10-129629305-C-T

Position:

• chr10-129629305-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002412.5(MGMT):​c.126-78590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,094 control chromosomes in the GnomAD database, including 15,988 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 0.45 (15988 hom., cov: 33)
• Consequence: MGMT NM_002412.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGMT	NM_002412.5	c.126-78590C>T		intron_variant		ENST00000651593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGMT	ENST00000651593.1	c.126-78590C>T		intron_variant			NM_002412.5	P1
MGMT	ENST00000306010.8	c.219-78590C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68746 AN: 151976 Hom.: 15981 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.452 AC: 68782 AN: 152094 Hom.: 15988 Cov.: 33 AF XY: 0.450 AC XY: 33451 AN XY: 74318

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.476

Alfa AF: 0.482 Hom.: 10350

Bravo AF: 0.452

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs531572; hg19: chr10-131427569;