Genetic Variant PPP2R2A:c.802+236T>C (chr8-26363084-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_002717.4(PPP2R2A):c.802+236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 397,138 control chromosomes in the GnomAD database, including 747 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 0.039 ( 177 hom., cov: 31)

Exomes 𝑓: 0.054 ( 570 hom. )

Consequence

PPP2R2A
NM_002717.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

Publications

2 publications found

Variant links:

Genes affected

PPP2R2A (HGNC:9304): (protein phosphatase 2 regulatory subunit Balpha) The product of this gene belongs to the phosphatase 2 regulatory subunit B family. Protein phosphatase 2 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 alpha isoform of the regulatory subunit B55 subfamily. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]

PPP2R2A 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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2A	NM_002717.4 link	c.802+236T>C		intron_variant	Intron 7 of 9	ENST00000380737.8	NP_002708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R2A	ENST00000380737.8 link	c.802+236T>C		intron_variant	Intron 7 of 9	1	NM_002717.4	ENSP00000370113.3

Frequencies

GnomAD3 genomes

AF:

0.0393

AC:

5977

AN:

152056

Hom.:

178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00947

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.0258

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.0677

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0493

Gnomad OTH

AF:

0.0297

GnomAD4 exome

AF:

0.0536

AC:

13142

AN:

244964

Hom.:

570

Cov.:

AF XY:

0.0584

AC XY:

7429

AN XY:

127304

show subpopulations

African (AFR)

AF:

0.00821

AC:

AN:

7552

American (AMR)

AF:

0.0239

AC:

207

AN:

8646

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

969

AN:

8368

East Asian (EAS)

AF:

0.000343

AC:

AN:

17514

South Asian (SAS)

AF:

0.137

AC:

2757

AN:

20186

European-Finnish (FIN)

AF:

0.0673

AC:

935

AN:

13888

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

1192

European-Non Finnish (NFE)

AF:

0.0481

AC:

7339

AN:

152624

Other (OTH)

AF:

0.0527

AC:

790

AN:

14994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

570

1140

1710

2280

2850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0393

AC:

5976

AN:

152174

Hom.:

177

Cov.:

AF XY:

0.0415

AC XY:

3089

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.00944

AC:

392

AN:

41526

American (AMR)

AF:

0.0258

AC:

394

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

414

AN:

3470

East Asian (EAS)

AF:

0.000579

AC:

AN:

5178

South Asian (SAS)

AF:

0.122

AC:

587

AN:

4818

European-Finnish (FIN)

AF:

0.0677

AC:

717

AN:

10592

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0493

AC:

3349

AN:

67980

Other (OTH)

AF:

0.0294

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

278

556

835

1113

1391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0516

Hom.:

123

Bravo

AF:

0.0319

Asia WGS

AF:

0.0470

AC:

165

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.20

(source)

DANN

Benign

0.61

PhyloP100

-1.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over