chr10-129509012-C-G

Variant names:

• chr10-129509012-C-G
• rs10741191
• NM_002412.5:c.-12-27229C>G

Variant summary

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

The NM_002412.5(MGMT):​c.-12-27229C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,022 control chromosomes in the GnomAD database, including 24,448 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 0.56 (24448 hom., cov: 32)
• Consequence: MGMT NM_002412.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGMT	NM_002412.5	c.-12-27229C>G		intron_variant	Intron 1 of 4	ENST00000651593.1	NP_002403.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGMT	ENST00000651593.1	c.-12-27229C>G		intron_variant	Intron 1 of 4		NM_002412.5	ENSP00000498729.1
MGMT	ENST00000306010.8	c.82-27229C>G		intron_variant	Intron 1 of 4	1		ENSP00000302111.7
MGMT	ENST00000482547.1	n.36-27229C>G		intron_variant	Intron 1 of 1	2
MGMT	ENST00000482653.1	n.69-27229C>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84641 AN: 151904 Hom.: 24438 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.557 AC: 84687 AN: 152022 Hom.: 24448 Cov.: 32 AF XY: 0.559 AC XY: 41583 AN XY: 74330

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.584

Alfa AF: 0.557 Hom.: 2864

Bravo AF: 0.556

Asia WGS AF: 0.774 AC: 2692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.72

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: rs10741191; hg19: chr10-131307276;