chr3:38627472:C>T Detail (hg19) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,627,472-38,627,472
hg38 chr3:38,585,981-38,585,981 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.2497G>A NP_000326.2:p.Gly833Arg
NM_198056.2:c.2497G>A NP_932173.1:p.Gly833Arg
NM_001099404.1:c.2497G>A NP_001092874.1:p.Gly833Arg
Summary

MGeND

Clinical significance
Variant entry
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 Conflicting classifications of pathogenicity
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 tgv12113199 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2024-01-24 criteria provided, conflicting interpretations not provided germline Detail
Uncertain significance 2014-06-01 no assertion criteria provided long QT syndrome germline Detail
Uncertain significance 2015-08-05 criteria provided, single submitter Brugada syndrome,long QT syndrome 3 unknown Detail
Uncertain significance 2015-08-05 criteria provided, single submitter Brugada syndrome,long QT syndrome 3 unknown Detail
Uncertain significance 2019-05-28 criteria provided, single submitter Brugada syndrome 1 unknown Detail
Uncertain significance 2023-11-20 criteria provided, multiple submitters, no conflicts Cardiac arrhythmia germline Detail
Uncertain significance 2023-11-16 criteria provided, single submitter germline 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.2497G>A (p.Gly833Arg) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.2497G>A (p.Gly833Arg) AND Long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.2497G>A (p.Gly833Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2497G>A (p.Gly833Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.2497G>A (p.Gly833Arg) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.2497G>A (p.Gly833Arg) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.2497G>A (p.Gly833Arg) AND Cardiovascular phenotype 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
rs45475899 dbSNP
Genome
hg19
Position
chr3:38,627,472-38,627,472
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
108.19
Standard deviation of sample read depth (HGVD)
54.10
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))
rs45475899
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0003
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4666050381326557E-4
Chromosome Counts in All Race (ExAC)
121172
Allele Counts in All Race (ExAC)
20
Heterozygous Counts in All Race (ExAC)
20
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.6505463308355065E-4
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