rs17197552
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002718.5(PPP2R3A):āc.1924A>Gā(p.Ser642Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,613,444 control chromosomes in the GnomAD database, including 75,959 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R3A | NM_002718.5 | c.1924A>G | p.Ser642Gly | missense_variant | 2/14 | ENST00000264977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R3A | ENST00000264977.8 | c.1924A>G | p.Ser642Gly | missense_variant | 2/14 | 1 | NM_002718.5 | P3 | |
PPP2R3A | ENST00000490467.5 | c.-213-23410A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38640AN: 151974Hom.: 5417 Cov.: 32
GnomAD3 exomes AF: 0.262 AC: 65660AN: 250754Hom.: 9979 AF XY: 0.274 AC XY: 37127AN XY: 135602
GnomAD4 exome AF: 0.303 AC: 442857AN: 1461352Hom.: 70545 Cov.: 39 AF XY: 0.305 AC XY: 222024AN XY: 727000
GnomAD4 genome ? AF: 0.254 AC: 38652AN: 152092Hom.: 5414 Cov.: 32 AF XY: 0.253 AC XY: 18777AN XY: 74338
ClinVar
Submissions by phenotype
PPP2R3A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 02, 2020 | 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