chr3:38592012:C>A Detail (hg19) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,592,012-38,592,012
hg38 chr3:38,550,521-38,550,521 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.5851G>T NP_000326.2:p.Val1951Leu
NM_198056.2:c.5851G>T NP_932173.1:p.Val1951Leu
NM_001099404.1:c.5851G>T NP_001092874.1:p.Val1951Leu
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.007
ToMMo:0.004
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600163 OMIM
HGNC 10593 HGNC
Ensembl ENSG00000183873 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12111308 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-01-08 no assertion criteria provided long QT syndrome germline Detail
Benign Likely benign 2015-07-01 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely benign 2014-06-01 no assertion criteria provided Brugada syndrome germline Detail
Likely benign 2014-08-15 no assertion criteria provided Ventricular tachycardia germline Detail
Likely benign 2013-06-24 criteria provided, single submitter atrial fibrillation,Brugada syndrome unknown Detail
Likely benign 2013-06-24 criteria provided, single submitter atrial fibrillation,Brugada syndrome unknown Detail
Benign 2015-08-05 criteria provided, single submitter germline Detail
Benign 2019-06-11 criteria provided, single submitter cardiomyopathy,long QT syndrome germline Detail
Benign 2019-06-11 criteria provided, single submitter cardiomyopathy,long QT syndrome germline Detail
Likely benign 2018-02-05 criteria provided, single submitter dilated cardiomyopathy 1E germline Detail
Likely benign 2018-02-05 criteria provided, single submitter Progressive familial heart block, type 1A germline Detail
Likely benign 2018-02-05 criteria provided, single submitter long QT syndrome 3 germline Detail
Likely benign 2018-02-05 criteria provided, single submitter Ventricular fibrillation, paroxysmal familial, type 1 germline Detail
Benign 2018-02-05 criteria provided, single submitter Sick sinus syndrome 1 germline Detail
Likely benign 2018-02-05 criteria provided, single submitter Brugada syndrome 1 germline Detail
Benign 2018-03-19 criteria provided, single submitter Cardiac arrhythmia germline Detail
Benign 2021-12-13 criteria provided, single submitter cardiomyopathy germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.120 Atrial Fibrillation Adverse Event NA CLINVAR Detail
0.240 Atrial fibrillation, familial, 10 Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. UNIPROT 18378609 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND not specified ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Brugada syndrome ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Dilated cardiomyopathy 1E ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Progressive familial heart block, type 1A ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Ventricular fibrillation, paroxysmal familial, type ... ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Sick sinus syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.5848G>T (p.Val1950Leu) AND Cardiomyopathy ClinVar Detail
NA DisGeNET Detail
Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs41315493 dbSNP
Genome
hg19
Position
chr3:38,592,012-38,592,012
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
44.89
Standard deviation of sample read depth (HGVD)
18.72
Number of reference allele (HGVD)
2397
Number of alternative allele (HGVD)
16
Allele Frequency (HGVD)
0.00663075010360547
Gene Symbol (HGVD)
SCN5A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs41315493
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0038
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
64
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8272
East Asian Allele Counts (ExAC)
25
East Asian Heterozygous Counts (ExAC)
25
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0030222437137330752
Chromosome Counts in All Race (ExAC)
115854
Allele Counts in All Race (ExAC)
627
Heterozygous Counts in All Race (ExAC)
615
Homozygous Counts in All Race (ExAC)
6
Allele Frequency in All Race (ExAC)
0.005411984048889119
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