rs9814557
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002718.5(PPP2R3A):c.200A>G(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. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). 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
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.200A>G | p.Asp67Gly | missense_variant | 2/14 | ENST00000264977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R3A | ENST00000264977.8 | c.200A>G | p.Asp67Gly | missense_variant | 2/14 | 1 | NM_002718.5 | P3 | |
PPP2R3A | ENST00000490467.5 | c.-213-25134A>G | intron_variant | 2 |
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 condition Benign:1
Benign, criteria provided, single submitter | 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