rs10764882

Variant names:

• chr10-129508232-C-G
• rs10764882
• NM_002412.5:c.-12-28009C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002412.5(MGMT):​c.-12-28009C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,920 control chromosomes in the GnomAD database, including 17,214 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17214 hom., cov: 32)
• Consequence: MGMT NM_002412.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 1 publications found

Genes affected

MGMT (HGNC:7059): (O-6-methylguanine-DNA methyltransferase) Alkylating agents are potent carcinogens that can result in cell death, mutation and cancer. The protein encoded by this gene is a DNA repair protein that is involved in cellular defense against mutagenesis and toxicity from alkylating agents. The protein catalyzes transfer of methyl groups from O(6)-alkylguanine and other methylated moieties of the DNA to its own molecule, which repairs the toxic lesions. Methylation of the genes promoter has been associated with several cancer types, including colorectal cancer, lung cancer, lymphoma and glioblastoma. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002412.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGMT	NM_002412.5	MANE Select	c.-12-28009C>G		intron	N/A	NP_002403.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGMT	ENST00000651593.1	MANE Select	c.-12-28009C>G		intron	N/A	ENSP00000498729.1
	MGMT	ENST00000306010.8	TSL:1	c.82-28009C>G		intron	N/A	ENSP00000302111.7
	MGMT	ENST00000482547.1	TSL:2	n.36-28009C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71321 AN: 151802 Hom.: 17214 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.490

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.470 AC: 71346 AN: 151920 Hom.: 17214 Cov.: 32 AF XY: 0.472 AC XY: 35027 AN XY: 74228

African (AFR) AF: 0.371 AC: 15347 AN: 41416

American (AMR) AF: 0.478 AC: 7297 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3243 AN: 5142

South Asian (SAS) AF: 0.561 AC: 2696 AN: 4806

European-Finnish (FIN) AF: 0.496 AC: 5237 AN: 10562

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34065 AN: 67946

Other (OTH) AF: 0.490 AC: 1033 AN: 2108

Alfa AF: 0.475 Hom.: 2180

Bravo AF: 0.462

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.74
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10764882; hg19: chr10-131306496;