11-64925917-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006244.4(PPP2R5B):c.183G>A(p.Pro61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000401 in 1,611,528 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 2 hom., cov: 31)
Exomes 𝑓: 0.00024 ( 1 hom. )
Consequence
PPP2R5B
NM_006244.4 synonymous
NM_006244.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.14
Genes affected
PPP2R5B (HGNC:9310): (protein phosphatase 2 regulatory subunit B'beta) 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 beta isoform of the regulatory subunit B56 subfamily. [provided by RefSeq, Jul 2008]
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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=-0.72).
BP6
Variant 11-64925917-G-A is Benign according to our data. Variant chr11-64925917-G-A is described in ClinVar as [Benign]. Clinvar id is 1589486.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BS2
High AC in GnomAd4 at 293 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5B | NM_006244.4 | c.183G>A | p.Pro61= | synonymous_variant | 2/14 | ENST00000164133.7 | |
PPP2R5B | XM_047427199.1 | c.183G>A | p.Pro61= | synonymous_variant | 1/13 | ||
PPP2R5B | XM_011545132.3 | c.96G>A | p.Pro32= | synonymous_variant | 3/15 | ||
PPP2R5B | XM_047427200.1 | c.96G>A | p.Pro32= | synonymous_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5B | ENST00000164133.7 | c.183G>A | p.Pro61= | synonymous_variant | 2/14 | 1 | NM_006244.4 | P1 | |
PPP2R5B | ENST00000526559.5 | c.183G>A | p.Pro61= | synonymous_variant | 2/5 | 5 | |||
PPP2R5B | ENST00000532850.1 | c.-76G>A | 5_prime_UTR_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00192 AC: 292AN: 152184Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.000630 AC: 155AN: 245904Hom.: 0 AF XY: 0.000440 AC XY: 59AN XY: 134022
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GnomAD4 exome AF: 0.000242 AC: 353AN: 1459226Hom.: 1 Cov.: 34 AF XY: 0.000244 AC XY: 177AN XY: 725880
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GnomAD4 genome AF: 0.00192 AC: 293AN: 152302Hom.: 2 Cov.: 31 AF XY: 0.00187 AC XY: 139AN XY: 74472
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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 | Jan 05, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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