8-9141261-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024607.4(PPP1R3B):c.391G>A(p.Asp131Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024607.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R3B | ENST00000310455.4 | c.391G>A | p.Asp131Asn | missense_variant | Exon 2 of 2 | 1 | NM_024607.4 | ENSP00000308318.3 | ||
PPP1R3B | ENST00000519699.1 | c.391G>A | p.Asp131Asn | missense_variant | Exon 2 of 2 | 2 | ENSP00000428642.1 | |||
ENSG00000254340 | ENST00000520017.1 | n.-163C>T | upstream_gene_variant | 3 | ||||||
ENSG00000254340 | ENST00000666082.1 | n.-166C>T | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251220Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135794
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461856Hom.: 0 Cov.: 35 AF XY: 0.0000289 AC XY: 21AN XY: 727222
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74316
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at