rs2974938
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002711.4(PPP1R3A):āc.2645T>Gā(p.Leu882Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L882H) has been classified as Benign.
Frequency
Consequence
NM_002711.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R3A | NM_002711.4 | c.2645T>G | p.Leu882Arg | missense_variant | 4/4 | ENST00000284601.4 | |
PPP1R3A | XM_005250473.4 | c.2042T>G | p.Leu681Arg | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R3A | ENST00000284601.4 | c.2645T>G | p.Leu882Arg | missense_variant | 4/4 | 1 | NM_002711.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249766Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135040
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460374Hom.: 0 Cov.: 73 AF XY: 0.00000138 AC XY: 1AN XY: 726548
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at