NM_005374.5:c.151-728G>A

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

1

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]

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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
MPP2NM_005374.5 linkc.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
MPP2ENST00000269095.9 linkc.151-728G>A intron_variant Intron 3 of 12 1 NM_005374.5 ENSP00000269095.4 D3DX48
MPP2ENST00000461854.5 linkc.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.:
32
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.:
0
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.:
32
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.

Other links and lift over

dbSNP: rs231518; hg19: chr17-41961451; API