rs77456357
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002711.4(PPP1R3A):āc.3259A>Gā(p.Ile1087Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,609,466 control chromosomes in the GnomAD database, including 28 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1087R) has been classified as Uncertain significance.
Frequency
Consequence
NM_002711.4 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 |
---|---|---|---|---|---|---|---|
PPP1R3A | NM_002711.4 | c.3259A>G | p.Ile1087Val | missense_variant | 4/4 | ENST00000284601.4 | |
PPP1R3A | XM_005250473.4 | c.2656A>G | p.Ile886Val | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R3A | ENST00000284601.4 | c.3259A>G | p.Ile1087Val | missense_variant | 4/4 | 1 | NM_002711.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00731 AC: 1111AN: 151986Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00194 AC: 485AN: 249786Hom.: 4 AF XY: 0.00141 AC XY: 190AN XY: 135010
GnomAD4 exome AF: 0.000728 AC: 1061AN: 1457362Hom.: 14 Cov.: 30 AF XY: 0.000619 AC XY: 449AN XY: 725310
GnomAD4 genome ? AF: 0.00736 AC: 1120AN: 152104Hom.: 14 Cov.: 32 AF XY: 0.00691 AC XY: 514AN XY: 74362
ClinVar
Submissions by phenotype
Monogenic diabetes Benign:1
Benign, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Dec 21, 2018 | ACMG criteria: BP4 (REVEL 0.027 + 10 predictors), BS2 (75 cases and 66 controls in T2DM), BA1 (2.6% MAF in gnomAD African)= benign - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at