10-129543865-A-C

Variant names:

• chr10-129543865-A-C
• rs3858300
• NM_002412.5:c.125+7488A>C

Variant summary

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

The NM_002412.5(MGMT):​c.125+7488A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,010 control chromosomes in the GnomAD database, including 35,312 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 0.68 (35312 hom., cov: 32)
• Consequence: MGMT NM_002412.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.980
• Publications: 22 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 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.125+7488A>C		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.125+7488A>C		intron	N/A	ENSP00000498729.1
	MGMT	ENST00000306010.8	TSL:1	c.218+7488A>C		intron	N/A	ENSP00000302111.7
	MGMT	ENST00000482653.1	TSL:3	n.205+7488A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102807 AN: 151892 Hom.: 35289 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.677 AC: 102878 AN: 152010 Hom.: 35312 Cov.: 32 AF XY: 0.679 AC XY: 50438 AN XY: 74282

African (AFR) AF: 0.737 AC: 30533 AN: 41452

American (AMR) AF: 0.687 AC: 10500 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.954 AC: 4933 AN: 5170

South Asian (SAS) AF: 0.745 AC: 3592 AN: 4820

European-Finnish (FIN) AF: 0.618 AC: 6517 AN: 10548

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42357 AN: 67956

Other (OTH) AF: 0.686 AC: 1444 AN: 2104

Alfa AF: 0.640 Hom.: 16722

Bravo AF: 0.685

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.5
DANN	Benign	0.65
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3858300; hg19: chr10-131342129; COSMIC: COSV60022562;