chr6:32609126:T>C Detail (hg19) (HLA-DQA1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:32,609,126-32,609,126 |
| hg38 | chr6:32,641,349-32,641,349 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002122.3:c.122T>C | NP_002113.2:p.Phe41Ser |
| Ensemble | ENST00000343139.11:c.122T>C | ENST00000343139.11:p.Phe41Ser |
| ENST00000374949.2:c.122T>C | ENST00000374949.2:p.Phe41Ser |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.356 |
| ToMMo:0.551 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.586 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2020-07-15 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Steroid-sensitive nephrotic syndrome | Four common single nucleotide polymorphisms (SNPs) in HLA-DQA1 and HLA-DQB1 (rs1... | BeFree | 25349203 | Detail |
| <0.001 | leprosy | We have conducted an association analysis of more than 1,500 individuals from di... | BeFree | 20617178 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002122.5(HLA-DQA1):c.122T>C (p.Phe41Ser) AND not provided | ClinVar | Detail |
| Four common single nucleotide polymorphisms (SNPs) in HLA-DQA1 and HLA-DQB1 (rs1129740, rs9273349, r... | DisGeNET | Detail |
| We have conducted an association analysis of more than 1,500 individuals from different case-control... | 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
- rs1071630 dbSNP
- Genome
- hg19
- Position
- chr6:32,609,126-32,609,126
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 878
- Mean of sample read depth (HGVD)
- 23.20
- Standard deviation of sample read depth (HGVD)
- 19.10
- Number of reference allele (HGVD)
- 1131
- Number of alternative allele (HGVD)
- 625
- Allele Frequency (HGVD)
- 0.3559225512528474
- Gene Symbol (HGVD)
- HLA-DQA1
- 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))
- rs1071630
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.5511
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 9214
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16718
- East Asian Chromosome Counts (ExAC)
- 8406
- East Asian Allele Counts (ExAC)
- 4924
- East Asian Heterozygous Counts (ExAC)
- 2064
- East Asian Homozygous Counts (ExAC)
- 1430
- East Asian Allele Frequency (ExAC)
- 0.5857720675707828
- Chromosome Counts in All Race (ExAC)
- 118834
- Allele Counts in All Race (ExAC)
- 66155
- Heterozygous Counts in All Race (ExAC)
- 27503
- Homozygous Counts in All Race (ExAC)
- 19326
- Allele Frequency in All Race (ExAC)
- 0.5567009441742262
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