3-136002075-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The ENST00000264977.8(PPP2R3A):āc.577C>Gā(p.Leu193Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000474 in 1,614,094 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
ENST00000264977.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP2R3A | NM_002718.5 | c.577C>G | p.Leu193Val | missense_variant | 2/14 | ENST00000264977.8 | NP_002709.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP2R3A | ENST00000264977.8 | c.577C>G | p.Leu193Val | missense_variant | 2/14 | 1 | NM_002718.5 | ENSP00000264977 | P3 | |
PPP2R3A | ENST00000490467.5 | c.-213-24757C>G | intron_variant | 2 | ENSP00000419344 |
Frequencies
GnomAD3 genomes AF: 0.000729 AC: 111AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00151 AC: 379AN: 251050Hom.: 2 AF XY: 0.00133 AC XY: 180AN XY: 135742
GnomAD4 exome AF: 0.000448 AC: 655AN: 1461782Hom.: 3 Cov.: 39 AF XY: 0.000446 AC XY: 324AN XY: 727166
GnomAD4 genome AF: 0.000722 AC: 110AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000846 AC XY: 63AN XY: 74468
ClinVar
Submissions by phenotype
PPP2R3A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at