3-136001730-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002718.5(PPP2R3A):c.232G>A(p.Gly78Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00435 in 1,614,088 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002718.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R3A | NM_002718.5 | c.232G>A | p.Gly78Arg | missense_variant | 2/14 | ENST00000264977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R3A | ENST00000264977.8 | c.232G>A | p.Gly78Arg | missense_variant | 2/14 | 1 | NM_002718.5 | P3 | |
PPP2R3A | ENST00000490467.5 | c.-213-25102G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00273 AC: 416AN: 152176Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00277 AC: 696AN: 250952Hom.: 1 AF XY: 0.00303 AC XY: 411AN XY: 135620
GnomAD4 exome AF: 0.00452 AC: 6604AN: 1461794Hom.: 21 Cov.: 45 AF XY: 0.00443 AC XY: 3225AN XY: 727188
GnomAD4 genome AF: 0.00273 AC: 416AN: 152294Hom.: 1 Cov.: 33 AF XY: 0.00238 AC XY: 177AN XY: 74472
ClinVar
Submissions by phenotype
PPP2R3A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 31, 2022 | This variant is classified as likely 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