chr10-129731172-G-A

Variant names:

• chr10-129731172-G-A
• rs7898151
• NM_002412.5:c.274+23129G>A

Variant summary

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

The NM_002412.5(MGMT):​c.274+23129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,854 control chromosomes in the GnomAD database, including 21,931 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 0.53 (21931 hom., cov: 30)
• Consequence: MGMT NM_002412.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.635 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.274+23129G>A		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.274+23129G>A		intron	N/A	ENSP00000498729.1
	MGMT	ENST00000306010.8	TSL:1	c.367+23129G>A		intron	N/A	ENSP00000302111.7

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80747 AN: 151734 Hom.: 21901 Cov.: 30

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.705

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.532 AC: 80819 AN: 151854 Hom.: 21931 Cov.: 30 AF XY: 0.538 AC XY: 39903 AN XY: 74180

African (AFR) AF: 0.437 AC: 18084 AN: 41408

American (AMR) AF: 0.645 AC: 9854 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2341 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3320 AN: 5124

South Asian (SAS) AF: 0.654 AC: 3145 AN: 4810

European-Finnish (FIN) AF: 0.520 AC: 5463 AN: 10504

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36792 AN: 67940

Other (OTH) AF: 0.539 AC: 1138 AN: 2110

Alfa AF: 0.402 Hom.: 1127

Bravo AF: 0.536

Asia WGS AF: 0.641 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.48
PhyloP100		0.12
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: rs7898151; hg19: chr10-131529436;