chr10:131565170:A>G Detail (hg19) (MGMT)

Information

Genome

Assembly Position
hg19 chr10:131,565,170-131,565,170
hg38 chr10:129,766,906-129,766,906 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002412.4:c.626A>G NP_002403.2:p.Lys209Arg
Ensemble ENST00000306010.8:c.626A>G ENST00000306010.8:p.Lys209Arg
ENST00000651593.1:c.533A>G ENST00000651593.1:p.Lys178Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.008

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 156569 OMIM
HGNC 7059 HGNC
Ensembl ENSG00000170430 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41120478 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-10-07 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Malignant neoplasm of lung The association between lung cancer risk and 2 polymorphisms, rs12268840 and rs2... BeFree 17957803 Detail
<0.001 Carcinoma of lung The association between lung cancer risk and 2 polymorphisms, rs12268840 and rs2... BeFree 17957803 Detail
0.033 colorectal cancer Of note, the MGMT Lys(178)Arg (rs2308237) SNP, in linkage disequilibrium with th... BeFree 18268114 Detail
0.014 colorectal carcinoma Of note, the MGMT Lys(178)Arg (rs2308237) SNP, in linkage disequilibrium with th... BeFree 18268114 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.008 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
0.003 Lymphoma, Follicular The following genotypes in combination with hair dye use before 1980 were associ... BeFree 25178586 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002412.5(MGMT):c.533A>G (p.Lys178Arg) AND not provided ClinVar Detail
The association between lung cancer risk and 2 polymorphisms, rs12268840 and rs2308327 (codon K178R)... DisGeNET Detail
The association between lung cancer risk and 2 polymorphisms, rs12268840 and rs2308327 (codon K178R)... DisGeNET Detail
Of note, the MGMT Lys(178)Arg (rs2308237) SNP, in linkage disequilibrium with the previously reporte... DisGeNET Detail
Of note, the MGMT Lys(178)Arg (rs2308237) SNP, in linkage disequilibrium with the previously reporte... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... DisGeNET Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B... 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
rs2308327 dbSNP
Genome
hg19
Position
chr10:131,565,170-131,565,170
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
62.71
Standard deviation of sample read depth (HGVD)
28.52
Number of reference allele (HGVD)
2408
Number of alternative allele (HGVD)
6
Allele Frequency (HGVD)
0.0024855012427506215
Gene Symbol (HGVD)
MGMT
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))
rs2308327
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
33
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8568
East Asian Allele Counts (ExAC)
66
East Asian Heterozygous Counts (ExAC)
66
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.007703081232492998
Chromosome Counts in All Race (ExAC)
118058
Allele Counts in All Race (ExAC)
11184
Heterozygous Counts in All Race (ExAC)
9862
Homozygous Counts in All Race (ExAC)
661
Allele Frequency in All Race (ExAC)
0.09473309729116197
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