rs12720452

Positions:

chr3-38603758-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4

The NM_001099404.2(SCN5A):c.1844G>A(p.Gly615Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00053 in 1,537,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00028 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00056 ( 0 hom. )

Consequence

SCN5A
NM_001099404.2 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:12B:1O:1

Conservation

PhyloP100: 0.210

Variant links:

Genes affected

SCN5A (HGNC:10593): (sodium voltage-gated channel alpha subunit 5) The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene have been associated with long QT syndrome type 3 (LQT3), atrial fibrillation, cardiomyopathy, and Brugada syndrome 1, all autosomal dominant cardiac diseases. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2022]

SCN5A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP2

Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SCN5A. . Gene score misZ 2.7504 (greater than the threshold 3.09). Trascript score misZ 4.7729 (greater than threshold 3.09). GenCC has associacion of gene with progressive familial heart block, type 1A, Brugada syndrome, familial sick sinus syndrome, short QT syndrome, paroxysmal familial ventricular fibrillation, progressive familial heart block, long QT syndrome 3, familial atrial fibrillation, catecholaminergic polymorphic ventricular tachycardia, dilated cardiomyopathy, dilated cardiomyopathy 1E, arrhythmogenic right ventricular cardiomyopathy, Brugada syndrome 1, atrial standstill, familial isolated dilated cardiomyopathy, familial long QT syndrome, sick sinus syndrome 1.

BP4

Computational evidence support a benign effect (MetaRNN=0.36050773).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN5A	NM_001099404.2 linkuse as main transcript	c.1844G>A	p.Gly615Glu	missense_variant	12/28	ENST00000413689.6
SCN5A	NM_000335.5 linkuse as main transcript	c.1844G>A	p.Gly615Glu	missense_variant	12/28	ENST00000423572.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN5A	ENST00000413689.6 linkuse as main transcript	c.1844G>A	p.Gly615Glu	missense_variant	12/28	5	NM_001099404.2	P4
SCN5A	ENST00000423572.7 linkuse as main transcript	c.1844G>A	p.Gly615Glu	missense_variant	12/28	1	NM_000335.5	A1	Q14524-2

Frequencies

GnomAD3 genomes

AF:

0.000276

AC:

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

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:

0.000529

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000286

AC:

AN:

196144

Hom.:

AF XY:

0.000299

AC XY:

AN XY:

103844

show subpopulations

Gnomad AFR exome

AF:

0.000134

Gnomad AMR exome

AF:

0.000114

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000563

Gnomad FIN exome

AF:

0.0000556

Gnomad NFE exome

AF:

0.000518

Gnomad OTH exome

AF:

0.000219

GnomAD4 exome

AF:

0.000558

AC:

773

AN:

1385874

Hom.:

Cov.:

AF XY:

0.000533

AC XY:

362

AN XY:

679522

show subpopulations

Gnomad4 AFR exome

AF:

0.0000956

Gnomad4 AMR exome

AF:

0.0000842

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000397

Gnomad4 NFE exome

AF:

0.000689

Gnomad4 OTH exome

AF:

0.000456

GnomAD4 genome

AF:

0.000276

AC:

AN:

152120

Hom.:

Cov.:

AF XY:

0.000215

AC XY:

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.0000483

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000529

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.000432

Hom.:

Bravo

AF:

0.000264

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000595

AC:

ExAC

AF:

0.000207

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2Uncertain:12Benign:1Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 12, 2020	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2023	Reported in association with LQTS (Kapplinger et al., 2009; Marschall et al., 2019) and CPVT (Gerber et al., 2020), and as part of postmortem genetic testing for unexplained deaths (Albert et al., 2008; Methner et al., 2016; Sanchez et al., 2016; Munroe et al., 2018); Reported in patients with Brugada syndrome; however, at least one individual also harbored a second variant in the SCN5A gene that was deemed deleterious (Kapplinger et al., 2010; Le Scouarnec et al., 2015; Berthome et al., 2019); Identified in several individuals who developed torsades de pointe after exposure to a QT-prolonging drug (Yang et al., 2002; Ramirez et al., 2013); Identified in a patient with neonatal onset DCM who also harbored an additional variant in the VCL gene (Hawley et al., 2020); family studies identified the p.(G615E) variant in the proband's unaffected mother who was negative for the VCL variant, as well as in three siblings with no symptoms but reported to have a prolonged QT interval; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24055113, 19841300, 34461752, 22378279, 23414114, 25637381, 24713084, 23631430, 24613995, 15840476, 14760488, 19862833, 23861362, 27930701, 27435932, 22584458, 27153395, 26746457, 28412158, 29874177, 29728395, 28798025, 31262209, 30193851, 31737537, 32553227, 20129283, 19716085, 18071069, 11997281, 25650408, 32516855, 30203441, 30079003) -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2017	- -

not specified

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 11, 2019	The p.Gly615Glu variant in SCN5A has been reported in at least 10 individuals with LQTS, 4 individuals with sudden death, 1 individual with Brugada syndrome, 1 individual with HCM and 1 individual with delayed enhancement in LV (Albert 2008, Beyder 2010, Itoh 2016, Kapplinger 2009, Le Scouarnec 2015, Lieve 2013, Methner 2016, Ng 2013, Paulussen 2004, Sanchez 2016, Tester 2005, Yang 2002). In vitro functional studies provide some evidence that the p.Gly615Glu variant may impact protein function (Beyder 2014, Albert 2008). However, these types of assays may not accurately represent biological function. This variant has also been reported in ClinVar (Variation ID 67691) and has been identified in 50/106156 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs12720452). Computational prediction tools and conservation analysis suggest that the p.Gly615Glu variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, due to conflicting data, the p.Gly615Glu variant is uncertain. ACMG/AMP Criteria applied: PS4, PP3, PS3_S, BS1 (Richards 2015). -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 16, 2021	Variant summary: SCN5A c.1844G>A (p.Gly615Glu) results in a non-conservative amino acid change located in the Voltage-gated Na+ ion channel, cytoplasmic domain of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00028 in 199960 control chromosomes. The observed variant frequency is approximately 13 fold of the estimated maximal expected allele frequency for a pathogenic variant in SCN5A causing Long QT Syndrome With Sudden Cardiac Death phenotype (2.1e-05), strongly suggesting that the variant is benign. c.1844G>A has been reported in the literature in multiple LQTS patients, including some diagnosed with Sudden Cardiac Death and LQTS triggered by quinidine (e.g. Lieve_2013, Sanchez_2016, Methner_2016, Anderson_2017, Marschall_2019). In addition, this variant was also reported in one proband with neonatal DCM, one family member with episode of chest pain with normal QT interval, and three aymptomatic family members with prolonged QT interval (Hawley_2020). These data do not provide unequivocal conclusions about association of the variant with LQTS or other diseases. Functional studies have reported conflicting results with no effect on the peak amplitude of voltage-gated sodium current (Yang_2002), positive shifts in voltage dependence of activation, with altered activation kinetics and slower activation than wildtype associated with this variant (Beyder_2014), and disruptions in mechanosensitivity (Strege_2019). Ten clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (Pathogenic n=2, VUS n=8). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -

Long QT syndrome, drug-associated

Uncertain:1Benign:1

Likely benign, criteria provided, single submitter	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jun 24, 2013	- -
Uncertain significance, no assertion criteria provided	research	CSER _CC_NCGL, University of Washington	Jun 01, 2014	- -

Death in infancy

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Forensic Genetics Laboratory, Harris County Institute of Forensic Sciences

Mar 27, 2015

- -

Death in early adulthood

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Forensic Genetics Laboratory, Harris County Institute of Forensic Sciences

Mar 28, 2015

- -

Brugada syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Nov 01, 2022

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 615 of the SCN5A protein (p.Gly615Glu). This variant is present in population databases (rs12720452, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of SCN5A-related conditions (PMID: 11997281, 15840476, 19716085, 20129283, 23631430, 24613995, 30079003, 32516855). ClinVar contains an entry for this variant (Variation ID: 67691). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on SCN5A function (PMID: 11997281, 24613995, 31262209). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 25, 2023

The p.G615E variant (also known as c.1844G>A), located in coding exon 11 of the SCN5A gene, results from a G to A substitution at nucleotide position 1844. The glycine at codon 615 is replaced by glutamic acid, an amino acid with similar properties. This alteration has been reported in subjects with acquired long QT syndrome, long QT syndrome, Brugada syndrome, and dilated cardiomyopathy; however, in some cases, clinical details were limited and/or additional cardiac variants were detected (Yang P et al. Circulation, 2002 Apr;105:1943-8; Kapplinger JD et al. Heart Rhythm, 2009 Sep;6:1297-303; Lieve KV et al. Genet Test Mol Biomarkers, 2013 Jul;17:553-61; Le Scouarnec S et al. Hum. Mol. Genet., 2015 May;24:2757-63; Hawley MH et al. Hum Mutat, 2020 09;41:1577-1587). It has also been reported in sudden death and stillbirth cohorts (Albert CM et al. Circulation, 2008 Jan;117:16-23; Methner DN et al. Genome Res., 2016 Sep;26:1170-7; Munroe PB et al. Circ Genom Precis Med, 2018 01;11:e001817). This variant has also been seen in exome cohorts, as well as an irritable bowel syndrome cohort (Dorschner MO et al. Am J Hum Genet. 2013;93(4):631-40; Beyder A et al. Gastroenterology, 2014 Jun;146:1659-68; Amendola LM et al. Genome Res. 2015;25(3):305-15; Maxwell KN et al. Am. J. Hum. Genet., 2016 May;98:801-17). Functional studies have shown little or no impact on voltage function, but possible mechanosensitivity effects; however, the clinical relevance of these findings is uncertain (Yang P et al. Circulation, 2002 Apr;105:1943-8; Albert CM et al. Circulation, 2008 Jan;117:16-23; Strege PR et al. Channels (Austin), 2019 12;13:287-298). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

Long QT syndrome 3

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues

Apr 06, 2017

- -

Cardiac arrhythmia

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Dec 21, 2022

This missense variant replaces glycine with glutamic acid at codon 615 of the SCN5A protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown that this variant may alter sodium channel activation and inactivation kinetics (PMID: 18071069, 24613995) Additionally, one functional study has shown that the mutant channel affects mechanosensitivity of voltage-dependent gating compared to the wild type channel (PMID: 31262209). This variant has been reported in individuals affected with Brugada syndrome (PMID: 20129283), irritable bowel syndrome (PMID: 24613995) and sudden cardiac death (PMID: 18071069). This variant has been reported in an individual affected with long QT syndrome, who also carried a pathogenic variant in the KCNQ1 gene (PMID: 23631430) and in an individual affected with catecholaminergic polymorphic ventricular tachycardia (PMID: 32553227). This variant has also been reported in one individual affected with neonatal dilated cardiomyopathy and three individuals with prolonged QT intervals in one family (PMID: 32516855). This variant has been identified in 66/227496 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Congenital long QT syndrome

Other:1

not provided, no classification provided

literature only

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

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:14760488;PMID:15840476;PMID:19716085;PMID:19841300). 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 v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

CardioboostCm

Benign

0.0037

BayesDel_addAF

Benign

-0.082

BayesDel_noAF

Uncertain

0.070

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.61

.;.;.;.;.;D;.;.;.

Eigen

Benign

-0.035

Eigen_PC

Benign

-0.074

FATHMM_MKL

Benign

0.53

LIST_S2

Benign

0.77

.;T;T;T;T;T;T;.;T

M_CAP

Pathogenic

0.42

MetaRNN

Benign

0.36

T;T;T;T;T;T;T;T;T

MetaSVM

Uncertain

0.27

MutationAssessor

Uncertain

2.3

.;M;.;.;.;M;.;.;.

MutationTaster

Benign

0.71

N;N;N;N;N;N;N;N;N;N

PrimateAI

Benign

0.44

PROVEAN

Benign

-2.1

N;N;N;N;N;N;N;N;N

REVEL

Uncertain

0.63

Sift

Benign

0.091

T;T;T;T;T;T;T;T;T

Sift4G

Benign

0.66

T;T;T;T;T;T;T;T;T

Polyphen

0.85

P;D;.;P;.;D;D;.;.

Vest4

0.53

MVP

0.84

MPC

1.2

ClinPred

0.046

GERP RS

4.2

Varity_R

0.12

gMVP

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over