chr3-136001831-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002718.5(PPP2R3A):āc.333T>Cā(p.Asp111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,613,946 control chromosomes in the GnomAD database, including 76,651 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.27 ( 5787 hom., cov: 33)
Exomes š: 0.30 ( 70864 hom. )
Consequence
PPP2R3A
NM_002718.5 synonymous
NM_002718.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.17
Genes affected
PPP2R3A (HGNC:9307): (protein phosphatase 2 regulatory subunit B''alpha) This gene encodes one of the regulatory subunits of the protein phosphatase 2. Protein phosphatase 2 (formerly named type 2A) is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2 holoenzymes are heterotrimeric proteins composed of a structural subunit A, a catalytic subunit C, and a regulatory subunit B. The regulatory subunit is encoded by a diverse set of genes that have been grouped into the B/PR55, B'/PR61, and B''/PR72 families. These different regulatory subunits confer distinct enzymatic specificities and intracellular localizations to the holozenzyme. The product of this gene belongs to the B'' family. The B'' family has been further divided into subfamilies. The product of this gene belongs to the alpha subfamily of regulatory subunit B''. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 3-136001831-T-C is Benign according to our data. Variant chr3-136001831-T-C is described in ClinVar as [Benign]. Clinvar id is 3055572.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.17 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R3A | NM_002718.5 | c.333T>C | p.Asp111= | synonymous_variant | 2/14 | ENST00000264977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R3A | ENST00000264977.8 | c.333T>C | p.Asp111= | synonymous_variant | 2/14 | 1 | NM_002718.5 | P3 | |
PPP2R3A | ENST00000490467.5 | c.-213-25001T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.266 AC: 40491AN: 152114Hom.: 5790 Cov.: 33
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GnomAD3 exomes AF: 0.265 AC: 66223AN: 250286Hom.: 10081 AF XY: 0.276 AC XY: 37293AN XY: 135302
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GnomAD4 exome AF: 0.304 AC: 444793AN: 1461714Hom.: 70864 Cov.: 44 AF XY: 0.306 AC XY: 222850AN XY: 727140
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GnomAD4 genome AF: 0.266 AC: 40508AN: 152232Hom.: 5787 Cov.: 33 AF XY: 0.264 AC XY: 19658AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PPP2R3A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at