16-79532-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPG	NM_001015052.3	c.132C>G	p.Ser44Ser	synonymous_variant	Exon 2 of 4	ENST00000356432.8	NP_001015052.1
MPG	NM_002434.4	c.147C>G	p.Ser49Ser	synonymous_variant	Exon 3 of 5		NP_002425.2
MPG	NM_001015054.3	c.96C>G	p.Ser32Ser	synonymous_variant	Exon 2 of 4		NP_001015054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPG	ENST00000356432.8	c.132C>G	p.Ser44Ser	synonymous_variant	Exon 2 of 4	1	NM_001015052.3	ENSP00000348809.4

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

GnomAD3 exomes AF: 0.00472 AC: 1177 AN: 249566 Hom.: 3 AF XY: 0.00467 AC XY: 633 AN XY: 135450

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 SAS exome AF: 0.00353

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

Gnomad4 AFR exome AF: 0.00149

Gnomad4 AMR exome AF: 0.00369

Gnomad4 ASJ exome AF: 0.00800

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00334

Gnomad4 FIN exome AF: 0.00247

Gnomad4 NFE exome AF: 0.00951

Gnomad4 OTH exome AF: 0.00762

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

Gnomad4 AFR AF: 0.00156

Gnomad4 AMR AF: 0.00549

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00435

Gnomad4 FIN AF: 0.00170

Gnomad4 NFE AF: 0.00800

Gnomad4 OTH AF: 0.00522

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.097
DANN	Benign	0.55

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: rs2259275; hg19: chr16-129531;