rs2562182

chr16-83947-G-A

Variant summary

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

The NM_001015052.3(MPG):c.505+691G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,924 control chromosomes in the GnomAD database, including 41,739 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 0.71 (41739 hom., cov: 30)
• Consequence: MPG NM_001015052.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73

Genes affected

MPG (HGNC:7211): (N-methylpurine DNA glycosylase) Predicted to enable alkylbase DNA N-glycosylase activity. Predicted to be involved in base-excision repair. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPG	NM_001015052.3	c.505+691G>A		intron_variant		ENST00000356432.8
MPG	NM_001015054.3	c.469+691G>A		intron_variant
MPG	NM_002434.4	c.520+691G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPG	ENST00000356432.8	c.505+691G>A		intron_variant		1	NM_001015052.3	P2
MPG	ENST00000219431.4	c.520+691G>A		intron_variant		3		A2
MPG	ENST00000397817.5	c.469+691G>A		intron_variant		2		A2
MPG	ENST00000436333.5	c.469+691G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108365 AN: 151806 Hom.: 41717 Cov.: 30

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.714 AC: 108407 AN: 151924 Hom.: 41739 Cov.: 30 AF XY: 0.717 AC XY: 53228 AN XY: 74266

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.757

Alfa AF: 0.826 Hom.: 69089

Bravo AF: 0.696

Asia WGS AF: 0.775 AC: 2696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.2
Dann	Benign	0.41

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: rs2562182; hg19: chr16-133946; COSMIC: COSV54739645; COSMIC: COSV54739645;