rs45620037

Positions:

chr3-38613787-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PP2PP3BP4_Moderate

The NM_000335.5(SCN5A):c.659C>T(p.Thr220Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00084 in 1,611,012 control chromosomes in the GnomAD database, including 1 homozygotes. 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 0.00063 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00086 ( 1 hom. )

Consequence

SCN5A
NM_000335.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:6B:6O:1

Conservation

PhyloP100: 10.0

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 4.8279 (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.

PP3

Multiple lines of computational evidence support a deleterious effect 10: AlphaMissense, BayesDel_addAF, BayesDel_noAF, Cadd, Dann, Eigen, M_CAP, phyloP100way_vertebrate, PROVEAN, REVEL [when CardioboostCm, max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]

BP4

Computational evidence support a benign effect (MetaRNN=0.12240586).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN5A	NM_000335.5 linkuse as main transcript	c.659C>T	p.Thr220Ile	missense_variant	6/28	ENST00000423572.7	NP_000326.2
SCN5A	NM_001099404.2 linkuse as main transcript	c.703+188C>T		intron_variant		ENST00000413689.6	NP_001092874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN5A	ENST00000423572.7 linkuse as main transcript	c.659C>T	p.Thr220Ile	missense_variant	6/28	1	NM_000335.5	ENSP00000398266	A1	Q14524-2
SCN5A	ENST00000413689.6 linkuse as main transcript	c.703+188C>T		intron_variant		5	NM_001099404.2	ENSP00000410257	P4

Frequencies

GnomAD3 genomes

AF:

0.000631

AC:

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

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:

0.00349

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000808

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.000663

AC:

162

AN:

244430

Hom.:

AF XY:

0.000611

AC XY:

AN XY:

132490

show subpopulations

Gnomad AFR exome

AF:

0.0000669

Gnomad AMR exome

AF:

0.000147

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00394

Gnomad NFE exome

AF:

0.000631

Gnomad OTH exome

AF:

0.000336

GnomAD4 exome

AF:

0.000862

AC:

1258

AN:

1458692

Hom.:

Cov.:

AF XY:

0.000816

AC XY:

592

AN XY:

725282

show subpopulations

Gnomad4 AFR exome

AF:

0.0000897

Gnomad4 AMR exome

AF:

0.000135

Gnomad4 ASJ exome

AF:

0.0000384

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00464

Gnomad4 NFE exome

AF:

0.000871

Gnomad4 OTH exome

AF:

0.000564

GnomAD4 genome

AF:

0.000630

AC:

AN:

152320

Hom.:

Cov.:

AF XY:

0.000537

AC XY:

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.0000722

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00349

Gnomad4 NFE

AF:

0.000809

Gnomad4 OTH

AF:

0.000474

Alfa

AF:

0.000619

Hom.:

Bravo

AF:

0.000310

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000476

AC:

ExAC

AF:

0.000669

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2Uncertain:6Benign:6Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Uncertain:1Benign:3

Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 02, 2015	p.Thr220Ile in exon 6 of SCN5A: This variant has was initially believed to be di sease causing based on its detection 12 probands with a range of SCN5-related di sorders (CSD, DCM, LQTS) and absence from controls (Benson 2003, Olson 2005, Kap plinger 2010, Oleson 2012, Crottie 2013, GeneDx, pers. comm.) as well as some in vitro functional data (Benson 2003, Butters 2010, Gui 2010). However, the varia nt is unlikely disease causing on its own based on its frequency in the general population (detected in 0.7% (30/4290) of European (Finnish) chromosomes and 0.1 % (46/43544) European (Non-Finnish) chromosomes screened by the Exome Aggregatio n Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs45620037). It remain s possible that the Thr220Ile variant represents a modifier or risk allele. -
Likely benign, criteria provided, single submitter	clinical testing	Blueprint Genetics	Feb 24, 2015	- -
Uncertain significance, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Mar 12, 2012	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. p.Thr220Ile (c.659 C>T) in the SCN5A gene (NM_198056.2) Given the abundance of case data, it seems likely that this variant contributes to disease in some fashion. What is challenging is determining whether it is sufficient on its own to cause disease or whether it is a modifer of some sort, given the presence of another variant in several reported cases and the presence of the variant in general population samples. Given this, we consider this variant a variant of uncertain significance, probably disease causing. The variant has been seen in one patient with sick sinus syndrome who was a compound heterozygote for this variant and a nonsense variant, one family with familial DCM, two patients with Brugada (one was a compound heterozygote for this variant and another missense variant), one patient with early-onset lone atrial fibrillation, two unrelated cases of pediatric onset atrial standstill (both cases were compound heterozygotes), one case of intrauterine death, one case of sudden unexplained death, and one case of irritable bowel syndrome. Using a candidate gene approach, Benson et al (2003) sequenced SCN5A in 10 patients with pediatric onset sick sinus syndrome from 7 families. Probands from three of the families were compound heterozygotes for two SCN5A variants (6 variants in total). One proband inherited p.Thr220Ile from his father and p.Arg1623Ter from his mother. His mother and two other maternal relatives who carry p.Arg1623Ter have first degree heart block. The two other maternal relatives also had prolonged QRS. His father was not available for study, however the paternal grandmother carried p.Thr220Ile and had a normal evaluation. Ancestry is not noted. The researchers are from various American academic medical centers. Olson et al (2005) observed the variant in one of 156 unrelated patients with DCM who underwent analysis of SCN5A. The patient had familial DCM (ischemic disease was ruled out) with atrial fibrillation and heart block. He never had documented ventricular tachycardia. The authors do not note if an arrhythmic phenotype preceded the cardiomyopathic phenotype. A first cousin had DCM, incomplete bundle branch block and also carried the variant. Ancestry is not noted. The patients were seen at Mayo in Minnesota or Latter Day Saints in Utah. The variant is reported in a compendium of SCN5A variants seen in individuals referred for Brugada syndrome genetic testing at various centers around the world (Kapplinger et al 2010). The authors note that patients were included if the physician who referred for genetic tesitng had made a possible or definite diagnosis of Brugada. Phenotype was not confirmed by the investigators so presumably some individuals included in the compendium do not in fact have Brugada syndrome. Two patients carried the variant. One patient was studied by the Brugada group and the other was studied by a Dutch group (likely same case reported by the Dutch group in Amin et al 2011). One patient also carried another SCN5A variant, p.Glu439Lys. He was diagnosed with Brugada at 26 years of age. Oleson et al (2012) observed the variant in 1 of 192 individuals with early onset lone atrial fibrillation. The patient had paroxysmal lone atrial fibrillation starting at 35 years of age. QTc was 422 ms, sodium blocking challenge (ex. Procainamide) was not done, and there was no family history of atrial fibrillation. Individual ancestry is not reported, but the subjects were recruited in Denmark. At the 2014 HRS meeting Baskar et al reported an 11yo girl with atrial standstill who was a compound heterozygote for this variant and a frameshift in SCN5A. The missense variant was inherited fr -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 30, 2024	Variant summary: SCN5A c.659C>T (p.Thr220Ile) results in a non-conservative amino acid change located in the Ion-transport domain (IPR005821) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00065 in 250790 control chromosomes. The observed variant frequency is approximately 6.5-fold of the estimated maximal expected allele frequency for a pathogenic variant in SCN5A causing Arrhythmia phenotype (0.0001), suggesting that the variant is benign. c.659C>T has been reported in the literature in individuals affected with Arrhythmia and other cardiac phenotypes (e.g. Benson_2003, Olson_2005, Kapplinger_2010, Amin_2011, Olesen_2012, Baskar_2014, Celestino-Soper_2015, Ceyhan-Birsoy_2015, Marschall_2019, Raju_2019), but without strong evidence for causality. In several of the reports, the variant was identified in unaffected family members, indicating that the variant may not co-segregate with disease (e.g. Benson_2003, Baskar_2014). In addition, co-occurrences with other pathogenic/likely pathogenic variants have been reported [SCN5A c.3142_3153delins11 (Baskar_2014); SCN5A p.Arg1623X (Benson_2003); SCN5A c.3512-1G>C (internal sample)], providing supporting evidence for a benign role. Several publications report experimental evidence evaluating an impact on protein function and indicate that the variant may alter the properties or functions of sodium channels to varying degrees in-vitro (e.g. Benson_2003, Butters_2010, Gui_2010). The following publications have been ascertained in the context of this evaluation (PMID: 15671429, 20129283, 14523039, 20539757, 20448214, 22677073, 21273195, 24055113, 23571586, 22685113, 25637381, 24784157, 24762805, 25171853, 26636822, 27066507, 24613995, 31737537, 31337358, 32048431). ClinVar contains an entry for this variant (Variation ID: 9396). Based on the evidence outlined above, the variant was classified as likely benign. -

not provided

Uncertain:1Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 17, 2024	Reported in multiple patients with several different clinical phenotypes, including cardiomyopathy, sick sinus syndrome (SSS), Brugada syndrome, Long QT syndrome (LQTS), intrauterine fetal demise (IUFD), sudden death, and complete heart block; however, several of these individuals also harbored a second variant in SCN5A or in another gene, and some individuals who harbored only the p.(T220I) variant were clinically unaffected (PMID: 14523039, 15671429, 20129283, 21273195, 23571586, 24136861, 26636822, 26884609, 24762805, 26743238, 29709244, 27332903, 27066507, 32048431, 20539757, 25351510, 31737537, 22677073); Published studies examined the functional effect of the p.(T220I) variant, with the general conclusion that this variant impairs sodium ion channel function; however, it is unclear how these studies may translate to a pathogenic role in vivo (PMID: 20539757, 14523039, 20448214, 38196587); 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: 26636822, 24055113, 22685113, 20448214, 23414114, 24613995, 24784157, 25637381, 25171853, 20129283, 23571586, 21273195, 15671429, 24136861, 26884609, 28150151, 34426522, 30203441, 20539757, 14523039, 37937776, 29709244, 27332903, 26743238, 32048431, 31737537, 24762805, 25351510, 22677073, 35197637, 31337358, 27066507, 20384651, 21596231, 22581653, 24059039, 38196587) -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 27, 2024	- -

Dilated cardiomyopathy 1E

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 26, 2005

- -

Sick sinus syndrome 1

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 26, 2005

- -

SCN5A-related disorder

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Primary familial dilated cardiomyopathy

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Apr 21, 2017

- -

AV junctional rhythm

Uncertain:1

Uncertain significance, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

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

Feb 17, 2018

- -

Cardiovascular phenotype

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

May 18, 2021

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Cardiac arrhythmia

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Aug 31, 2018

- -

Brugada 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 Brugada syndrome in the following publications (PMID:14523039;PMID:15671429;PMID:20129283;PMID:20448214;PMID:20539757;PMID:22685113). 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

Pathogenic

0.93

CardioboostCm

Benign

0.031

BayesDel_addAF

Pathogenic

0.24

BayesDel_noAF

Pathogenic

0.49

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.97

.;D;.

Eigen

Pathogenic

0.83

Eigen_PC

Pathogenic

0.77

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.94

D;D;D

M_CAP

Pathogenic

0.92

MetaRNN

Benign

0.12

T;T;T

MetaSVM

Pathogenic

1.1

MutationAssessor

Uncertain

2.2

M;M;.

MutationTaster

Benign

1.0

A;A;A;A;A;A;A;A;A;A

PROVEAN

Pathogenic

-5.8

D;D;D

REVEL

Pathogenic

0.96

Sift

Pathogenic

0.0

D;D;D

Sift4G

Benign

0.11

T;T;T

Polyphen

1.0

D;D;.

Vest4

0.95

MVP

0.98

ClinPred

0.14

GERP RS

4.3

Varity_R

0.91

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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