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rs7626962

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(G;G) 0 common in clinvar
(G;T) 3 increased susceptibility to long QT syndrome
(T;T) 4 increased susceptibility to long QT syndrome
ReferenceGRCh38 38.1/141
Chromosome3
Position38579416
GeneSCN5A
is asnp
is mentioned by
dbSNPrs7626962
ebirs7626962
HLIrs7626962
Exacrs7626962
Varsomers7626962
Maprs7626962
PheGenIrs7626962
hapmaprs7626962
1000 genomesrs7626962
hgdprs7626962
ensemblrs7626962
gopubmedrs7626962
geneviewrs7626962
scholarrs7626962
googlers7626962
pharmgkbrs7626962
gwascentralrs7626962
openSNPrs7626962
23andMers7626962
23andMe allrs7626962
SNP Nexus

SNPshotrs7626962
SNPdbers7626962
MSV3drs7626962
GWAS Ctlgrs7626962
GMAF0.01194
Max Magnitude4

rs7626962, also known as Ser1103Tyr or S1103Y, is a SNP in the cardiac sodium channel SCN5A gene.

Although relatively common (for a rare allele; 10 - 20% of individuals) in those of African ancestry, in all populations the rs7626962(T) allele has been reported to increase the risk for cardiac issues such as long QT syndrome but also arrhythmias and even sudden infant death syndrome.

The odds ratio for displaying signs of arrhythmia for anyone carrying a rs7626962(T) allele is reported as 8.7 (CI 3.2 - 23.9) [PMID 12193783]; as for sudden infant death syndrome, at least in African-ancestry populations, the odds ratio for the same allele is reported as 4.9, leading to an odds ratio of 24 for rs7626962(T;T) homozygotes.[PMID 16453024OA-icon.png]

This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about.[PMID 23788249OA-icon.png]

? (G;G) (G;T) (T;T) 28
OMIM600163
DescLONG QT SYNDROME 3, ACQUIRED, SUSCEPTIBILITY TO
Variant0024
Relatedalso



ClinVar
Risk rs7626962(T;T)
Alt rs7626962(T;T)
Reference rs7626962(G;G)
Significance Other
Disease Long qt syndrome 3 SUDDEN INFANT DEATH SYNDROME not specified not provided Cardiac arrhythmia Brugada syndrome
Variation info
Gene SCN5A
CLNDBN Long qt syndrome 3, acquired, susceptibility to SUDDEN INFANT DEATH SYNDROME not specified not provided Cardiac arrhythmia Brugada syndrome
Reversed 0
HGVS NC_000003.11:g.38620907G>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000009992.2, RCV000009993.2, RCV000041615.4, RCV000058563.2, RCV000171820.2, RCV000204216.1,



[PMID 19214780OA-icon.png] In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs).


[PMID 19530973OA-icon.png] Genetic variation in the rhythmonome: ethnic variation and haplotype structure in candidate genes for arrhythmias.


[PMID 21347284OA-icon.png] Genome-wide association studies of the PR interval in African Americans.


[PMID 12193783] Variant of SCN5A sodium channel implicated in risk of cardiac arrhythmia.


[PMID 15161528] Single nucleotide polymorphisms of the SCN5A gene in Han Chinese and their relation with Brugada syndrome.


[PMID 19841300OA-icon.png] Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants.


GET Evidence
SCN5A-S1103Y
aa_change Ser1103Tyr
aa_change_short S1103Y
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.015625
summary This is a common variant in individuals of African descent (African American allele frequency 6.8%). It is associated with an increased risk of cardiac arrhythmia (odds ratio of 8.7 for both homozygous and heterozygous carriers) and of sudden infant death syndrome (24-fold increase for homozygous).