chr6:32661360:T>G Detail (hg38) (HLA-DQB1)

Information

Genome

Assembly Position
hg19 chr6:32,629,137-32,629,137 View the variant detail on this assembly version.
hg38 chr6:32,661,360-32,661,360

HGVS

Type Transcript Protein
RefSeq NM_001243961.1:c.759A>C NP_001230890.1:p.Gln253His
NM_002123.4:c.759A>C NP_002114.3:p.Gln253His
Ensemble ENST00000374943.8:c.759A>C ENST00000374943.8:p.Gln253His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.440
ToMMo:0.552
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.073

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 604305 OMIM
HGNC 4944 HGNC
Ensembl ENSG00000179344 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24851337 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
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
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
-
Genome
hg38
Position
chr6:32,661,360-32,661,360
Variant Type
snv
Reference Allele
T
Alternative Allele
G
Filtering Status (HGVD)
LowQual
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
948
Mean of sample read depth (HGVD)
48.02
Standard deviation of sample read depth (HGVD)
31.34
Number of reference allele (HGVD)
1061
Number of alternative allele (HGVD)
835
Allele Frequency (HGVD)
0.4404008438818565
Gene Symbol (HGVD)
HLA-DQB1
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))
rs1140343
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.552
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9252
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
3206
East Asian Allele Counts (ExAC)
234
East Asian Heterozygous Counts (ExAC)
172
East Asian Homozygous Counts (ExAC)
31
East Asian Allele Frequency (ExAC)
0.07298814722395508
Chromosome Counts in All Race (ExAC)
63916
Allele Counts in All Race (ExAC)
9329
Heterozygous Counts in All Race (ExAC)
5985
Homozygous Counts in All Race (ExAC)
1672
Allele Frequency in All Race (ExAC)
0.14595719381688466
Genome browser