chr10:129467281:C>T Detail (hg38) (MGMT)

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Information

Genome

Assembly	Position
hg19	chr10:131,265,545-131,265,545 View the variant detail on this assembly version.
hg38	chr10:129,467,281-129,467,281

Summary

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	tgv41112844	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
not provided	2016-03-10	no assertion provided	glioblastoma	somatic	Detail

CIViC

Disease	Drug	EL	ET	ED	CS	VO	TR	Pubmed	Links
glioblastoma	Temozolomide	B	Predictive	Supports	Sensitivity/Response	Common Germline	3	25910840	Detail

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	malignant pleural mesothelioma	Methylation of MGMT in malignant pleural mesothelioma occurs in a subset of pati...	BeFree	20627446	Detail
0.033	colorectal cancer	MGMT methylation is associated primarily with the germline C>T SNP (rs1690625...	BeFree	19734844	Detail
0.015	adenocarcinoma	The A/G allele of rs16906252 predicts for MGMT methylation and is selectively si...	BeFree	21355081	Detail
0.003	Precancerous Conditions	The A/G allele of rs16906252 predicts for MGMT methylation and is selectively si...	BeFree	21355081	Detail
0.014	colorectal carcinoma	MGMT methylation is associated primarily with the germline C>T SNP (rs1690625...	BeFree	19734844	Detail
0.202	glioblastoma	The T genotype of the MGMT C>T (rs16906252) enhancer single-nucleotide polymo...	BeFree	22975219	Detail

Annotation

Descrption	Source	Links
The T allele of the rs16906252 SNP was associated with MGMT methylation and low protein expression. ...	CIViC Evidence	Detail
NM_002412.5(MGMT):c.-28C>T AND Glioblastoma	ClinVar	Detail
Methylation of MGMT in malignant pleural mesothelioma occurs in a subset of patients and is associat...	DisGeNET	Detail
MGMT methylation is associated primarily with the germline C>T SNP (rs16906252) in colorectal can...	DisGeNET	Detail
The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premaligna...	DisGeNET	Detail
The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premaligna...	DisGeNET	Detail
MGMT methylation is associated primarily with the germline C>T SNP (rs16906252) in colorectal can...	DisGeNET	Detail
The T genotype of the MGMT C>T (rs16906252) enhancer single-nucleotide polymorphism (SNP) is asso...	DisGeNET	Detail

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs16906252 dbSNP
Genome: hg38
Position: chr10:129,467,281-129,467,281
Variant Type: snv
Reference Allele: C
Alternative Allele: T
Filtering Status (HGVD): PASS
Filtering Status (HGVD): LowQual
# of samples (HGVD): 1174
Mean of sample read depth (HGVD): 93.72
Standard deviation of sample read depth (HGVD): 45.13
Number of reference allele (HGVD): 2347
Number of alternative allele (HGVD): 1
Allele Frequency (HGVD): 4.2589437819420784E-4
Gene Symbol (HGVD): MGMT
East Asian Chromosome Counts (ExAC): 480
East Asian Allele Counts (ExAC): 0
East Asian Heterozygous Counts (ExAC): 0
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 0.0
Chromosome Counts in All Race (ExAC): 16070
Allele Counts in All Race (ExAC): 1102
Heterozygous Counts in All Race (ExAC): 1010
Homozygous Counts in All Race (ExAC): 46
Allele Frequency in All Race (ExAC): 0.0685749844430616
Variant (CIViC) (CIViC Variant): RS16906252
Transcript 1 (CIViC Variant): ENST00000306010.7
Variant URL (CIViC Variant): https://civic.genome.wustl.edu/links/variants/338

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