5-146638376-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3BP4_StrongBP6BS2
The NM_181675.4(PPP2R2B):c.665C>T(p.Thr222Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,611,790 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_181675.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000307 AC: 77AN: 250682Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135474
GnomAD4 exome AF: 0.000151 AC: 220AN: 1459452Hom.: 2 Cov.: 31 AF XY: 0.000154 AC XY: 112AN XY: 726106
GnomAD4 genome AF: 0.000151 AC: 23AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74494
ClinVar
Submissions by phenotype
PPP2R2B-related disorder Benign:1
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