Genetic Variant NM_001015052.3:c.25-470C>T (chr16-78955-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0840

Publications

11 publications found

Variant links:

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)

MPG links:

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new If you want to explore the variant's impact on the transcript NM_001015052.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MPG	NM_001015052.3	MANE Select	c.25-470C>T	intron	N/A	NP_001015052.1	P29372-4
MPG	NM_002434.4		c.-154-184C>T	intron	N/A	NP_002425.2	Q1W6H1
MPG	NM_001015054.3		c.-12-470C>T	intron	N/A	NP_001015054.1	P29372-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MPG	ENST00000356432.8	TSL:1 MANE Select	c.25-470C>T	intron	N/A	ENSP00000348809.4	P29372-4
MPG	ENST00000219431.4	TSL:3	c.-154-184C>T	intron	N/A	ENSP00000219431.4	P29372-1
MPG	ENST00000397817.5	TSL:2	c.-12-470C>T	intron	N/A	ENSP00000380918.1	P29372-5

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104148

AN:

151878

Hom.:

39808

Cov.:

show subpopulations

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.:

AF XY:

0.683

AC XY:

50778

AN XY:

74296

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1288

2576

3863

5151

6439

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

784

1568

2352

3136

3920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.9

(source)

DANN

Benign

0.48

PhyloP100

0.084

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over