Genetic Variant NM_005374.5:c.151-728G>A (chr17-43884083-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005374.5(MPP2):c.151-728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 702,314 control chromosomes in the GnomAD database, including 5,916 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 0.12 ( 1147 hom., cov: 32)

Exomes 𝑓: 0.12 ( 4769 hom. )

Consequence

MPP2
NM_005374.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.263

Variant links:

Genes affected

MPP2 (HGNC:7220): (MAGUK p55 scaffold protein 2) Palmitoylated membrane protein 2 is a member of a family of membrane-associated proteins termed MAGUKs (membrane-associated guanylate kinase homologs). MAGUKs interact with the cytoskeleton and regulate cell proliferation, signaling pathways, and intracellular junctions. Palmitoylated membrane protein 2 contains a conserved sequence, called the SH3 (src homology 3) motif, found in several other proteins that associate with the cytoskeleton and are suspected to play important roles in signal transduction. [provided by RefSeq, Jul 2008]

MPP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPP2	NM_005374.5 link	c.151-728G>A		intron_variant	Intron 3 of 12	ENST00000269095.9	NP_005365.4	Q14168D3DX48

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPP2	ENST00000269095.9 link	c.151-728G>A		intron_variant	Intron 3 of 12	1	NM_005374.5	ENSP00000269095.4		D3DX48
MPP2	ENST00000461854.5 link	c.222+1G>A		splice_donor_variant, intron_variant	Intron 4 of 13	1		ENSP00000428286.1		D3DX49

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17627

AN:

152082

Hom.:

1146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0989

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.0857

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.000960

Gnomad SAS

AF:

0.0910

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.115

GnomAD4 exome

AF:

0.122

AC:

66965

AN:

550114

Hom.:

4769

Cov.:

AF XY:

0.122

AC XY:

36313

AN XY:

297780

show subpopulations

Gnomad4 AFR exome

AF:

0.104

Gnomad4 AMR exome

AF:

0.0669

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.000218

Gnomad4 SAS exome

AF:

0.0969

Gnomad4 FIN exome

AF:

0.156

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.116

AC:

17628

AN:

152200

Hom.:

1147

Cov.:

AF XY:

0.114

AC XY:

8507

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0988

Gnomad4 AMR

AF:

0.0856

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.000962

Gnomad4 SAS

AF:

0.0907

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.136

Gnomad4 OTH

AF:

0.114

Alfa

AF:

0.130

Hom.:

865

Bravo

AF:

0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over