16-79532-C-G

Variant names:

• chr16-79532-C-G
• rs2259275
• NM_001015052.3:c.132C>G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_001015052.3(MPG):​c.132C>G​(p.Ser44Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00785 in 1,612,976 control chromosomes in the GnomAD database, including 72 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 0.0050 (5 hom., cov: 33)
  • Exomes 𝑓: 0.0081 (67 hom.)
• Consequence: MPG NM_001015052.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38
• Publications: 15 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP7: Synonymous conserved (PhyloP=-3.38 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 5 Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001015052.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPG	NM_001015052.3	MANE Select	c.132C>G	p.Ser44Ser	synonymous	Exon 2 of 4	NP_001015052.1
	MPG	NM_002434.4		c.147C>G	p.Ser49Ser	synonymous	Exon 3 of 5	NP_002425.2
	MPG	NM_001015054.3		c.96C>G	p.Ser32Ser	synonymous	Exon 2 of 4	NP_001015054.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPG	ENST00000356432.8	TSL:1 MANE Select	c.132C>G	p.Ser44Ser	synonymous	Exon 2 of 4	ENSP00000348809.4
	MPG	ENST00000219431.4	TSL:3	c.147C>G	p.Ser49Ser	synonymous	Exon 3 of 5	ENSP00000219431.4
	MPG	ENST00000397817.5	TSL:2	c.96C>G	p.Ser32Ser	synonymous	Exon 2 of 4	ENSP00000380918.1

Frequencies

GnomAD3 genomes AF: 0.00505 AC: 769 AN: 152174 Hom.: 5 Cov.: 33

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00550

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00800

Gnomad OTH AF: 0.00527

GnomAD2 exomes AF: 0.00472 AC: 1177 AN: 249566 AF XY: 0.00467

Gnomad AFR exome AF: 0.00187

Gnomad AMR exome AF: 0.00313

Gnomad ASJ exome AF: 0.00711

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00218

Gnomad NFE exome AF: 0.00693

Gnomad OTH exome AF: 0.00559

GnomAD4 exome AF: 0.00814 AC: 11891 AN: 1460684 Hom.: 67 Cov.: 32 AF XY: 0.00805 AC XY: 5849 AN XY: 726658

African (AFR) AF: 0.00149 AC: 50 AN: 33478

American (AMR) AF: 0.00369 AC: 165 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00800 AC: 209 AN: 26122

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00334 AC: 288 AN: 86248

European-Finnish (FIN) AF: 0.00247 AC: 129 AN: 52330

Middle Eastern (MID) AF: 0.00208 AC: 12 AN: 5766

European-Non Finnish (NFE) AF: 0.00951 AC: 10578 AN: 1111950

Other (OTH) AF: 0.00762 AC: 460 AN: 60378

GnomAD4 genome AF: 0.00505 AC: 769 AN: 152292 Hom.: 5 Cov.: 33 AF XY: 0.00469 AC XY: 349 AN XY: 74458

African (AFR) AF: 0.00156 AC: 65 AN: 41562

American (AMR) AF: 0.00549 AC: 84 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00435 AC: 21 AN: 4826

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00800 AC: 544 AN: 68022

Other (OTH) AF: 0.00522 AC: 11 AN: 2108

Alfa AF: 0.00286 Hom.: 0

Bravo AF: 0.00534

EpiCase AF: 0.00872

EpiControl AF: 0.00836

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.097
DANN	Benign	0.55
PhyloP100		-3.4
Mutation Taster		=100/0	polymorphism

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: rs2259275; hg19: chr16-129531;