rs917948
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_006247.4(PPP5C):c.132C>T(p.Tyr44=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,613,882 control chromosomes in the GnomAD database, including 17,160 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 0.12 ( 1662 hom., cov: 33)
Exomes 𝑓: 0.12 ( 15498 hom. )
Consequence
PPP5C
NM_006247.4 synonymous
NM_006247.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.975
Genes affected
PPP5C (HGNC:9322): (protein phosphatase 5 catalytic subunit) This gene encodes a serine/threonine phosphatase which is a member of the protein phosphatase catalytic subunit family. Proteins in this family participate in pathways regulated by reversible phosphorylation at serine and threonine residues; many of these pathways are involved in the regulation of cell growth and differentiation. The product of this gene has been shown to participate in signaling pathways in response to hormones or cellular stress, and elevated levels of this protein may be associated with breast cancer development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP7
?
Synonymous conserved (PhyloP=0.975 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP5C | NM_006247.4 | c.132C>T | p.Tyr44= | synonymous_variant | 2/13 | ENST00000012443.9 | |
PPP5C | NM_001204284.2 | c.132C>T | p.Tyr44= | synonymous_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP5C | ENST00000012443.9 | c.132C>T | p.Tyr44= | synonymous_variant | 2/13 | 1 | NM_006247.4 | P1 | |
PPP5C | ENST00000478046.5 | c.129C>T | p.Tyr43= | synonymous_variant, NMD_transcript_variant | 2/14 | 1 | |||
PPP5C | ENST00000391919.1 | c.-187C>T | 5_prime_UTR_variant | 2/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.120 AC: 18275AN: 152128Hom.: 1663 Cov.: 33
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GnomAD3 exomes AF: 0.174 AC: 43551AN: 250558Hom.: 6354 AF XY: 0.160 AC XY: 21681AN XY: 135528
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GnomAD4 exome AF: 0.124 AC: 180887AN: 1461636Hom.: 15498 Cov.: 32 AF XY: 0.121 AC XY: 87813AN XY: 727134
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GnomAD4 genome ? AF: 0.120 AC: 18296AN: 152246Hom.: 1662 Cov.: 33 AF XY: 0.128 AC XY: 9551AN XY: 74440
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at