chr6:32641328:G>A Detail (hg38) (HLA-DQA1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:32,609,105-32,609,105 View the variant detail on this assembly version. |
| hg38 | chr6:32,641,328-32,641,328 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002122.3:c.101G>A | NP_002113.2:p.Cys34Tyr |
| Ensemble | ENST00000343139.11:c.101G>A | ENST00000343139.11:p.Cys34Tyr |
| ENST00000374949.2:c.101G>A | ENST00000374949.2:p.Cys34Tyr |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.401 |
| ToMMo:0.552 | |
| 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 |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002122.5(HLA-DQA1):c.101G>A (p.Cys34Tyr) AND not provided | ClinVar | Detail |
| Four common single nucleotide polymorphisms (SNPs) in HLA-DQA1 and HLA-DQB1 (rs1129740, rs9273349, r... | 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
- rs1129740 dbSNP
- Genome
- hg38
- Position
- chr6:32,641,328-32,641,328
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- # of samples (HGVD)
- 857
- Mean of sample read depth (HGVD)
- 18.37
- Standard deviation of sample read depth (HGVD)
- 19.71
- Number of reference allele (HGVD)
- 1027
- Number of alternative allele (HGVD)
- 687
- Allele Frequency (HGVD)
- 0.4008168028004667
- 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))
- rs1129740
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.5515
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 9216
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16712
- East Asian Chromosome Counts (ExAC)
- 8392
- East Asian Allele Counts (ExAC)
- 4914
- East Asian Heterozygous Counts (ExAC)
- 2048
- East Asian Homozygous Counts (ExAC)
- 1433
- East Asian Allele Frequency (ExAC)
- 0.5855576739752145
- Chromosome Counts in All Race (ExAC)
- 119046
- Allele Counts in All Race (ExAC)
- 66325
- Heterozygous Counts in All Race (ExAC)
- 27503
- Homozygous Counts in All Race (ExAC)
- 19411
- Allele Frequency in All Race (ExAC)
- 0.5571375770710482
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