NM_005374.5:c.151-728G>A
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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
NM_005374.5 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.263
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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17627AN: 152082Hom.: 1146 Cov.: 32
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GnomAD4 exome AF: 0.122 AC: 66965AN: 550114Hom.: 4769 Cov.: 0 AF XY: 0.122 AC XY: 36313AN XY: 297780
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GnomAD4 genome AF: 0.116 AC: 17628AN: 152200Hom.: 1147 Cov.: 32 AF XY: 0.114 AC XY: 8507AN XY: 74400
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at