chr11-64927831-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.426G>A(p.Pro142=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,611,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
PPP2R5B
NM_006244.4 synonymous
NM_006244.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.43
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=-0.73).
BP6
Variant 11-64927831-G-A is Benign according to our data. Variant chr11-64927831-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2990603.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.43 with no splicing effect.
BS2
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5B | NM_006244.4 | c.426G>A | p.Pro142= | synonymous_variant | 4/14 | ENST00000164133.7 | |
PPP2R5B | XM_047427199.1 | c.426G>A | p.Pro142= | synonymous_variant | 3/13 | ||
PPP2R5B | XM_011545132.3 | c.339G>A | p.Pro113= | synonymous_variant | 5/15 | ||
PPP2R5B | XM_047427200.1 | c.339G>A | p.Pro113= | synonymous_variant | 5/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5B | ENST00000164133.7 | c.426G>A | p.Pro142= | synonymous_variant | 4/14 | 1 | NM_006244.4 | P1 | |
PPP2R5B | ENST00000526559.5 | c.426G>A | p.Pro142= | synonymous_variant | 4/5 | 5 | |||
PPP2R5B | ENST00000532850.1 | c.168G>A | p.Pro56= | synonymous_variant | 4/5 | 3 | |||
PPP2R5B | ENST00000528530.1 | n.98G>A | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151946Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251446Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135900
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GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459908Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726380
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
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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 | Aug 27, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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