rs1800171

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PM2_SupportingPS3PS4PP3PP4

This summary comes from the ClinGen Evidence Repository: NM_000218.3(KCNQ1):c.1032G>A is a synonymous variant (p.Ala344=) predicted to affect KCNQ1 mRNA splicing. The computational splicing predictor SpliceAI gives scores of 0.49 for donor gain and 0.38 for donor loss, which are higher than the ClinGen Potassium Channel Arrhythmia VCEP PP3 threshold of greater than or equal to 0.2 and predict that the variant disrupts KCNQ1 splicing (PP3). The variant is observed at an extremely low frequency in the population with a maximum allele frequency (gnomAD 4.1.0) of 0.000001701, with 2 in 1,175,668 individuals of European (non-Finnish) ancestry (PM2_Supporting). Functional studies have been performed on this variant and meet criteria with demonstrated deleterious effects on electrophysiology and RNA metabolism (PS3, PMID:29857160, 10477533, 17292394). There are 23 reported probands in the literature with a clinical diagnosis of Long QT syndrome (PS4; PMID:26118460, PMID:21810471, PMID:9654228, PMID:29497013, PMID:17292394). An additional case reports provides specific details that are highly specific for a diagnosis of Long QT syndrome in an individual with the variant who had a significantly prolonged QTc at rest and exercise-triggered events (PP4, PMID:21810471). In summary, this variant meets the criteria to be classified as pathogenic for long QT syndrome 1 based on the ACMG/AMP criteria applied, as specified by the ClinGen Potassium Channel Arrhythmia VCEP: PS3, PS4, PM2_Supporting, PP3, and PP4. (VCEP specifications version 1.0.0; date of approval 03/04/2025). LINK:https://erepo.genome.network/evrepo/ui/classification/CA005005/MONDO:0100316/112

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

KCNQ1
NM_000218.3 splice_region, synonymous

Scores

Splicing: ADA: 0.9999

Clinical Significance

Pathogenic reviewed by expert panel P:17

Conservation

PhyloP100: 1.79

Publications

27 publications found

Variant links:

Genes affected

KCNQ1 (HGNC:6294): (potassium voltage-gated channel subfamily Q member 1) This gene encodes a voltage-gated potassium channel required for repolarization phase of the cardiac action potential. This protein can form heteromultimers with two other potassium channel proteins, KCNE1 and KCNE3. Mutations in this gene are associated with hereditary long QT syndrome 1 (also known as Romano-Ward syndrome), Jervell and Lange-Nielsen syndrome, and familial atrial fibrillation. This gene exhibits tissue-specific imprinting, with preferential expression from the maternal allele in some tissues, and biallelic expression in others. This gene is located in a region of chromosome 11 amongst other imprinted genes that are associated with Beckwith-Wiedemann syndrome (BWS), and itself has been shown to be disrupted by chromosomal rearrangements in patients with BWS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]

KCNQ1 Gene-Disease associations (from GenCC):

long QT syndrome
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
long QT syndrome 1
Inheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
Jervell and Lange-Nielsen syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Jervell and Lange-Nielsen syndrome 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
atrial fibrillation, familial, 3
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
short QT syndrome
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet
short QT syndrome type 2
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
familial atrial fibrillation
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Jervell and Lange-Nielsen syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
hypertrophic cardiomyopathy
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

KCNQ1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 11 ACMG points.

PS3

For more information check the summary or visit ClinGen Evidence Repository.

PS4

For more information check the summary or visit ClinGen Evidence Repository.

PM2

For more information check the summary or visit ClinGen Evidence Repository.

PP3

For more information check the summary or visit ClinGen Evidence Repository.

PP4

For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNQ1	NM_000218.3 link	c.1032G>A	p.Ala344Ala	splice_region_variant, synonymous_variant	Exon 7 of 16	ENST00000155840.12	NP_000209.2	P51787-1Q96AI9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNQ1	ENST00000155840.12 link	c.1032G>A	p.Ala344Ala	splice_region_variant, synonymous_variant	Exon 7 of 16	1	NM_000218.3	ENSP00000155840.2		P51787-1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000398

AC:

AN:

251186

AF XY:

0.00000736

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000881

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

6.86e-7

AC:

AN:

1456938

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

725086

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33374

American (AMR)

AF:

0.00

AC:

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26110

East Asian (EAS)

AF:

0.00

AC:

AN:

39668

South Asian (SAS)

AF:

0.00

AC:

AN:

86160

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53286

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5756

European-Non Finnish (NFE)

AF:

9.03e-7

AC:

AN:

1107640

Other (OTH)

AF:

0.00

AC:

AN:

60228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152222

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41456

American (AMR)

AF:

0.00

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00

AC:

AN:

4836

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68028

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Long QT syndrome 1

Pathogenic:7

Jan 01, 2014

Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:research

- -

May 22, 2022

3billion

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Functional studies provide moderate evidence of the variant having a damaging effect on the gene or gene product (PMID:10477533, 21810471). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID:10477533, 21810471, 27485560, 29255176, 31589614, 31737537). The variant has been reported to co-segregate with the disease in at least 5 similarly affected relatives/individuals in the same family or similarly affected unrelated families (PMID:10477533).Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

Feb 02, 2022

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative, loss of function and gain of function are known mechanisms of disease in this gene. Gain of function variants result exclusively in Short QT syndrome (MIM#609621), while dominant negative and loss of function variants can cause Long QT syndrome (LQTS, MIM#192500), atrial fibrillation (MIM#607554) and Jervell and Lange-Nielsen syndrome (JLNS, MIM#220400) (OMIM, PMIDs: 19632626, 28438721). (I) 0108 - This gene is known to be associated with both recessive and dominant disease. JLNS is characterized by congenital, bilateral deafness and variable degrees of QT prolongation, and is the only condition caused by biallelic mutations (PMID: 28438721). (I) 0112 - The condition associated with this gene has incomplete penetrance (GeneReviews, OMIM). (I) 0209 - Splice site variant proven to affect splicing of the transcript with uncertain effect on protein sequence. This variant has been shown to result in several splicing errors, including the skipping of exon 7, exon 8, or both exon 7 and 8. Quantitative analysis confirmed only 55% of wildtype transcript remained (PMID: 21810471). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2, v3) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. Multiple pathogenic variants at the same residue have been reported as pathogenic, and it is described as the 2nd most mutated codon (Decipher, PMID: 10477533). (SP) 0703 - Other synonymous splice variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. Alternative changes at the same nucleotide position (c.1032G>C, c.1032G>T) have been reported as pathogenic, likely pathogenic and in a family with LQTS (ClinVar, PMID: 10477533). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic and in multiple families with LQTS (ClinVar, PMID: 21810471, PMID: 10477533). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Jul 01, 2025

ClinGen Potassium Channel Arrhythmia Variant Curation Expert Panel, ClinGen

Significance:Pathogenic

Review Status:reviewed by expert panel

Collection Method:curation

NM_000218.3(KCNQ1):c.1032G>A is a synonymous variant (p.Ala344=) predicted to affect KCNQ1 mRNA splicing. The computational splicing predictor SpliceAI gives scores of 0.49 for donor gain and 0.38 for donor loss, which are higher than the ClinGen Potassium Channel Arrhythmia VCEP PP3 threshold of greater than or equal to 0.2 and predict that the variant disrupts KCNQ1 splicing (PP3). The variant is observed at an extremely low frequency in the population with a maximum allele frequency (gnomAD 4.1.0) of 0.000001701, with 2 in 1,175,668 individuals of European (non-Finnish) ancestry (PM2_Supporting). Functional studies have been performed on this variant and meet criteria with demonstrated deleterious effects on electrophysiology and RNA metabolism (PS3, PMID: 29857160, 10477533, 17292394). There are 23 reported probands in the literature with a clinical diagnosis of Long QT syndrome (PS4; PMID: 26118460, PMID: 21810471, PMID: 9654228, PMID: 29497013, PMID: 17292394). An additional case reports provides specific details that are highly specific for a diagnosis of Long QT syndrome in an individual with the variant who had a significantly prolonged QTc at rest and exercise-triggered events (PP4, PMID: 21810471). In summary, this variant meets the criteria to be classified as pathogenic for long QT syndrome 1 based on the ACMG/AMP criteria applied, as specified by the ClinGen Potassium Channel Arrhythmia VCEP: PS3, PS4, PM2_Supporting, PP3, and PP4. (VCEP specifications version 1.0.0; date of approval 03/04/2025). -

Aug 01, 2023

Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 07, 1999

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Jan 12, 2024

KardioGenetik, Herz- und Diabeteszentrum NRW

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Pathogenic:3

Nov 01, 2021

GeneDx

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); A different nucleotide change at the same position (c.1032 G>C, A344A) has also been reported to affect splicing and was found to segregate with a LQTS phenotype in a multi-generation family (Murray et al., 1999); Reported in ClinVar as pathogenic (ClinVar Variant ID# 3135; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 21810471, 29857160, 9570196, 26318259, 10973849, 19716085, 29497013, 10477533, 22629021, 9654228, 26118460, 29255176, 27485560, 28438721, 17292394, 31737537, 31589614) -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 06, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The KCNQ1 c.1032G>A; p.Ala344= variant (rs1800171) is reported in the literature in individuals and families affected with long QT syndrome (Gao 2012, Kanters 1998, Tsuji 2007, Tsuji-Wakisaka 2011). This variant is also reported in ClinVar (Variation ID: 3135). It is only found on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. This is a synonymous variant in the last nucleotide of exon 7, and mRNA assays have shown this variant causes exon skipping (Tsuji 2007, Tsuji-Wakisaka 2011). Based on available information, this variant is considered to be pathogenic. References: Gao Y et al. Genotype-phenotype analysis of three Chinese families with Jervell and Lange-Nielsen syndrome. J Cardiovasc Dis Res. 2012 Apr;3(2):67-75. PMID: 22629021. Kanters JK et al. Novel donor splice site mutation in the KVLQT1 gene is associated with long QT syndrome. J Cardiovasc Electrophysiol. 1998 Jun;9(6):620-4. PMID: 9654228. Tsuji K et al. Mechanistic basis for the pathogenesis of long QT syndrome associated with a common splicing mutation in KCNQ1 gene. J Mol Cell Cardiol. 2007 Mar;42(3):662-9. PMID: 17292394. Tsuji-Wakisaka K et al. Identification and functional characterization of KCNQ1 mutations around the exon 7-intron 7 junction affecting the splicing process. Biochim Biophys Acta. 2011 Nov;1812(11):1452-9. PMID: 21810471. -

Long QT syndrome

Pathogenic:3

May 13, 2019

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant summary: KCNQ1 c.1032G>A (p.Ala344Ala) alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a 5' splicing donor site. Three predict the variant weakens a 5' donor site. At least two publications reported experimental evidence that this variant affects mRNA splicing (Murray 1999, Tsuji-Wakisaka 2011), causing a partial exon skipping, decreasing the wild type mRNA level to about 55% (Tsuji-Wakisaka 2011). The variant allele was found at a frequency of 4e-06 in 251186 control chromosomes (gnomAD). c.1032G>A has been reported in the literature in multiple individuals affected with Long QT Syndrome (Kanters 1998, Li 1998, Murray 1999, Tsuji-Wakisaka 2011), and in two large families the variant co-segregated with the disease (Li 1998, Murray 1999). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, and demonstrated significant reduction in currents compared to control (Tsuji-Wakisaka 2011). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Oct 16, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change affects codon 344 of the KCNQ1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the KCNQ1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs1800171, gnomAD 0.0009%). This variant has been observed in individuals with Jervell and Lange-Nielsen syndrome and/or long QT syndrome (PMID: 9654228, 10973849, 21810471, 22629021). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3135). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 7, but is expected to preserve the integrity of the reading-frame (PMID: 21810471). For these reasons, this variant has been classified as Pathogenic. -

Jan 08, 2024

All of Us Research Program, National Institutes of Health

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.1032G>A (p.Ala344=) variant in the KCNQ1 gene has been reported in multiple individuals with long QT syndrome and Jervell and Lange-Nielsen syndrome (PMID: 17292394, 9654228, 10973849, 29857160, 32893267). RNA studies have shown that this variant causes exon 7 skipping (PMID: 21810471). This variant has been demonstrated to disrupt protein function (PMID: 17292394). This variant has been reported in ClinVar as pathogenic (ID: 3135). The overall frequency of this variant in the population database (gnomAD) is 1/251186 chromosomes. Based on this evidence, the c.1032G>A (p.Ala344=) variant in the KCNQ1 gene has been classified as pathogenic. -

Long QT syndrome 2

Pathogenic:1

Feb 09, 2017

Center for Human Genetics, University of Leuven

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

ACMG score pathogenic -

Beckwith-Wiedemann syndrome

Pathogenic:1

May 04, 2022

Mendelics

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital long QT syndrome

Pathogenic:1

Jul 16, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The p.Ala344Ala variant in KCNQ1 has been reported in >20 heterozygous individuals with Long QT syndrome (LQTS) and in one compound heterozygous individual with Jervell and Lange-Nielsen syndrome (JLNS). It segregated with LQTS in > 10 relatives from multiple families (Kanters 1998, Struijk 2006, Tsuji 2007, Gao 2012, Itoh 2015, Vyas 2016, Robyns 2017). This variant has also been reported in ClinVar (Variation ID: 3135) and has been identified in 1/111614 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs1800171). This variant is located at the last base of exon 7, which is part of the 5’ splice region. Computational tools and functional studies using patient mRNAs suggest that the p.Ala344ala variant impacts splicing, resulting mainly in the skipping of exon 7 but other aberrant mRNA transcripts were also reported (Wuriyanghai 2018, Tsuji 2007). In summary, this variant meets criteria to be classified as pathogenic for LQTS in an autosomal dominant manner based upon presence in multiple affected individuals, segregation studies, predicted impact to the protein, and functional studies. ACMG/AMP criteria applied: PS4, PP1_Strong, PM4, PS3_Moderate, PM2. -

Cardiovascular phenotype

Pathogenic:1

Jul 18, 2024

Ambry Genetics

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.1032G>A pathogenic mutation (also known as p.A344A) is located in coding exon 7 of the KCNQ1 gene. This variant results from a G to A substitution at nucleotide position 1032. This nucleotide substitution does not change the amino acid at codon 344. However, this change occurs in the last base pair of coding exon 7, which makes it likely to have some effect on normal mRNA splicing. This alteration has been reported in multiple families with long QT syndrome (LQTS) and Jervell and Lange-Nielsen syndrome, including at least one reported de novo case of LQTS (Kanters JK et al. J. Cardiovasc. Electrophysiol., 1998 Jun;9:620-4; Murray A et al. Circulation, 1999 Sep;100:1077-84; Tsuji-Wakisaka K et al. Biochim. Biophys. Acta, 2011 Nov;1812:1452-9; Gao Y et al. J Cardiovasc Dis Res, 2012 Apr;3:67-75). RNA studies have demonstrated that this alteration leads to exon skipping with the loss of exon 7 as the most frequently observed effect (Murray A et al. Circulation, 1999 Sep;100:1077-84; Tsuji-Wakisaka K et al. Biochim. Biophys. Acta, 2011 Nov;1812:1452-9). In addition, in vitro functional studies have shown significant suppression of potassium channel currents (Tsuji-Wakisaka K et al. Biochim. Biophys. Acta, 2011 Nov;1812:1452-9). This nucleotide position is not well conserved in available vertebrate species. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Uncertain

(source)

DANN

Benign

0.95

PhyloP100

1.8

Mutation Taster

=22/78

disease causing (ClinVar)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

1.0

SpliceAI score (max)

0.49

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.49

Position offset: 15

DS_DL_spliceai

0.38

Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over