chr3:38550521:C>T Detail (hg38) (SCN5A)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:38,592,012-38,592,012 View the variant detail on this assembly version. |
| hg38 | chr3:38,550,521-38,550,521 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000335.4:c.5851G>A | NP_000326.2:p.Val1951Met |
| NM_198056.2:c.5851G>A | NP_932173.1:p.Val1951Met | |
| NM_001099404.1:c.5851G>A | NP_001092874.1:p.Val1951Met |
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 | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
not provided
|
no assertion provided | atrial fibrillation |
germline
|
Detail | |
Uncertain significance
|
2023-12-22 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Uncertain significance
|
2015-08-31 | criteria provided, single submitter | long QT syndrome 2 |
germline
|
Detail |
Likely benign
|
2022-11-17 | criteria provided, single submitter |
germline
|
Detail | |
|
Uncertain significance
|
2017-04-28 | criteria provided, single submitter | Brugada syndrome 1 |
germline
|
Detail |
|
Uncertain significance
|
2017-04-28 | criteria provided, single submitter | Sick sinus syndrome 1 |
germline
|
Detail |
|
Uncertain significance
|
2017-04-28 | criteria provided, single submitter | Ventricular fibrillation, paroxysmal familial, type 1 |
germline
|
Detail |
|
Uncertain significance
|
2017-04-28 | criteria provided, single submitter | Progressive familial heart block, type 1A |
germline
|
Detail |
|
Uncertain significance
|
2017-04-28 | criteria provided, single submitter | dilated cardiomyopathy 1E |
germline
|
Detail |
|
Likely benign
|
2017-04-28 | criteria provided, single submitter | long QT syndrome 3 |
germline
|
Detail |
|
Uncertain significance
|
2022-09-12 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Likely benign
|
2018-12-06 | criteria provided, single submitter | Cardiac arrhythmia |
germline
|
Detail |
|
Uncertain significance
|
2023-05-16 | 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
| Descrption | Source | Links |
|---|---|---|
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Atrial fibrillation | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND not provided | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Long QT syndrome 2 | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Cardiovascular phenotype | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Brugada syndrome 1 | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Sick sinus syndrome 1 | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Ventricular fibrillation, paroxysmal familial, type ... | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Progressive familial heart block, type 1A | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Dilated cardiomyopathy 1E | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Long QT syndrome 3 | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND not specified | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) AND Cardiac arrhythmia | ClinVar | Detail |
| NM_000335.5(SCN5A):c.5848G>A (p.Val1950Met) 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
- hg38
- Position
- chr3:38,550,521-38,550,521
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- 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)
- 1
- Allele Frequency (HGVD)
- 4.170141784820684E-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))
- rs41315493
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0007
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 11
- 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)
- 5
- East Asian Heterozygous Counts (ExAC)
- 5
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 6.044487427466151E-4
- Chromosome Counts in All Race (ExAC)
- 115854
- Allele Counts in All Race (ExAC)
- 10
- Heterozygous Counts in All Race (ExAC)
- 10
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 8.63155350700019E-5
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