dbSNP rs1152449: PPP2R5E:c.157+24464A>G (chr14-63515065-T-C) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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.157+24464A>G	intron	N/A	NP_006237.1	Q16537-1
PPP2R5E	NM_001282179.3		c.157+24464A>G	intron	N/A	NP_001269108.1	Q16537-1
PPP2R5E	NM_001282180.3		c.157+24464A>G	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.157+24464A>G	intron	N/A	ENSP00000337641.3	Q16537-1
PPP2R5E	ENST00000555899.1	TSL:1	c.157+24464A>G	intron	N/A	ENSP00000452396.1	Q16537-2
PPP2R5E	ENST00000553266.5	TSL:1	n.740+24464A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.410

AC:

62290

AN:

151892

Hom.:

16205

Cov.:

show subpopulations

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.:

AF XY:

0.405

AC XY:

30111

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.752

AC:

31157

AN:

41444

American (AMR)

AF:

0.259

AC:

3961

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

1134

AN:

3470

East Asian (EAS)

AF:

0.350

AC:

1810

AN:

5174

South Asian (SAS)

AF:

0.279

AC:

1346

AN:

4820

European-Finnish (FIN)

AF:

0.291

AC:

3075

AN:

10552

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.277

AC:

18822

AN:

67956

Other (OTH)

AF:

0.366

AC:

773

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1536

3072

4609

6145

7681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<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:

0.334

Hom.:

1998

Bravo

AF:

0.419

Asia WGS

AF:

0.376

AC:

1305

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.7

(source)

DANN

Benign

0.71

PhyloP100

0.059

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