3-136002009-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002718.5(PPP2R3A):c.511G>T(p.Ala171Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,613,636 control chromosomes in the GnomAD database, including 68,852 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). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002718.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP2R3A | NM_002718.5 | c.511G>T | p.Ala171Ser | 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.511G>T | p.Ala171Ser | missense_variant | 2/14 | 1 | NM_002718.5 | ENSP00000264977.3 | ||
PPP2R3A | ENST00000490467.5 | c.-213-24823G>T | intron_variant | 2 | ENSP00000419344.1 |
Frequencies
GnomAD3 genomes AF: 0.344 AC: 52276AN: 151878Hom.: 9972 Cov.: 32
GnomAD3 exomes AF: 0.294 AC: 73668AN: 250950Hom.: 11499 AF XY: 0.289 AC XY: 39236AN XY: 135616
GnomAD4 exome AF: 0.280 AC: 408563AN: 1461642Hom.: 58870 Cov.: 67 AF XY: 0.280 AC XY: 203302AN XY: 727116
GnomAD4 genome AF: 0.344 AC: 52321AN: 151994Hom.: 9982 Cov.: 32 AF XY: 0.344 AC XY: 25558AN XY: 74308
ClinVar
Submissions by phenotype
PPP2R3A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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