chr7-113879268-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_002711.4(PPP1R3A):c.1824C>T(p.Ser608=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,440 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000015 ( 1 hom. )
Consequence
PPP1R3A
NM_002711.4 synonymous
NM_002711.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
PPP1R3A (HGNC:9291): (protein phosphatase 1 regulatory subunit 3A) The glycogen-associated form of protein phosphatase-1 (PP1) derived from skeletal muscle is a heterodimer composed of a 37-kD catalytic subunit and a 124-kD targeting and regulatory subunit. This gene encodes the regulatory subunit which binds to muscle glycogen with high affinity, thereby enhancing dephosphorylation of glycogen-bound substrates for PP1 such as glycogen synthase and glycogen phosphorylase kinase. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP7
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| PPP1R3A | NM_002711.4 | c.1824C>T | p.Ser608= | synonymous_variant | 4/4 | ENST00000284601.4 | |
| PPP1R3A | XM_005250473.4 | c.1221C>T | p.Ser407= | synonymous_variant | 5/5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PPP1R3A | ENST00000284601.4 | c.1824C>T | p.Ser608= | synonymous_variant | 4/4 | 1 | NM_002711.4 | P1 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 151914Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250648Hom.: 1 AF XY: 0.0000222 AC XY: 3AN XY: 135420
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461526Hom.: 1 Cov.: 71 AF XY: 0.00000963 AC XY: 7AN XY: 727072
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GnomAD4 genome 0.00000658 AC: 1AN: 151914Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74180
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ClinVar
Not reported inComputational scores
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CADD
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at