chr2:85697606:C>T Detail (hg38) (GNLY)

Information

Genome

Assembly Position
hg19 chr2:85,924,729-85,924,729 View the variant detail on this assembly version.
hg38 chr2:85,697,606-85,697,606

HGVS

Type Transcript Protein
RefSeq NM_006433.4:c.356C>T NP_006424.2:p.Thr119Ile
NM_012483.3:c.311C>T NP_036615.2:p.Thr104Ile
NM_001302758.1:c.437C>T NP_001289687.1:p.Thr146Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.587
ToMMo:0.580
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.581

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 188855 OMIM
HGNC 4414 HGNC
Ensembl ENSG00000115523 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv7693288 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 Chronic liver disease HLA-DQ (rs9275572) and GNLY (rs1866139 and rs11127) were genotyped in 310 subjec... BeFree 25644528 Detail
Annotation

Annotations

DescrptionSourceLinks
HLA-DQ (rs9275572) and GNLY (rs1866139 and rs11127) were genotyped in 310 subjects with HBV-related ... 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
chr2:85,697,606-85,697,606
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1149
Mean of sample read depth (HGVD)
46.16
Standard deviation of sample read depth (HGVD)
19.02
Number of reference allele (HGVD)
949
Number of alternative allele (HGVD)
1347
Allele Frequency (HGVD)
0.5866724738675958
Gene Symbol (HGVD)
GNLY
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))
rs11127
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5795
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9712
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
5017
East Asian Heterozygous Counts (ExAC)
2095
East Asian Homozygous Counts (ExAC)
1461
East Asian Allele Frequency (ExAC)
0.581209453197405
Chromosome Counts in All Race (ExAC)
121294
Allele Counts in All Race (ExAC)
46353
Heterozygous Counts in All Race (ExAC)
27427
Homozygous Counts in All Race (ExAC)
9463
Allele Frequency in All Race (ExAC)
0.3821541049021386
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