16-80894-G-C

Variant names:

• chr16-80894-G-C
• rs2858056
• NM_001015052.3:c.300+1194G>C

Variant summary

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

The NM_001015052.3(MPG):​c.300+1194G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,258 control chromosomes in the GnomAD database, including 45,604 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 0.75 (45604 hom., cov: 34)
• Consequence: MPG NM_001015052.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPG	NM_001015052.3	c.300+1194G>C		intron_variant	Intron 2 of 3	ENST00000356432.8	NP_001015052.1
MPG	NM_002434.4	c.315+1194G>C		intron_variant	Intron 3 of 4		NP_002425.2
MPG	NM_001015054.3	c.264+1194G>C		intron_variant	Intron 2 of 3		NP_001015054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPG	ENST00000356432.8	c.300+1194G>C		intron_variant	Intron 2 of 3	1	NM_001015052.3	ENSP00000348809.4
MPG	ENST00000219431.4	c.315+1194G>C		intron_variant	Intron 3 of 4	3		ENSP00000219431.4
MPG	ENST00000397817.5	c.264+1194G>C		intron_variant	Intron 2 of 3	2		ENSP00000380918.1
MPG	ENST00000436333.5	c.264+1194G>C		intron_variant	Intron 2 of 3	2		ENSP00000388097.1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113935 AN: 152140 Hom.: 45582 Cov.: 34

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.749 AC: 113988 AN: 152258 Hom.: 45604 Cov.: 34 AF XY: 0.750 AC XY: 55871 AN XY: 74450

African (AFR) AF: 0.437 AC: 18148 AN: 41518

American (AMR) AF: 0.846 AC: 12948 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3100 AN: 3470

East Asian (EAS) AF: 0.731 AC: 3791 AN: 5186

South Asian (SAS) AF: 0.891 AC: 4306 AN: 4832

European-Finnish (FIN) AF: 0.856 AC: 9073 AN: 10596

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59973 AN: 68028

Other (OTH) AF: 0.776 AC: 1641 AN: 2116

Alfa AF: 0.748 Hom.: 2676

Bravo AF: 0.731

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.34
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: rs2858056; hg19: chr16-130893;