NM_002412.5:c.414+2205A>T

Variant names:

• chr10-129761546-A-T
• rs12243174
• NM_002412.5:c.414+2205A>T

Variant summary

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

The NM_002412.5(MGMT):​c.414+2205A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,200 control chromosomes in the GnomAD database, including 3,528 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 0.19 (3528 hom., cov: 33)
• Consequence: MGMT NM_002412.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 7 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=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGMT	NM_002412.5	c.414+2205A>T		intron_variant	Intron 4 of 4	ENST00000651593.1	NP_002403.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGMT	ENST00000651593.1	c.414+2205A>T		intron_variant	Intron 4 of 4		NM_002412.5	ENSP00000498729.1
MGMT	ENST00000306010.8	c.507+2205A>T		intron_variant	Intron 4 of 4	1		ENSP00000302111.7

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29033 AN: 152082 Hom.: 3513 Cov.: 33

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.191 AC: 29051 AN: 152200 Hom.: 3528 Cov.: 33 AF XY: 0.196 AC XY: 14619 AN XY: 74410

African (AFR) AF: 0.0576 AC: 2394 AN: 41544

American (AMR) AF: 0.324 AC: 4947 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1554 AN: 5160

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2750 AN: 10600

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14668 AN: 68006

Other (OTH) AF: 0.187 AC: 396 AN: 2114

Alfa AF: 0.209 Hom.: 521

Bravo AF: 0.191

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	12
DANN	Benign	0.92
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: rs12243174; hg19: chr10-131559810;