Variant 8-26370083-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002717.4(PPP2R2A):c.1065-51A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,557,578 control chromosomes in the GnomAD database, including 21,216 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3207 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18009 hom. )

Consequence

PPP2R2A
NM_002717.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.712

Variant links:

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]

PPP2R2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 8-26370083-A-C is Benign according to our data. Variant chr8-26370083-A-C is described in ClinVar as [Benign]. Clinvar id is 1679072.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP2R2A	NM_002717.4 linkuse as main transcript	c.1065-51A>C		intron_variant		ENST00000380737.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP2R2A	ENST00000380737.8 linkuse as main transcript	c.1065-51A>C		intron_variant		1	NM_002717.4	P1	P63151-1

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28336

AN:

152000

Hom.:

3207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.180

GnomAD3 exomes

AF:

0.168

AC:

38415

AN:

228572

Hom.:

4018

AF XY:

0.163

AC XY:

20209

AN XY:

123882

show subpopulations

Gnomad AFR exome

AF:

0.293

Gnomad AMR exome

AF:

0.131

Gnomad ASJ exome

AF:

0.138

Gnomad EAS exome

AF:

0.423

Gnomad SAS exome

AF:

0.144

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.150

GnomAD4 exome

AF:

0.148

AC:

207801

AN:

1405458

Hom.:

18009

Cov.:

AF XY:

0.147

AC XY:

102362

AN XY:

695402

show subpopulations

Gnomad4 AFR exome

AF:

0.289

Gnomad4 AMR exome

AF:

0.128

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.464

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.122

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.156

GnomAD4 genome

AF:

0.186

AC:

28354

AN:

152120

Hom.:

3207

Cov.:

AF XY:

0.186

AC XY:

13821

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.135

Gnomad4 ASJ

AF:

0.139

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.153

Hom.:

438

Bravo

AF:

0.191

Asia WGS

AF:

0.276

AC:

959

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.0

DANN

Benign

0.79

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over