chr7-113879212-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002711.4(PPP1R3A):c.1880G>A(p.Arg627Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00595 in 1,613,512 control chromosomes in the GnomAD database, including 449 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002711.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R3A | NM_002711.4 | c.1880G>A | p.Arg627Lys | missense_variant | 4/4 | ENST00000284601.4 | |
PPP1R3A | XM_005250473.4 | c.1277G>A | p.Arg426Lys | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R3A | ENST00000284601.4 | c.1880G>A | p.Arg627Lys | missense_variant | 4/4 | 1 | NM_002711.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0308 AC: 4686AN: 151958Hom.: 240 Cov.: 32
GnomAD3 exomes AF: 0.00843 AC: 2114AN: 250648Hom.: 95 AF XY: 0.00614 AC XY: 831AN XY: 135442
GnomAD4 exome AF: 0.00336 AC: 4904AN: 1461436Hom.: 208 Cov.: 71 AF XY: 0.00292 AC XY: 2122AN XY: 727020
GnomAD4 genome ? AF: 0.0309 AC: 4693AN: 152076Hom.: 241 Cov.: 32 AF XY: 0.0288 AC XY: 2138AN XY: 74324
ClinVar
Submissions by phenotype
Monogenic diabetes Benign:1
Benign, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Nov 08, 2018 | ACMG criteria: BA1 (10.7% in African), BS2 (142 homo in ExAC), BP4 (REVEL score 0.015 + 9 predictors)=benign - |
PPP1R3A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 31, 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