chr22:23982936:G>A Detail (hg38) (GSTT2)

Information

Genome

Assembly Position
hg19 chr22:24,325,127-24,325,127 View the variant detail on this assembly version.
hg38 chr22:23,982,936-23,982,936

HGVS

Type Transcript Protein
RefSeq NR_126445.1:c.417G>A
Ensemble ENST00000402588.6:c.417G>A ENST00000402588.6:p.Met139Ile
ENST00000634759.1:c.417G>A ENST00000634759.1:p.Met139Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.009
ToMMo:0.008
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600437 OMIM
HGNC 4642 HGNC
Ensembl ENSG00000099984 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv65517310 TogoVar
COSMIC COSM3681400 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 Non-small cell lung carcinoma When we corrected for multiple testing using these statistical tools, three nove... BeFree 18258609 Detail
<0.001 Non-small cell lung carcinoma When we corrected for multiple testing using these statistical tools, three nove... BeFree 18258609 Detail
Annotation

Annotations

DescrptionSourceLinks
When we corrected for multiple testing using these statistical tools, three novel associations of NS... DisGeNET Detail
When we corrected for multiple testing using these statistical tools, three novel associations of NS... 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
chr22:23,982,936-23,982,936
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
234
Mean of sample read depth (HGVD)
20.18
Standard deviation of sample read depth (HGVD)
27.64
Number of reference allele (HGVD)
464
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.008547008547008548
Gene Symbol (HGVD)
GSTT2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.90to99.95
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs60718122
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0084
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
107
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12796
East Asian Chromosome Counts (ExAC)
4856
East Asian Allele Counts (ExAC)
13
East Asian Heterozygous Counts (ExAC)
13
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0026771004942339376
Chromosome Counts in All Race (ExAC)
35914
Allele Counts in All Race (ExAC)
134
Heterozygous Counts in All Race (ExAC)
132
Homozygous Counts in All Race (ExAC)
1
Allele Frequency in All Race (ExAC)
0.0037311354903380297
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