chr3:38585981:C>T Detail (hg38) (SCN5A)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr3:38,627,472-38,627,472 View the variant detail on this assembly version. |
hg38 | chr3:38,585,981-38,585,981 |
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 |
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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 | Conflicting classifications of pathogenicity |
Review star | ![]() |
Show details |
Disease area statistics
MGeND
Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
---|---|---|---|---|---|---|---|---|---|
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other |
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MGS000001
(TMGS000178) |
Kenjiro Kosaki | Keio University |
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
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2024-01-24 | criteria provided, conflicting interpretations | not provided |
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Detail |
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2014-06-01 | no assertion criteria provided | long QT syndrome |
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Detail |
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2015-08-05 | criteria provided, single submitter | Brugada syndrome,long QT syndrome 3 |
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Detail |
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2015-08-05 | criteria provided, single submitter | Brugada syndrome,long QT syndrome 3 |
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Detail |
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2019-05-28 | criteria provided, single submitter | Brugada syndrome 1 |
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Detail |
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2023-11-20 | criteria provided, multiple submitters, no conflicts | Cardiac arrhythmia |
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Detail |
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2023-11-16 | criteria provided, single submitter |
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Detail |
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
0.335 | long QT syndrome | NA | CLINVAR | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
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
- hg38
- Position
- chr3:38,585,981-38,585,981
- 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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