dbSNP rs1951212: PPP2R5E:c.158-24380C>T (chr14-63478265-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006246.5(PPP2R5E):c.158-24380C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,006 control chromosomes in the GnomAD database, including 10,879 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 0.33 ( 10879 hom., cov: 32)

Consequence

PPP2R5E
NM_006246.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

1 publications found

Variant links:

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]

PPP2R5E links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PPP2R5E	NM_006246.5	MANE Select	c.158-24380C>T	intron	N/A	NP_006237.1	Q16537-1
PPP2R5E	NM_001282179.3		c.158-24380C>T	intron	N/A	NP_001269108.1	Q16537-1
PPP2R5E	NM_001282180.3		c.158-24380C>T	intron	N/A	NP_001269109.1	Q16537-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PPP2R5E	ENST00000337537.8	TSL:1 MANE Select	c.158-24380C>T	intron	N/A	ENSP00000337641.3	Q16537-1
PPP2R5E	ENST00000555899.1	TSL:1	c.158-24380C>T	intron	N/A	ENSP00000452396.1	Q16537-2
PPP2R5E	ENST00000553266.5	TSL:1	n.741-56171C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49756

AN:

151888

Hom.:

10845

Cov.:

show subpopulations

Gnomad AFR

AF:

0.623

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.311

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

GnomAD4 genome

AF:

0.328

AC:

49837

AN:

152006

Hom.:

10879

Cov.:

AF XY:

0.325

AC XY:

24156

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.623

AC:

25836

AN:

41444

American (AMR)

AF:

0.208

AC:

3167

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

753

AN:

3470

East Asian (EAS)

AF:

0.388

AC:

2007

AN:

5176

South Asian (SAS)

AF:

0.208

AC:

1005

AN:

4824

European-Finnish (FIN)

AF:

0.231

AC:

2436

AN:

10544

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.203

AC:

13809

AN:

67972

Other (OTH)

AF:

0.313

AC:

662

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1439

2878

4318

5757

7196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.281

Hom.:

981

Bravo

AF:

0.338

Asia WGS

AF:

0.349

AC:

1210

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.097

(source)

DANN

Benign

0.40

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over