rs9814557
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000264977.8(PPP2R3A):āc.200A>Gā(p.Asp67Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,613,762 control chromosomes in the GnomAD database, including 73,912 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 (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D67N) has been classified as Benign.
Frequency
Consequence
ENST00000264977.8 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.200A>G | p.Asp67Gly | 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.200A>G | p.Asp67Gly | missense_variant | 2/14 | 1 | NM_002718.5 | ENSP00000264977 | P3 | |
PPP2R3A | ENST00000490467.5 | c.-213-25134A>G | intron_variant | 2 | ENSP00000419344 |
Frequencies
GnomAD3 genomes AF: 0.231 AC: 35137AN: 152010Hom.: 4885 Cov.: 32
GnomAD3 exomes AF: 0.252 AC: 63197AN: 250856Hom.: 9460 AF XY: 0.264 AC XY: 35814AN XY: 135546
GnomAD4 exome AF: 0.299 AC: 436365AN: 1461634Hom.: 69030 Cov.: 45 AF XY: 0.300 AC XY: 218463AN XY: 727116
GnomAD4 genome AF: 0.231 AC: 35131AN: 152128Hom.: 4882 Cov.: 32 AF XY: 0.229 AC XY: 17047AN XY: 74350
ClinVar
Submissions by phenotype
PPP2R3A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 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