19-46387103-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_006247.4(PPP5C):c.915G>A(p.Glu305=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00111 in 1,614,272 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00065 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 2 hom. )
Consequence
PPP5C
NM_006247.4 synonymous
NM_006247.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.57
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 19-46387103-G-A is Benign according to our data. Variant chr19-46387103-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3037600.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 99 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP5C | NM_006247.4 | c.915G>A | p.Glu305= | synonymous_variant | 8/13 | ENST00000012443.9 | |
LOC105372426 | XR_007067275.1 | n.405-4579C>T | intron_variant, non_coding_transcript_variant | ||||
PPP5C | NM_001204284.2 | c.849G>A | p.Glu283= | synonymous_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP5C | ENST00000012443.9 | c.915G>A | p.Glu305= | synonymous_variant | 8/13 | 1 | NM_006247.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000650 AC: 99AN: 152270Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000497 AC: 125AN: 251384Hom.: 1 AF XY: 0.000537 AC XY: 73AN XY: 135878
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GnomAD4 exome AF: 0.00116 AC: 1697AN: 1461884Hom.: 2 Cov.: 31 AF XY: 0.00110 AC XY: 800AN XY: 727242
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GnomAD4 genome AF: 0.000650 AC: 99AN: 152388Hom.: 0 Cov.: 33 AF XY: 0.000456 AC XY: 34AN XY: 74528
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PPP5C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 29, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at