rs1564577

Positions:

• chr8-26307207-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002717.4(PPP2R2A):​c.82+13467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,008 control chromosomes in the GnomAD database, including 26,695 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (26695 hom., cov: 32)
• Consequence: PPP2R2A NM_002717.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2R2A	NM_002717.4	c.82+13467G>A		intron_variant		ENST00000380737.8	NP_002708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2R2A	ENST00000380737.8	c.82+13467G>A		intron_variant		1	NM_002717.4	ENSP00000370113	P1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89525 AN: 151890 Hom.: 26651 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.568

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.590 AC: 89625 AN: 152008 Hom.: 26695 Cov.: 32 AF XY: 0.591 AC XY: 43904 AN XY: 74270

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.571

Alfa AF: 0.597 Hom.: 3400

Bravo AF: 0.578

Asia WGS AF: 0.536 AC: 1864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.062
DANN	Benign	0.15

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: rs1564577; hg19: chr8-26164723;