rs616322

chr11-64923403-G-C

Variant summary

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

The ENST00000526559.5(PPP2R5B):c.-264-2068G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,236 control chromosomes in the GnomAD database, including 1,038 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 0.10 (1038 hom., cov: 32)
• Consequence: PPP2R5B ENST00000526559.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

Genes affected

PPP2R5B (HGNC:9310): (protein phosphatase 2 regulatory subunit B'beta) The product of this gene belongs to the phosphatase 2A regulatory subunit B family. Protein phosphatase 2A 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 a beta isoform of the regulatory subunit B56 subfamily. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP2R5B	XM_011545132.3	c.27-2445G>C		intron_variant
PPP2R5B	XM_047427200.1	c.27-2445G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP2R5B	ENST00000526559.5	c.-264-2068G>C		intron_variant		5
PPP2R5B	ENST00000413292.1	n.288+301G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15151 AN: 152118 Hom.: 1037 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.0995 AC: 15150 AN: 152236 Hom.: 1038 Cov.: 32 AF XY: 0.105 AC XY: 7817 AN XY: 74420

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0992

Alfa AF: 0.107 Hom.: 119

Bravo AF: 0.0823

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	4.8
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs616322; hg19: chr11-64690875;