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
Links
Type Database ID Link
Gene MIM 146880 OMIM
HGNC 4942 HGNC
Ensembl ENSG00000196735 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24849390 TogoVar
COSMIC
MONDO
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

DescrptionSourceLinks
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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