chr3:38620965:C>T Detail (hg19) (SCN5A, LOC110121269)

Information

Genome

Assembly Position
hg19 chr3:38,620,965-38,620,965
hg38 chr3:38,579,474-38,579,474 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001099404.1:c.3250G>A NP_001092874.1:p.Gly1084Ser
NM_001160160.1:c.3250G>A NP_001153632.1:p.Gly1084Ser
NM_000335.4:c.3250G>A NP_000326.2:p.Gly1084Ser
Summary

MGeND

Clinical significance 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:[No Data.]

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 tgv12112779 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
not provided no assertion provided sudden infant death syndrome germline Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2021-08-20 criteria provided, single submitter Sick sinus syndrome 1,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1,sudden infant death syndrome,Atrial fibrillation, familial, 10 unknown Detail
Uncertain significance 2024-01-17 criteria provided, single submitter not provided germline Detail
Uncertain significance 2023-06-15 criteria provided, single submitter Brugada syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.386 sudden infant death syndrome NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND SUDDEN INFANT DEATH SYNDROME ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.3247G>A (p.Gly1083Ser) AND Brugada syndrome 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
rs199473190 dbSNP
Genome
hg19
Position
chr3:38,620,965-38,620,965
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
962
Mean of sample read depth (HGVD)
20.29
Standard deviation of sample read depth (HGVD)
11.33
Number of reference allele (HGVD)
1922
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
0.0010395010395010396
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))
rs199473190
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0005
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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