Variant rs2738364 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013239.5(PPP2R3B):c.1086-8C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 1,611,780 control chromosomes in the GnomAD database, including 513,198 homozygotes. There are 638,742 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 48997 hom., 59354 hem., cov: 34)

Exomes 𝑓: 0.80 ( 464201 hom. 579388 hem. )

Consequence

PPP2R3B
NM_013239.5 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0190

Variant links:

Genes affected

PPP2R3B (HGNC:13417): (protein phosphatase 2 regulatory subunit B''beta) Protein phosphatase 2 (formerly named type 2A) is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2 holoenzymes are heterotrimeric proteins composed of a structural subunit A, a catalytic subunit C, and a regulatory subunit B. The regulatory subunit is encoded by a diverse set of genes that have been grouped into the B/PR55, B'/PR61, and B''/PR72 families. These different regulatory subunits confer distinct enzymatic specificities and intracellular localizations to the holozenzyme. The product of this gene belongs to the B'' family. The B'' family has been further divided into subfamilies. The product of this gene belongs to the beta subfamily of regulatory subunit B''. [provided by RefSeq, Apr 2010]

PPP2R3B links:

PPP2R3B (HGNC:):

PPP2R3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2R3B	NM_013239.5 linkuse as main transcript	c.1086-8C>G		splice_region_variant, intron_variant		ENST00000390665.9	NP_037371.2	Q9Y5P8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2R3B	ENST00000390665.9 linkuse as main transcript	c.1086-8C>G		splice_region_variant, intron_variant		1	NM_013239.5	ENSP00000375080.3		Q9Y5P8-1

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

121744

AN:

152048

Hom.:

48980

Cov.:

AF XY:

0.798

AC XY:

59273

AN XY:

74254

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.700

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.811

Gnomad SAS

AF:

0.817

Gnomad FIN

AF:

0.785

Gnomad MID

AF:

0.864

Gnomad NFE

AF:

0.801

Gnomad OTH

AF:

0.811

GnomAD3 exomes

AF:

0.780

AC:

193521

AN:

248100

Hom.:

76239

AF XY:

0.789

AC XY:

106469

AN XY:

135022

show subpopulations

Gnomad AFR exome

AF:

0.843

Gnomad AMR exome

AF:

0.608

Gnomad ASJ exome

AF:

0.798

Gnomad EAS exome

AF:

0.815

Gnomad SAS exome

AF:

0.822

Gnomad FIN exome

AF:

0.790

Gnomad NFE exome

AF:

0.803

Gnomad OTH exome

AF:

0.803

GnomAD4 exome

AF:

0.797

AC:

1162618

AN:

1459614

Hom.:

464201

Cov.:

AF XY:

0.798

AC XY:

579388

AN XY:

726022

show subpopulations

Gnomad4 AFR exome

AF:

0.845

Gnomad4 AMR exome

AF:

0.619

Gnomad4 ASJ exome

AF:

0.797

Gnomad4 EAS exome

AF:

0.796

Gnomad4 SAS exome

AF:

0.820

Gnomad4 FIN exome

AF:

0.785

Gnomad4 NFE exome

AF:

0.801

Gnomad4 OTH exome

AF:

0.798

GnomAD4 genome

AF:

0.800

AC:

121805

AN:

152166

Hom.:

48997

Cov.:

AF XY:

0.798

AC XY:

59354

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.840

Gnomad4 AMR

AF:

0.699

Gnomad4 ASJ

AF:

0.791

Gnomad4 EAS

AF:

0.811

Gnomad4 SAS

AF:

0.817

Gnomad4 FIN

AF:

0.785

Gnomad4 NFE

AF:

0.801

Gnomad4 OTH

AF:

0.806

Bravo

AF:

0.796

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.1

DANN

Benign

0.39

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over