chr1:109737079:C>T Detail (hg38) (GSTM3)

Information

Genome

Assembly Position
hg19 chr1:110,279,701-110,279,701 View the variant detail on this assembly version.
hg38 chr1:109,737,079-109,737,079

HGVS

Type Transcript Protein
RefSeq NM_000849.4:c.670G>A NP_000840.2:p.Val224Ile
NR_024537.1:c.670G>A
Ensemble ENST00000256594.7:c.670G>A ENST00000256594.7:p.Val224Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.758
ToMMo:0.757
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.738

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 138390 OMIM
HGNC 4635 HGNC
Ensembl ENSG00000134202 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2762617 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
0.012 Malignant neoplasm of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.041 Malignant neoplasm of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.005 Malignant neoplasm of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.057 Malignant neoplasm of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.002 Carcinoma of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.033 Malignant neoplasm of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.009 Carcinoma of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.002 Carcinoma of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
0.007 Carcinoma of lung Heterozygote carriers of SNPs in CYP1A2 1545T>C, -164C>A and -740T>G; C... BeFree 17259654 Detail
<0.001 Carcinoma of lung Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; C... BeFree 17259654 Detail
0.016 Malignant neoplasm of lung Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; C... BeFree 17259654 Detail
0.007 Carcinoma of lung Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; C... BeFree 17259654 Detail
<0.001 osteoporosis The results of our study demonstrate the genetic association between detoxifying... BeFree 22327174 Detail
<0.001 osteoporosis The results of our study demonstrate the genetic association between detoxifying... BeFree 22327174 Detail
Annotation

Annotations

DescrptionSourceLinks
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
Heterozygote carriers of SNPs in CYP1A2 1545T&gt;C, -164C&gt;A and -740T&gt;G; CYP2A6 -47A&gt;C; MDR... DisGeNET Detail
The results of our study demonstrate the genetic association between detoxifying enzyme GSTM3 and BM... DisGeNET Detail
The results of our study demonstrate the genetic association between detoxifying enzyme GSTM3 and BM... 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
chr1:109,737,079-109,737,079
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
59.33
Standard deviation of sample read depth (HGVD)
24.24
Number of reference allele (HGVD)
585
Number of alternative allele (HGVD)
1835
Allele Frequency (HGVD)
0.7582644628099173
Gene Symbol (HGVD)
GSTM3
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))
rs7483
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7575
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12696
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8636
East Asian Allele Counts (ExAC)
6372
East Asian Heterozygous Counts (ExAC)
1698
East Asian Homozygous Counts (ExAC)
2337
East Asian Allele Frequency (ExAC)
0.7378415933302455
Chromosome Counts in All Race (ExAC)
121314
Allele Counts in All Race (ExAC)
41425
Heterozygous Counts in All Race (ExAC)
24875
Homozygous Counts in All Race (ExAC)
8275
Allele Frequency in All Race (ExAC)
0.3414692450994939
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