NM_006246.5:c.158-35964A>T

Variant names:

• chr14-63489849-T-A
• rs4902230
• NM_006246.5:c.158-35964A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006246.5(PPP2R5E):​c.158-35964A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,030 control chromosomes in the GnomAD database, including 1,760 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 0.15 (1760 hom., cov: 32)
• Consequence: PPP2R5E NM_006246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006246.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP2R5E	NM_006246.5	MANE Select	c.158-35964A>T		intron	N/A	NP_006237.1
	PPP2R5E	NM_001282179.3		c.158-35964A>T		intron	N/A	NP_001269108.1
	PPP2R5E	NM_001282180.3		c.158-35964A>T		intron	N/A	NP_001269109.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP2R5E	ENST00000337537.8	TSL:1 MANE Select	c.158-35964A>T		intron	N/A	ENSP00000337641.3
	PPP2R5E	ENST00000555899.1	TSL:1	c.158-35964A>T		intron	N/A	ENSP00000452396.1
	PPP2R5E	ENST00000553266.5	TSL:1	n.740+49680A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22221 AN: 151910 Hom.: 1756 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.146 AC: 22245 AN: 152030 Hom.: 1760 Cov.: 32 AF XY: 0.149 AC XY: 11056 AN XY: 74324

African (AFR) AF: 0.125 AC: 5173 AN: 41496

American (AMR) AF: 0.118 AC: 1797 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 480 AN: 3458

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5174

South Asian (SAS) AF: 0.163 AC: 784 AN: 4816

European-Finnish (FIN) AF: 0.177 AC: 1868 AN: 10536

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10588 AN: 67980

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.152 Hom.: 243

Bravo AF: 0.139

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.80
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4902230; hg19: chr14-63956567;