8-26370071-AT-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_002717.4(PPP2R2A):c.1065-59del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00365 in 1,530,798 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0023 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0038 (15 hom.)
• Consequence: PPP2R2A NM_002717.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0750

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]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 8-26370071-AT-A is Benign according to our data. Variant chr8-26370071-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 1679071.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 348 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP2R2A	NM_002717.4	c.1065-59del		intron_variant		ENST00000380737.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP2R2A	ENST00000380737.8	c.1065-59del		intron_variant		1	NM_002717.4	P1

Frequencies

GnomAD3 genomes AF: 0.00229 AC: 348 AN: 152178 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000676

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00281

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00348

Gnomad OTH AF: 0.000956

GnomAD4 exome AF: 0.00380 AC: 5241 AN: 1378502 Hom.: 15 AF XY: 0.00382 AC XY: 2611 AN XY: 682894

Gnomad4 AFR exome AF: 0.000617

Gnomad4 AMR exome AF: 0.00165

Gnomad4 ASJ exome AF: 0.000335

Gnomad4 EAS exome AF: 0.0000258

Gnomad4 SAS exome AF: 0.00259

Gnomad4 FIN exome AF: 0.00181

Gnomad4 NFE exome AF: 0.00439

Gnomad4 OTH exome AF: 0.00392

GnomAD4 genome AF: 0.00229 AC: 348 AN: 152296 Hom.: 0 Cov.: 32 AF XY: 0.00187 AC XY: 139 AN XY: 74472

Gnomad4 AFR AF: 0.000674

Gnomad4 AMR AF: 0.00281

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00348

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.00216 Hom.: 0

Bravo AF: 0.00241

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary breast ovarian cancer syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

National Health Laboratory Service, Universitas Academic Hospital and University of the Free State

Apr 19, 2022

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs142234242; hg19: chr8-26227587;