chr14-101819008-A-G
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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.259+32825A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000593 in 1,550,806 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 7 hom., cov: 32)
Exomes 𝑓: 0.00031 ( 2 hom. )
Consequence
PPP2R5C
NM_001352913.2 intron
NM_001352913.2 intron
Scores
14
Clinical Significance
Conservation
PhyloP100: -0.554
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 (MetaRNN=0.0031365454).
BP6
Variant 14-101819008-A-G is Benign according to our data. Variant chr14-101819008-A-G is described in ClinVar as [Benign]. Clinvar id is 1570998.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 483 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5C | NM_001352913.2 | c.259+32825A>G | intron_variant | ENST00000694906.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5C | ENST00000694906.1 | c.259+32825A>G | intron_variant | NM_001352913.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00315 AC: 480AN: 152168Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.000753 AC: 116AN: 154040Hom.: 1 AF XY: 0.000575 AC XY: 47AN XY: 81736
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GnomAD4 exome AF: 0.000312 AC: 437AN: 1398520Hom.: 2 Cov.: 30 AF XY: 0.000257 AC XY: 177AN XY: 689842
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GnomAD4 genome AF: 0.00317 AC: 483AN: 152286Hom.: 7 Cov.: 32 AF XY: 0.00303 AC XY: 226AN XY: 74466
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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 | Jun 15, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N;N;N
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at