11-2583544-C-T

Variant names:

• chr11-2583544-C-T
• rs199472763
• NM_000218.3:c.1031C>T

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PM1 PM5 PP2 PP3 PP5_Very_Strong

The NM_000218.3(KCNQ1):​c.1031C>T​(p.Ala344Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,607,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A344T) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000055 (0 hom.)
• Consequence: KCNQ1 NM_000218.3 missense, splice_region
• Scores: Splicing: ADA: 0.9786
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:13 O:1
• Conservation: PhyloP100: 7.38
• Publications: 31 publications found

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

ACMG classification

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PM1: In a hotspot region, there are 24 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 14 uncertain in NM_000218.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-2583543-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 449042.
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 212 curated pathogenic missense variants (we use a threshold of 10). The gene has 12 curated benign missense variants. Gene score misZ: 1.8321 (below the threshold of 3.09). Trascript score misZ: 0.90233 (below the threshold of 3.09). GenCC associations: The gene is linked to short QT syndrome type 2, long QT syndrome 1, Jervell and Lange-Nielsen syndrome 1, long QT syndrome, short QT syndrome, Jervell and Lange-Nielsen syndrome, hypertrophic cardiomyopathy, familial atrial fibrillation, atrial fibrillation, familial, 3.
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 11-2583544-C-T is Pathogenic according to our data. Variant chr11-2583544-C-T is described in ClinVar as Pathogenic. ClinVar VariationId is 52936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000218.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNQ1	NM_000218.3	MANE Select	c.1031C>T	p.Ala344Val	missense splice_region	Exon 7 of 16	NP_000209.2
	KCNQ1	NM_001406836.1		c.1031C>T	p.Ala344Val	missense splice_region	Exon 7 of 15	NP_001393765.1
	KCNQ1	NM_001406837.1		c.761C>T	p.Ala254Val	missense splice_region	Exon 8 of 17	NP_001393766.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNQ1	ENST00000155840.12	TSL:1 MANE Select	c.1031C>T	p.Ala344Val	missense splice_region	Exon 7 of 16	ENSP00000155840.2
	KCNQ1	ENST00000335475.6	TSL:1	c.650C>T	p.Ala217Val	missense splice_region	Exon 7 of 16	ENSP00000334497.5
	KCNQ1	ENST00000713725.1		c.890C>T	p.Ala297Val	missense splice_region	Exon 6 of 15	ENSP00000519029.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152222 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000550 AC: 8 AN: 1455416 Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3 AN XY: 724372

African (AFR) AF: 0.00 AC: 0 AN: 33336

American (AMR) AF: 0.00 AC: 0 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26106

East Asian (EAS) AF: 0.00 AC: 0 AN: 39656

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86126

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53286

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5752

European-Non Finnish (NFE) AF: 0.00000633 AC: 7 AN: 1106262

Other (OTH) AF: 0.00 AC: 0 AN: 60178

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152222 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74362

African (AFR) AF: 0.0000241 AC: 1 AN: 41460

American (AMR) AF: 0.00 AC: 0 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68030

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Long QT syndrome 1 Pathogenic:4

Aug 11, 2023

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1031C>T variant in KCNQ1 has previously been reported in individuals with long QT syndrome (PMID: 9386136, 28944242, 31737537, 34505893) and it has been deposited in ClinVar [ClinVar ID: 52936] as Pathogenic by multiple submitters with affected status provided. The c.1031C>T variant is observed in 1 allele (~0.00017% minor allele frequency with 0 homozygote) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8, All of Us), suggesting it is not a common benign variant in the populations represented in those databases. The c.1031C>T variant in KCNQ1 is located in exon 7 of this 16-exon gene and is predicted to replace an evolutionarily conserved alanine amino acid with valine at position 344 (p.(Ala344Val) in the ion transport domain of the encoded protein [UniProt ID: P51787]. Functional studies demonstrated loss of potassium channel function (PMID: 34505893). Different missense variants affecting the same aminoacid residue (p.Ala344) and neighbouring residues within the S segment have been reported in individuals with long QT syndrome in the literature [PMID: 28349240]. Based on available evidence this c.1031C>T p.(Ala344Val) variant identified in KCNQ1 is classified as Pathogenic.

Aug 01, 2023

Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Dec 18, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jun 11, 2020

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_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0103 - Both loss- and gain-of-function are known mechanisms of disease for this gene (PMID: 19632626). (N) 0104 - Dominant Negative is a mechanism of disease for this gene. Long QT syndrome has been associated with variants resulting in both loss-of-function and dominant negative effects (PMID: 19632626). (N) 0108 - This gene is known to be associated with both recessive and dominant disease. Long QT syndrome is caused predominantly by heterozygous pathogenic variants (OMIM). (N) 0200 - Variant is predicted to result in a missense amino acid change from an alanine to a valine (exon 7). (N) 0251 - Variant is heterozygous. (N) 0302 - Variant is present in gnomAD <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (P) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (N) 0600 - Variant is located in an annotated domain or motif (S6 transmembrane helix of the ion transport domain; NCBI, PDB, Decipher, PMID: 10508236). (N) 0703 - Comparable variants have moderate previous evidence for pathogenicity. At least two different variants in the same codon resulting in a change to a threonine and a glycine have been reported as likely pathogenic (ClinVar). (P) 0801 - Strong previous evidence of pathogenicity in unrelated individuals. This variant has been has described as a mild variant and has been previously reported as pathogenic in multiple patients with long QT syndrome (ClinVar, LOVD, PMID: 10508236, PMID: 28944242). (P) 1002 - Moderate functional evidence supporting abnormal protein function. Studies show that this variant induces voltage-dependent inactivation in KCNQ1 channels and shifts the voltage dependence of KCNQ1/KCNE1 complex activation (PMID: 16931984). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

Long QT syndrome Pathogenic:4

Apr 18, 2025

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.1031C>T (p.Ala344Val) results in a non-conservative amino acid change in the Ion transport domain (IPR005821) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens the canonical 5' donor site. One predict the variant creates the canonical 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251186 control chromosomes. c.1031C>T has been observed at a heterozygous state in multiple families affected with long QT syndrome 1 (examples, Donger_1997 and Schwartz_2021) and at a homozygous state in at least three individuals affected with severe long QT syndrome without hearing loss (example, Al-Hassnan_2017). In the families with homozygous affected, the variant was also observed at a heterozygous state in 7 family members including consanguineous parents, who reported no severe arrhythmic events such as syncope, but the QTC intervals appeared to be prolonged (Al-Hassnan_2017). These data indicate that the variant is very likely to be associated with disease. c.1031C>T has also been observed in multiple unaffected heterozygous individuals (Schwartz_2021), suggesting a reduced penetrance for long QT syndrome. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in a voltage-dependent inactivation of the macroscopic current in X. Oocytes and CHO cells (Siebrands_2006). The following publications have been ascertained in the context of this evaluation (PMID: 28438721, 9386136, 34505893, 16931984). ClinVar contains an entry for this variant (Variation ID: 52936). Based on the evidence outlined above, the variant was classified as pathogenic.

Jan 08, 2024

Dept of Medical Biology, Uskudar University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

Criteria: PS4_Strong, PS3_Moderate, PM1, PM2, PP3

Aug 16, 2023

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been reported in multiple individuals with long QT syndrome (PMID: 9386136, 15466642, 15840476, 19716085, 9570196, 17470695, 32893267, 36102233). This variant is absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant is located in a well-established functional domain of the protein where other pathogenic or likely pathogenic variants have been described (PMID: 19716085). It is predicted to be deleterious by in silico analysis. Functional studies suggest that this variant results in a deleterious effect on the protein (PMID: 16931984).

Jan 19, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 344 of the KCNQ1 protein (p.Ala344Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 9386136, 16922724, 17088455, 17470695, 19490272, 24217263). ClinVar contains an entry for this variant (Variation ID: 52936). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on KCNQ1 protein function. Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 16931984). For these reasons, this variant has been classified as Pathogenic.

not provided Pathogenic:3

Jul 16, 2015

Stanford Center for Inherited Cardiovascular Disease, Stanford University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. KCNQ1 p.Ala344Val This variant has been published in multiple cases of long QT syndrome. Donger et al (1997) reported the variant in 6 members of one family with long QT syndrome. It’s not clear how many of those family members actually had clinically diagnosed long QT. The average QTc among those family members was 471 ms (+/-32) and 2 of the 6 carriers were symptomatic (syncope). Tester et al (2005) reported the variant in three cases of long QT syndrome referred to Mayo Clinic’s Sudden Death Genomics Laboratory for genetic testing. In a study on genotype-phenotype correlations, Moss et al (2007) reported 17 individuals with this variant, though it is not clear if they all had a clinical diagnosis of long QT syndrome. Another missense variant at the same codon has been reported in someone with long QT syndrome: p.Ala344Glu (Tester et al 2005). Tester et al (2005) did not see the variant in more than 750 control individuals of varied ancestry. Donger et al (1997) did not observe the variant in 100 control subjects, for a total of 1050 control individuals. As of Oct 2013: It is not present in the NHLBI Exome Sequencing Project dataset of approximately 6500 individuals of Caucasian and African American ancestry. Based on these data it is very likely that this variant causes long QT syndrome and that the risk of cardiac events is increased because of the location of this variant. It affects a highly conserved amino acid residue in an important functional domain of the protein: the S6 transmembrane domain. Of note, variants like this one that are located in the transmembrane region of the channel are correlated with a higher risk of cardiac events (hazard ratio 2.06), independent of traditional clinical risk factors such as age, gender, and QTc length (Moss et al 2007).

May 17, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect on KCNQ1 channel function (Siebrands et al., 2006); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15840476, 19716085, 29444113, 16931984, 12388934, 22095730, 15466642, 9386136, 17470695, 28944242, 9570196, 29033053, 31589614, 28438721, 31737537, 34505893)

Jul 31, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP3, PM2, PS3, PS4

Cardiovascular phenotype Pathogenic:1

Jul 25, 2025

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.A344V pathogenic mutation (also known as c.1031C>T), located in coding exon 7 of the KCNQ1 gene, results from a C to T substitution at nucleotide position 1031. The alanine at codon 344 is replaced by valine, an amino acid with similar properties. This variant was reported in individual(s) with features consistent with long QT syndrome (LQTS) (Donger C et al. Circulation. 1997;96(9):2778-81; Choi G et al. Circulation. 2004;110(15):2119-24; Shimizu W et al. J. Am. Coll. Cardiol. 2004;44:117-25; Tester DJ et al. Heart Rhythm. 2005;2(5):507-17; Millat G et al. Clin. Genet. 2006;70(3):214-27; Moss AJ et al. Circulation. 2007;115(19):2481-9; Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303; Schwartz PJ et al. Eur Heart J. 2021 12;42(46):4743-4755). This variant has also been detected in the homozygous state in several individuals with severe LQTS phenotypes reminiscent recessive Jervell and Lange-Nielsen syndrome (JLNS), but without hearing loss (Al-Hassnan ZN et al. Heart Rhythm. 2017;epub; Bdier AT et al. Mol Gen & Gen Med. 2017:epub). Asymptomatic heterozygous carriers of this variant have also been detected, suggesting it may result in a mild phenotype and/or exhibit reduced penetrance in the heterozygous state in some cases (Al-Hassnan ZN et al. Heart Rhythm. 2017;epub; Schwartz PJ et al. Eur Heart J. 2021 12;42(46):4743-4755). In multiple assays testing KCNQ1 function, this variant showed functionally abnormal results (Siebrands CC et al. Anesthesiology. 2006 Sep;105(3):511-20; Heijman J et al. Circ. Res. 2012 Jan;110(2):211-9; Schwartz PJ et al. Eur Heart J. 2021 12;42(46):4743-4755). Based on internal structural analysis, this variant is anticipated to disrupt a region of known function (Sun J et al. Cell. 2020 01;180(2):340-347.e9; Sun J et al. Cell. 2017 Jun;169(6):1042-1050.e9). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

Cardiac arrhythmia Pathogenic:1

Oct 03, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces alanine with valine at codon 344 of the KCNQ1 protein. This variant is found within a highly conserved region in transmembrane domain S6 (a.a. 328-348). Rare non-truncating variants in this region have been shown to be significantly overrepresented in individuals with long QT syndrome (PMID: 32893267). Functional studies have shown that this variant affects gating properties and increases channel sensitivity to anesthetics (PMID: 16931984, 32015334 ). This variant has been reported in heterozygous state in over ten unrelated individuals affected with long QT syndrome (PMID: 9386136, 15840476, 19716085, 20851114, 24217263, 26669661, 27920829, 32298319, 32893267, 34505893, 34884666) and in homozygous state in at least three individuals affected with severe long QT syndrome without hearing loss (PMID: 28438721, 28944242). This variant has been report to be a de novo occurrence in a child with severe long QT syndrome in compound heterozygous state with p.Ala300Thr variant in the same gene (PMID: 34884666). This variant has also been observed in over twenty unaffected heterozygous individuals (PMID: 9386136, 28438721, 28944242, 34505893). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

Congenital long QT syndrome Other:1

Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:9386136;PMID:15466642;PMID:15840476;PMID:19716085;PMID:9570196;PMID:17470695). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
CardioboostArm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	35
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.96	D
Eigen	Uncertain	0.50
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Pathogenic	0.98	D
M_CAP	Pathogenic	0.90	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Benign	1.1	L
PhyloP100		7.4
PrimateAI	Pathogenic	0.88	D
PROVEAN	Uncertain	-3.6	D
REVEL	Pathogenic	0.91
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.93
MutPred		0.87		Loss of glycosylation at S349 (P = 0.2359)
MVP		0.98
MPC		1.2
ClinPred		0.97	D
GERP RS		3.8
Varity_R		0.94
gMVP		0.96
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.98
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs199472763; hg19: chr11-2604774;