chr14-101882226-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001352913.2(PPP2R5C):c.525G>A(p.Pro175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000181 in 1,613,680 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00018 ( 0 hom. )
Consequence
PPP2R5C
NM_001352913.2 synonymous
NM_001352913.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.104
Genes affected
PPP2R5C (HGNC:9311): (protein phosphatase 2 regulatory subunit B'gamma) The product of this gene belongs to the phosphatase 2A regulatory subunit B family. Protein phosphatase 2A is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a gamma isoform of the regulatory subunit B56 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 14-101882226-G-A is Benign according to our data. Variant chr14-101882226-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2052196.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.104 with no splicing effect.
BS2
High AC in GnomAd4 at 29 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5C | NM_001352913.2 | c.525G>A | p.Pro175= | synonymous_variant | 5/16 | ENST00000694906.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5C | ENST00000694906.1 | c.525G>A | p.Pro175= | synonymous_variant | 5/16 | NM_001352913.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152132Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000163 AC: 41AN: 250916Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135632
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GnomAD4 exome AF: 0.000180 AC: 263AN: 1461430Hom.: 0 Cov.: 30 AF XY: 0.000182 AC XY: 132AN XY: 727004
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GnomAD4 genome AF: 0.000190 AC: 29AN: 152250Hom.: 1 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74444
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
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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