIANT chr19:g.43674852CT>C [0/1] rs531773492 (variation viewer)

Variant score: 0.112 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: Best Score: 0.11243534; CADD: 0.112 (0.518)

Frequency Data:: No frequency data

Other passed variants:

C1QBP

Exomiser Score: 0.000

Phenotype Score: 0.254

Variant Score: 0.087

Phenotype matches:

Proximity score 0.508 in interactome to GP1BB and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with GP1BB.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:617713 Combined oxidative phosphorylation deficiency 33 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.254

Variant Score: 0.087

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr17:g.5434464CT>C [0/1] rs576803401 (variation viewer)

Variant score: 0.087 CONTRIBUTING VARIANT

Transcripts:: C1QBP:ENST00000225698.8:c.477+408del:p.(=); C1QBP:ENST00000574444.5:c.165+408del:p.(=)

Pathogenicity Data:: Best Score: 0.087148786; CADD: 0.087 (0.396)

Frequency Data:: No frequency data

Other passed variants:

RTN4R

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.081

Phenotype matches:

Proximity score 0.502 in interactome to MT-ND1 and phenotypic similarity 0.864 to MELAS associated with MT-ND1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:181500 Schizophrenia, susceptibility to (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.251

Variant Score: 0.081

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.20262040C>T [0/1] rs189655443 (variation viewer)

Variant score: 0.097 CONTRIBUTING VARIANT

Transcripts:: RTN4R:ENST00000043402.8:c.22+6031G>A:p.(=)

Pathogenicity Data:: Best Score: 0.110798895; CADD: 0.111 (0.510)

Frequency Data:: 1000Genomes: 0.1398%; TOPMed: 0.3592%; UK10K: 0.4232%; gnomAD_G_AFR: 0.2179%; gnomAD_G_AMR: 0.4773%; gnomAD_G_ASJ: 0.6623%; gnomAD_G_FIN: 0.0286%; gnomAD_G_NFE: 0.3803%; gnomAD_G_OTH: 0.1020%

CODING_TRANSCRIPT_INTRON_VARIANT chr22:g.20246674G>A [0|1] rs147783068 (variation viewer)

Variant score: 0.065 CONTRIBUTING VARIANT

Transcripts:: RTN4R:ENST00000043402.8:c.23-3564C>T:p.(=)

Pathogenicity Data:: Best Score: 0.14807767; CADD: 0.148 (0.696)

Frequency Data:: 1000Genomes: 0.6789%; TOPMed: 1.0300%; UK10K: 1.6398%; gnomAD_G_AFR: 0.3674%; gnomAD_G_AMR: 1.0740%; gnomAD_G_ASJ: 1.3245%; gnomAD_G_FIN: 1.3459%; gnomAD_G_NFE: 1.5713%; gnomAD_G_OTH: 1.2245%

Other passed variants:

UGT1A1

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.068

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:218800 Crigler-Najjar syndrome, type I - autosomal recessive; OMIM:237900 Hyperbilirubinemia, familial transient neonatal - autosomal recessive; OMIM:606785 Crigler-Najjar syndrome, type II - autosomal recessive; ORPHA:79234 Crigler-Najjar syndrome type 1; ORPHA:79235 Crigler-Najjar syndrome type 2

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.068

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr2:g.233768582CT>C [-/1] rs139595073 (variation viewer)

Variant score: 0.068 CONTRIBUTING VARIANT

Transcripts:: UGT1A1:ENST00000305208.10:c.1304+144del:p.(=)

Pathogenicity Data:: Best Score: 0.06846321; CADD: 0.068 (0.308)

Frequency Data:: No frequency data

Other passed variants:

NDUFA13

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.066

Phenotype matches:

Phenotypic similarity 0.479 to Leigh syndrome with leukodystrophy associated with NDUFA13.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0000712, Emotional lability

Proximity score 0.504 in interactome to MT-ND6 and phenotypic similarity 0.864 to MELAS associated with MT-ND6.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:618249 ?Mitochondrial complex I deficiency, nuclear type 28 (unconfirmed); ORPHA:255241 Leigh syndrome with leukodystrophy

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.066

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr19:g.19519045A>AT [0/1] rs71170693 (variation viewer)

Variant score: 0.066 CONTRIBUTING VARIANT

Transcripts:: NDUFA13:ENST00000428459.6:c.94+2713_94+2714insT:p.(=); NDUFA13:ENST00000503283.5:c.94+2713_94+2714insT:p.(=); NDUFA13:ENST00000507754.9:c.94+2713_94+2714insT:p.(=); NDUFA13:ENST00000555938.1:c.94+2713_94+2714insT:p.(=)

Pathogenicity Data:: Best Score: 0.066100836; CADD: 0.066 (0.297)

Frequency Data:: No frequency data

Other passed variants:

MYCN

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.054

Phenotype matches:

Proximity score 0.504 in interactome to DNMT3A and phenotypic similarity 0.906 to Tall stature-intellectual disability-facial dysmorphism syndrome associated with DNMT3A.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:164280 Feingold syndrome 1 - autosomal dominant; ORPHA:391641 Feingold syndrome type 1; ORPHA:391641 Feingold syndrome type 1; ORPHA:635 Neuroblastoma

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.054

Variants contributing to score:

INTERGENIC_VARIANT chr2:g.15959960TTCCTC>T [0/1] rs146561380 (variation viewer)

Variant score: 0.087 CONTRIBUTING VARIANT

Transcripts:: MYCN:ENST00000638417.1::; MYCN:ENST00000603389.1::

Pathogenicity Data:: Best Score: 0.094475925; CADD: 0.094 (0.431)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.3950%; UK10K: 0.4628%; gnomAD_G_AFR: 0.0688%; gnomAD_G_AMR: 0.2392%; gnomAD_G_NFE: 0.4738%; gnomAD_G_OTH: 0.1022%

REGULATORY_REGION_VARIANT chr2:g.15890063A>G [0/1] rs189277559 (variation viewer)

Variant score: 0.021 CONTRIBUTING VARIANT

Transcripts:: MYCN:ENST00000281043.4::; MYCN:ENST00000398740.2::

Pathogenicity Data:: Best Score: 0.02321273; CADD: 0.023 (0.102)

Frequency Data:: 1000Genomes: 0.2196%; TOPMed: 0.3345%; UK10K: 0.4232%; gnomAD_G_AFR: 0.0802%; gnomAD_G_AMR: 0.5967%; gnomAD_G_FIN: 0.0572%; gnomAD_G_NFE: 0.3799%; gnomAD_G_OTH: 0.2041%

Other passed variants:

SEC61A1

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.053

Phenotype matches:

Proximity score 0.504 in interactome to UFD1 and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with UFD1.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:617056 Hyperuricemic nephropathy, familial juvenile, 4 - autosomal dominant

Gene scores under compatible inheritance modes:

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.053

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr3:g.128058201A>AT [1/1] rs57508280 (variation viewer)

Variant score: 0.053 CONTRIBUTING VARIANT

Transcripts:: SEC61A1:ENST00000243253.8:c.352+1361_352+1362insT:p.(=); SEC61A1:ENST00000464451.5:c.370+1361_370+1362insT:p.(=); SEC61A1:ENST00000424880.2:c.-8-1901_-8-1900insT:p.(=)

Pathogenicity Data:: Best Score: 0.053326964; CADD: 0.053 (0.238)

Frequency Data:: No frequency data

Other passed variants:

ADH1B

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.021

Phenotype matches:

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.864 to 22q11.2 deletion syndrome associated with COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Proximity score 0.505 in interactome to COMT and phenotypic similarity 0.454 to mouse mutant of COMT.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - MP:0003106, abnormal fear-related response

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:103780 Alcohol dependence, protection against (susceptibility)

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.000

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99338444T>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: ADH1B:ENST00000639454.1:c.18+14214A>:p.(=); ADH1B:ENST00000515683.6:c.1103+1133A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

AUTOSOMAL_RECESSIVE

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.021

Variants contributing to score:

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99338438TATATATAC>T [0/1] rs1395921244 (variation viewer)

Variant score: 0.041 CONTRIBUTING VARIANT

Transcripts:: ADH1B:ENST00000639454.1:c.18+14212_18+14219del:p.(=); ADH1B:ENST00000515683.6:c.1103+1131_1103+1138del:p.(=)

Pathogenicity Data:: Best Score: 0.12622422; CADD: 0.126 (0.586)

Frequency Data:: gnomAD_G_AFR: 1.0573%; gnomAD_G_ASJ: 1.7857%; gnomAD_G_EAS: 0.4545%; gnomAD_G_FIN: 0.2732%; gnomAD_G_NFE: 0.4627%; gnomAD_G_OTH: 1.1628%

CODING_TRANSCRIPT_INTRON_VARIANT chr4:g.99338444T>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:: ADH1B:ENST00000639454.1:c.18+14214A>:p.(=); ADH1B:ENST00000515683.6:c.1103+1133A>:p.(=)

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

COA6

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.000

Phenotype matches:

Proximity score 0.504 in interactome to MT-CO3 and phenotypic similarity 0.864 to MELAS associated with MT-CO3.
Best Phenotype Matches:: HP:0007302, Bipolar affective disorder - HP:0007302, Bipolar affective disorder

Known diseases - observed variants incompatible with mode of inheritance:: OMIM:616501 Mitochondrial complex IV deficiency, nuclear type 13 - autosomal recessive

Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 0.000

Phenotype Score: 0.252

Variant Score: 0.000

Variants contributing to score:

REGULATORY_REGION_VARIANT chr1:g.234523969TATATATATATATATAGAGAGAG>* [-/1]

Variant score: 0.000 CONTRIBUTING VARIANT

Transcripts:

Pathogenicity Data:: No pathogenicity data

Frequency Data:: No frequency data

Other passed variants:

Unanalysed Variants

REGULATORY_REGION_VARIANT 1 9829797 CTT C [1/1] rs35897686 (variation viewer)

REGULATORY_REGION_VARIANT 1 65084099 CA C [0/1] rs34395027 (variation viewer)

REGULATORY_REGION_VARIANT 1 151195884 ATT A [-/1] rs1157195462 (variation viewer)

REGULATORY_REGION_VARIANT 1 151195884 A ATTTTT [-/1] rs1157195462 (variation viewer)

REGULATORY_REGION_VARIANT 1 182147338 C T [0/1] rs534735858 (variation viewer)

REGULATORY_REGION_VARIANT 1 234523969 TATATATATATATATAGAGAGAG * [-/1] . (variation viewer)

REGULATORY_REGION_VARIANT 2 8572803 G T [0/1] rs115148688 (variation viewer)

REGULATORY_REGION_VARIANT 2 8627059 TGTGAGAGAGGGA * [-/1] . (variation viewer)

REGULATORY_REGION_VARIANT 2 10013064 G T [0|1] rs796973306 (variation viewer)

REGULATORY_REGION_VARIANT 2 64212741 C CT [1/1] rs5831682 (variation viewer)

REGULATORY_REGION_VARIANT 2 231604701 CAGG * [-/1] . (variation viewer)

REGULATORY_REGION_VARIANT 2 231604712 CAGCA * [-/1] . (variation viewer)

REGULATORY_REGION_VARIANT 3 115792788 T C [0/1] rs139374383 (variation viewer)

REGULATORY_REGION_VARIANT 3 155746814 CA C [0/1] rs533773685 (variation viewer)

REGULATORY_REGION_VARIANT 3 171967352 A G [0/1] rs114242245 (variation viewer)

REGULATORY_REGION_VARIANT 3 180332744 C T [0|1] rs186577357 (variation viewer)

REGULATORY_REGION_VARIANT 3 194089713 G A [0/1] rs764012100 (variation viewer)

REGULATORY_REGION_VARIANT 5 53337910 G GAAAAAAA [1|1] rs1561251360 (variation viewer)

REGULATORY_REGION_VARIANT 5 74232153 C CT [0/1] rs770423775 (variation viewer)

REGULATORY_REGION_VARIANT 5 75057742 G A [0/1] rs112270430 (variation viewer)

REGULATORY_REGION_VARIANT 5 86358640 CTTTT C [1|1] rs71610472 (variation viewer)

CUSTOM 5 115547937 G GTGTGTGTGTATA [0/1] rs1284559247 (variation viewer)

CUSTOM 5 115642784 A T [0|1] rs11956382 (variation viewer)

CUSTOM 5 115699595 A ATATATATATATATATATATATTTTTTTTTT [0/1] . (variation viewer)

CUSTOM 5 115703003 CTATATATATATA C [-/1] rs59095437 (variation viewer)

REGULATORY_REGION_VARIANT 6 30806495 AGG A [0|1] rs9281051 (variation viewer)

REGULATORY_REGION_VARIANT 6 30806507 A G [0|1] rs141494988 (variation viewer)

REGULATORY_REGION_VARIANT 6 30806512 T A [0|1] . (variation viewer)

REGULATORY_REGION_VARIANT 6 110934109 T C [0/1] rs996355123 (variation viewer)

REGULATORY_REGION_VARIANT 7 140219509 CA C [0/1] rs71170957 (variation viewer)

REGULATORY_REGION_VARIANT 7 140324893 GT * [-/1] . (variation viewer)

REGULATORY_REGION_VARIANT 7 150755609 T TAGAGAGAGAGAGAGAG [-/1] rs58155618 (variation viewer)

REGULATORY_REGION_VARIANT 8 59158357 C CAA [1/1] rs11317853 (variation viewer)

REGULATORY_REGION_VARIANT 8 102426087 C CA [1/1] rs1183622039 (variation viewer)

REGULATORY_REGION_VARIANT 9 1665315 T TAAAAAA [0/1] rs570282901 (variation viewer)

REGULATORY_REGION_VARIANT 9 6681108 G A [0/1] rs560827314 (variation viewer)

REGULATORY_REGION_VARIANT 9 137173488 A G [0/1] rs765358052 (variation viewer)

REGULATORY_REGION_VARIANT 10 53014838 C CTTTTTT [-/1] rs71032683 (variation viewer)

REGULATORY_REGION_VARIANT 10 53014838 C CTTTTTTTTTTTT [-/1] rs71032683 (variation viewer)

REGULATORY_REGION_VARIANT 10 88062623 C T [0/1] rs145052648 (variation viewer)

REGULATORY_REGION_VARIANT 11 65149269 GTTTTTTTTTTTTTTTTTTT G [0/1] rs752895594 (variation viewer)

CUSTOM 11 78018600 G A [0/1] rs149724010 (variation viewer)

CUSTOM 11 78025086 G * [-/1] . (variation viewer)

CUSTOM 11 78033901 G GTGTGTGTGTACATATATATATATATA [0/1] rs781027862 (variation viewer)

REGULATORY_REGION_VARIANT 11 108648464 G A [0/1] rs1435947610 (variation viewer)

REGULATORY_REGION_VARIANT 11 112832286 A G [0|1] rs117169797 (variation viewer)

REGULATORY_REGION_VARIANT 12 120202435 CTTTTTTTTTT C [1/1] rs71072595 (variation viewer)

REGULATORY_REGION_VARIANT 13 76756464 C CA [-/1] rs57463502 (variation viewer)

REGULATORY_REGION_VARIANT 13 106418000 G GTTT [-/1] rs5806578 (variation viewer)

REGULATORY_REGION_VARIANT 14 22590191 G GTT [0/1] rs5807180 (variation viewer)

REGULATORY_REGION_VARIANT 15 100721147 T TTG [1/1] rs151054934 (variation viewer)

REGULATORY_REGION_VARIANT 16 31353277 G A [0/1] rs1044541962 (variation viewer)

REGULATORY_REGION_VARIANT 17 14748318 T TAAAAAAAAAAAAAAAA [1/1] rs55775289 (variation viewer)

REGULATORY_REGION_VARIANT 17 32397939 G A [0/1] rs116887675 (variation viewer)

CUSTOM 17 75991149 C CA [1/1] rs71361699 (variation viewer)

REGULATORY_REGION_VARIANT 17 80161459 CTTTTTT C [1/1] rs568182873 (variation viewer)

REGULATORY_REGION_VARIANT 17 81344384 T A [0/1] rs892980752 (variation viewer)

REGULATORY_REGION_VARIANT 19 27241216 G A [0/1] rs79112842 (variation viewer)

REGULATORY_REGION_VARIANT 19 27242097 C G [0/1] rs758525415 (variation viewer)

REGULATORY_REGION_VARIANT 19 27242159 A G [0/1] rs8108614 (variation viewer)

REGULATORY_REGION_VARIANT 19 27243215 T C [0/1] rs558548866 (variation viewer)

REGULATORY_REGION_VARIANT 19 27741622 G A [0/1] rs112236697 (variation viewer)

REGULATORY_REGION_VARIANT 19 43674852 CT C [0/1] rs531773492 (variation viewer)

REGULATORY_REGION_VARIANT 19 44736813 CT C [0/1] rs58455045 (variation viewer)

REGULATORY_REGION_VARIANT 19 49329622 CT C [0/1] rs71180620 (variation viewer)

REGULATORY_REGION_VARIANT 20 3175875 CTTTTTTTTTTTTT C [1/1] rs11477220 (variation viewer)

REGULATORY_REGION_VARIANT 22 29195727 G A [0/1] . (variation viewer)

REGULATORY_REGION_VARIANT 22 30273713 C G [0/1] rs188563973 (variation viewer)

REGULATORY_REGION_VARIANT 22 36884885 C A [0/1] rs549128459 (variation viewer)

REGULATORY_REGION_VARIANT 22 42132027 C T [1|1] rs139702605 (variation viewer)

REGULATORY_REGION_VARIANT X 133987408 A G [1/1] . (variation viewer)

About

The Exomizer is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file (version 4). The functional annotation code is based on Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates

Variants are prioritized according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, and model organism phenotype data. Predicted pathogenicity data was extracted from the dbNSFP resource.

Developed by the Computational Biology and Bioinformatics group at the Institute for Medical Genetics and Human Genetics of the Charité - Universitätsmedizin Berlin, the Mouse Informatics Group at the Sanger Institute and the Smedley group at Queen Mary University of London.

Problems, suggestions, or comments? Please let us know