16-78955-C-T

Variant names:

• chr16-78955-C-T
• rs1013358
• NM_001015052.3:c.25-470C>T

Variant summary

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

The NM_001015052.3(MPG):​c.25-470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,996 control chromosomes in the GnomAD database, including 39,809 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 0.69 (39809 hom., cov: 34)
• Consequence: MPG NM_001015052.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPG	NM_001015052.3	c.25-470C>T		intron_variant	Intron 1 of 3	ENST00000356432.8	NP_001015052.1
MPG	NM_002434.4	c.-154-184C>T		intron_variant	Intron 1 of 4		NP_002425.2
MPG	NM_001015054.3	c.-12-470C>T		intron_variant	Intron 1 of 3		NP_001015054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPG	ENST00000356432.8	c.25-470C>T		intron_variant	Intron 1 of 3	1	NM_001015052.3	ENSP00000348809.4

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104148 AN: 151878 Hom.: 39808 Cov.: 34

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.685 AC: 104159 AN: 151996 Hom.: 39809 Cov.: 34 AF XY: 0.683 AC XY: 50778 AN XY: 74296

African (AFR) AF: 0.321 AC: 13276 AN: 41328

American (AMR) AF: 0.758 AC: 11591 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3043 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3252 AN: 5150

South Asian (SAS) AF: 0.716 AC: 3453 AN: 4822

European-Finnish (FIN) AF: 0.803 AC: 8510 AN: 10594

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58566 AN: 68022

Other (OTH) AF: 0.711 AC: 1501 AN: 2112

Alfa AF: 0.780 Hom.: 98477

Bravo AF: 0.664

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.48
PhyloP100		0.084
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: rs1013358; hg19: chr16-128954;