rs3200031

chr8-26369968-C-T

Variant summary

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

The NM_002717.4(PPP2R2A):c.1065-166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 152,232 control chromosomes in the GnomAD database, including 247 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 0.048 (247 hom., cov: 32)
• Consequence: PPP2R2A NM_002717.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP2R2A	NM_002717.4	c.1065-166C>T		intron_variant		ENST00000380737.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP2R2A	ENST00000380737.8	c.1065-166C>T		intron_variant		1	NM_002717.4	P1

Frequencies

GnomAD3 genomes AF: 0.0481 AC: 7320 AN: 152112 Hom.: 248 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.0381

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0481 AC: 7318 AN: 152232 Hom.: 247 Cov.: 32 AF XY: 0.0476 AC XY: 3547 AN XY: 74440

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0500

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0381

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0506 Hom.: 30

Bravo AF: 0.0459

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.11
Dann	Benign	0.45

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: rs3200031; hg19: chr8-26227484;