chr14-101762885-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001352913.2(PPP2R5C):c.28-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000413 in 1,571,468 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 Benign (★).
Frequency
Genomes: 𝑓 0.0023 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
PPP2R5C
NM_001352913.2 intron
NM_001352913.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.475
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 14-101762885-C-T is Benign according to our data. Variant chr14-101762885-C-T is described in ClinVar as [Benign]. Clinvar id is 1663888.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 355 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5C | NM_001352913.2 | c.28-20C>T | intron_variant | ENST00000694906.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5C | ENST00000694906.1 | c.28-20C>T | intron_variant | NM_001352913.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00233 AC: 355AN: 152196Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000504 AC: 96AN: 190376Hom.: 0 AF XY: 0.000445 AC XY: 45AN XY: 101172
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GnomAD4 exome AF: 0.000207 AC: 294AN: 1419154Hom.: 1 Cov.: 30 AF XY: 0.000174 AC XY: 122AN XY: 701924
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GnomAD4 genome AF: 0.00233 AC: 355AN: 152314Hom.: 1 Cov.: 31 AF XY: 0.00208 AC XY: 155AN XY: 74474
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 15, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at