rs2562182

Variant names:

• chr16-83947-G-A
• rs2562182
• NM_001015052.3:c.505+691G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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]

MPG Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MPG	NM_001015052.3	c.505+691G>A		intron_variant	Intron 3 of 3	ENST00000356432.8	NP_001015052.1
MPG	NM_002434.4	c.520+691G>A		intron_variant	Intron 4 of 4		NP_002425.2
MPG	NM_001015054.3	c.469+691G>A		intron_variant	Intron 3 of 3		NP_001015054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPG	ENST00000356432.8	c.505+691G>A		intron_variant	Intron 3 of 3	1	NM_001015052.3	ENSP00000348809.4
MPG	ENST00000219431.4	c.520+691G>A		intron_variant	Intron 4 of 4	3		ENSP00000219431.4
MPG	ENST00000397817.5	c.469+691G>A		intron_variant	Intron 3 of 3	2		ENSP00000380918.1
MPG	ENST00000436333.5	c.469+691G>A		intron_variant	Intron 3 of 3	2		ENSP00000388097.1

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

African (AFR) AF: 0.400 AC: 16546 AN: 41374

American (AMR) AF: 0.821 AC: 12520 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2984 AN: 3470

East Asian (EAS) AF: 0.704 AC: 3621 AN: 5142

South Asian (SAS) AF: 0.857 AC: 4129 AN: 4818

European-Finnish (FIN) AF: 0.820 AC: 8666 AN: 10574

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57411 AN: 67980

Other (OTH) AF: 0.757 AC: 1598 AN: 2110

Alfa AF: 0.815 Hom.: 89425

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
PhyloP100		1.7
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: rs2562182; hg19: chr16-133946; COSMIC: COSV54739645; COSMIC: COSV54739645;