Genetic Variant PPP2R2D:c.*381C>G (chr10-131956344-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018461.5(PPP2R2D):c.*381C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 988,370 control chromosomes in the GnomAD database, including 31,315 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 0.28 ( 6028 hom., cov: 33)

Exomes 𝑓: 0.24 ( 25287 hom. )

Consequence

PPP2R2D
NM_018461.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

7 publications found

Variant links:

Genes affected

PPP2R2D (HGNC:23732): (protein phosphatase 2 regulatory subunit Bdelta) Predicted to enable protein phosphatase regulator activity. Predicted to be involved in exit from mitosis and peptidyl-serine dephosphorylation. Predicted to be part of protein phosphatase type 2A complex. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

PPP2R2D 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018461.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PPP2R2D	NM_018461.5	MANE Select	c.*381C>G	3_prime_UTR	Exon 9 of 9	NP_060931.2
PPP2R2D	NM_001291310.2		c.*381C>G	3_prime_UTR	Exon 10 of 10	NP_001278239.1	Q6IN90
PPP2R2D	NR_033191.3		n.1870C>G	non_coding_transcript_exon	Exon 10 of 10

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PPP2R2D	ENST00000455566.6	TSL:1 MANE Select	c.*381C>G	3_prime_UTR	Exon 9 of 9	ENSP00000399970.2	Q66LE6
PPP2R2D	ENST00000470416.5	TSL:1	n.*2546C>G	non_coding_transcript_exon	Exon 9 of 9	ENSP00000485636.1	A0A096LPI9
PPP2R2D	ENST00000616467.4	TSL:1	n.*1495C>G	non_coding_transcript_exon	Exon 10 of 10	ENSP00000481133.2	A0A0A6YYD6

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42398

AN:

151966

Hom.:

6019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.447

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.245

AC:

204718

AN:

836286

Hom.:

25287

Cov.:

AF XY:

0.244

AC XY:

94374

AN XY:

386304

show subpopulations

African (AFR)

AF:

0.291

AC:

4636

AN:

15928

American (AMR)

AF:

0.280

AC:

303

AN:

1082

Ashkenazi Jewish (ASJ)

AF:

0.342

AC:

1813

AN:

5300

East Asian (EAS)

AF:

0.473

AC:

1802

AN:

3808

South Asian (SAS)

AF:

0.279

AC:

4611

AN:

16506

European-Finnish (FIN)

AF:

0.238

AC:

AN:

390

Middle Eastern (MID)

AF:

0.300

AC:

490

AN:

1634

European-Non Finnish (NFE)

AF:

0.240

AC:

183729

AN:

764136

Other (OTH)

AF:

0.263

AC:

7241

AN:

27502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

9100

18200

27300

36400

45500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8642

17284

25926

34568

43210

<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:

0.279

AC:

42444

AN:

152084

Hom.:

6028

Cov.:

AF XY:

0.281

AC XY:

20915

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.287

AC:

11903

AN:

41484

American (AMR)

AF:

0.296

AC:

4532

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1230

AN:

3466

East Asian (EAS)

AF:

0.447

AC:

2300

AN:

5146

South Asian (SAS)

AF:

0.291

AC:

1404

AN:

4818

European-Finnish (FIN)

AF:

0.277

AC:

2929

AN:

10582

Middle Eastern (MID)

AF:

0.277

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.253

AC:

17217

AN:

67988

Other (OTH)

AF:

0.278

AC:

587

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1607

3213

4820

6426

8033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<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:

0.140

Hom.:

252

Bravo

AF:

0.283

Asia WGS

AF:

0.339

AC:

1180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.78

(source)

DANN

Benign

0.60

PhyloP100

-0.031

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over