chr4:6303022:C>T Detail (hg19) (WFS1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr4:6,303,022-6,303,022 |
| hg38 | chr4:6,301,295-6,301,295 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001145853.1:c.1500C>T | NP_001139325.1:p.Asn500= |
| NM_006005.3:c.1500C>T | NP_005996.2:p.Asn500= | |
| Ensemble | ENST00000503569.5:c.1500C>T | ENST00000503569.5:p.Asn500= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.979 |
| ToMMo:0.987 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.944 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
autosomal dominant hereditary sensorineural hearing loss |
germline
|
MGS000082
(TMGS000165) |
Kenjiro Kosaki Kenjiro Kosaki |
Keio University Mutation View |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2013-07-30 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2018-01-12 | criteria provided, single submitter | Autosomal dominant nonsyndromic hearing loss 6 |
germline
|
Detail |
|
Benign
|
2018-01-12 | criteria provided, single submitter | WFS1-Related Spectrum Disorders |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
Uncertain significance
|
criteria provided, single submitter | type 2 diabetes mellitus |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.336 | Diabetes Mellitus, Non-Insulin-Dependent | Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be... | BeFree | 23144361 | Detail |
| 0.452 | Diabetes Mellitus, Non-Insulin-Dependent | Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be... | BeFree | 23144361 | Detail |
| 0.614 | Diabetes Mellitus, Non-Insulin-Dependent | Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be... | BeFree | 23144361 | Detail |
| 0.327 | Diabetes Mellitus, Non-Insulin-Dependent | Twelve type 2 diabetes susceptibility loci identified through large-scale associ... | GWASCAT | 20581827 | Detail |
| 0.327 | Diabetes Mellitus, Non-Insulin-Dependent | Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be... | BeFree | 23144361 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_006005.3(WFS1):c.1500C>T (p.Asn500=) AND not specified | ClinVar | Detail |
| NM_006005.3(WFS1):c.1500C>T (p.Asn500=) AND Autosomal dominant nonsyndromic hearing loss 6 | ClinVar | Detail |
| NM_006005.3(WFS1):c.1500C>T (p.Asn500=) AND WFS1-Related Spectrum Disorders | ClinVar | Detail |
| NM_006005.3(WFS1):c.1500C>T (p.Asn500=) AND not provided | ClinVar | Detail |
| NM_006005.3(WFS1):c.1500C>T (p.Asn500=) AND Type 2 diabetes mellitus | ClinVar | Detail |
| Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be associated with T2D... | DisGeNET | Detail |
| Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be associated with T2D... | DisGeNET | Detail |
| Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be associated with T2D... | DisGeNET | Detail |
| Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. | DisGeNET | Detail |
| Seven of the 29 single nucleotide polymorphisms (SNPs) examined were found to be associated with T2D... | 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
- rs1801214 dbSNP
- Genome
- hg19
- Position
- chr4:6,303,022-6,303,022
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 226.03
- Standard deviation of sample read depth (HGVD)
- 107.50
- Number of reference allele (HGVD)
- 50
- Number of alternative allele (HGVD)
- 2370
- Allele Frequency (HGVD)
- 0.9793388429752066
- Gene Symbol (HGVD)
- WFS1
- 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))
- rs1801214
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.9868
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16537
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 8168
- East Asian Heterozygous Counts (ExAC)
- 446
- East Asian Homozygous Counts (ExAC)
- 3861
- East Asian Allele Frequency (ExAC)
- 0.9440591770688858
- Chromosome Counts in All Race (ExAC)
- 121226
- Allele Counts in All Race (ExAC)
- 79949
- Heterozygous Counts in All Race (ExAC)
- 26009
- Homozygous Counts in All Race (ExAC)
- 26970
- Allele Frequency in All Race (ExAC)
- 0.6595037368221338
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