chr3:38597925:C>T Detail (hg38) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,639,416-38,639,416 View the variant detail on this assembly version.
hg38 chr3:38,597,925-38,597,925

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.2066G>A NP_000326.2:p.Arg689His
NM_198056.2:c.2066G>A NP_932173.1:p.Arg689His
NM_001099404.1:c.2066G>A NP_001092874.1:p.Arg689His
Summary

MGeND

Clinical significance Likely benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Uncertain significance
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 tgv12113530 TogoVar
COSMIC COSM2986674 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely benign brugada syndrome germline MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2024-01-28 criteria provided, multiple submitters, no conflicts not provided germline Detail
Uncertain significance 2018-04-05 criteria provided, single submitter long QT syndrome germline unknown Detail
Uncertain significance 2015-08-03 criteria provided, single submitter not specified germline Detail
Uncertain significance 2023-02-06 criteria provided, single submitter germline Detail
Uncertain significance 2019-01-07 criteria provided, single submitter SCN5A-Related Arrhythmias germline Detail
Uncertain significance 2019-05-28 criteria provided, single submitter Brugada syndrome 1 unknown Detail
Uncertain significance 2024-02-05 criteria provided, multiple submitters, no conflicts Cardiac arrhythmia germline Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
Uncertain significance 2021-10-13 criteria provided, single submitter Sick sinus syndrome 1,Atrial fibrillation, familial, 10,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.335 long QT syndrome NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND Long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND not specified ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND SCN5A-Related Arrhythmias ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2066G>A (p.Arg689His) AND multiple conditions ClinVar Detail
NA 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
rs199473145 dbSNP
Genome
hg38
Position
chr3:38,597,925-38,597,925
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
156.02
Standard deviation of sample read depth (HGVD)
72.52
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
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))
rs199473145
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0006
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.3185717597959656E-4
Chromosome Counts in All Race (ExAC)
120204
Allele Counts in All Race (ExAC)
14
Heterozygous Counts in All Race (ExAC)
14
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.1646866992778943E-4
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