rs1152449

Variant names:

• chr14-63515065-T-C
• rs1152449
• NM_006246.5:c.157+24464A>G

Variant summary

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

The NM_006246.5(PPP2R5E):​c.157+24464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,008 control chromosomes in the GnomAD database, including 16,253 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 0.41 (16253 hom., cov: 32)
• Consequence: PPP2R5E NM_006246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

PPP2R5E (HGNC:9313): (protein phosphatase 2 regulatory subunit B'epsilon) The protein encoded by 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 an epsilon isoform of the regulatory subunit B56 subfamily. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R5E	NM_006246.5	c.157+24464A>G		intron_variant	Intron 2 of 13	ENST00000337537.8	NP_006237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R5E	ENST00000337537.8	c.157+24464A>G		intron_variant	Intron 2 of 13	1	NM_006246.5	ENSP00000337641.3
PPP2R5E	ENST00000555899.1	c.157+24464A>G		intron_variant	Intron 2 of 13	1		ENSP00000452396.1
PPP2R5E	ENST00000553266.5	n.740+24464A>G		intron_variant	Intron 2 of 11	1
PPP2R5E	ENST00000556878.1	n.759+24464A>G		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62290 AN: 151892 Hom.: 16205 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.410 AC: 62382 AN: 152008 Hom.: 16253 Cov.: 32 AF XY: 0.405 AC XY: 30111 AN XY: 74328

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.366

Alfa AF: 0.334 Hom.: 1998

Bravo AF: 0.419

Asia WGS AF: 0.376 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.71

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: rs1152449; hg19: chr14-63981783;