8-26293766-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002717.4(PPP2R2A):c.82+26T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000911 in 1,606,422 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0050 ( 9 hom., cov: 32)
Exomes 𝑓: 0.00048 ( 6 hom. )
Consequence
PPP2R2A
NM_002717.4 intron
NM_002717.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00
Genes affected
PPP2R2A (HGNC:9304): (protein phosphatase 2 regulatory subunit Balpha) The product of this gene belongs to the phosphatase 2 regulatory subunit B family. Protein phosphatase 2 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 an alpha isoform of the regulatory subunit B55 subfamily. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 8-26293766-T-G is Benign according to our data. Variant chr8-26293766-T-G is described in ClinVar as [Benign]. Clinvar id is 1679062.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00504 (768/152330) while in subpopulation AFR AF= 0.0179 (743/41576). AF 95% confidence interval is 0.0168. There are 9 homozygotes in gnomad4. There are 377 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 756 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R2A | NM_002717.4 | c.82+26T>G | intron_variant | ENST00000380737.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R2A | ENST00000380737.8 | c.82+26T>G | intron_variant | 1 | NM_002717.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00497 AC: 756AN: 152212Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00115 AC: 288AN: 250156Hom.: 2 AF XY: 0.000776 AC XY: 105AN XY: 135296
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GnomAD4 exome AF: 0.000478 AC: 695AN: 1454092Hom.: 6 Cov.: 28 AF XY: 0.000403 AC XY: 292AN XY: 723874
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary breast ovarian cancer syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | National Health Laboratory Service, Universitas Academic Hospital and University of the Free State | Apr 19, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
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