3-38613787-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM1PM2PP2PP3BP4_Moderate
The ENST00000423572.7(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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T220A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000423572.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN5A | NM_000335.5 | c.659C>T | p.Thr220Ile | missense_variant | 6/28 | ENST00000423572.7 | NP_000326.2 | |
SCN5A | NM_001099404.2 | 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 | c.659C>T | p.Thr220Ile | missense_variant | 6/28 | 1 | NM_000335.5 | ENSP00000398266 | A1 | |
SCN5A | ENST00000413689.6 | c.703+188C>T | intron_variant | 5 | NM_001099404.2 | ENSP00000410257 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000663 AC: 162AN: 244430Hom.: 0 AF XY: 0.000611 AC XY: 81AN XY: 132490
GnomAD4 exome AF: 0.000862 AC: 1258AN: 1458692Hom.: 1 Cov.: 30 AF XY: 0.000816 AC XY: 592AN XY: 725282
GnomAD4 genome AF: 0.000630 AC: 96AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:3
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 | 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 | 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 | - - |
Cardiac arrhythmia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Aug 31, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Sep 23, 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. - |
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at