rs616322

Variant names:

• chr11-64923403-G-C
• rs616322
• ENST00000526559.5:c.-264-2068G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PPP2R5B	XM_011545132.3	c.27-2445G>C		intron_variant	Intron 2 of 14		XP_011543434.1
PPP2R5B	XM_047427200.1	c.27-2445G>C		intron_variant	Intron 2 of 14		XP_047283156.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R5B	ENST00000526559.5	c.-264-2068G>C		intron_variant	Intron 1 of 4	5		ENSP00000437088.1
PPP2R5B	ENST00000413292.1	n.288+301G>C		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.0227 AC: 942 AN: 41558

American (AMR) AF: 0.0799 AC: 1223 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3470

East Asian (EAS) AF: 0.137 AC: 711 AN: 5176

South Asian (SAS) AF: 0.114 AC: 549 AN: 4830

European-Finnish (FIN) AF: 0.254 AC: 2679 AN: 10568

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8099 AN: 68014

Other (OTH) AF: 0.0992 AC: 210 AN: 2116

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
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs616322; hg19: chr11-64690875;