Variant 14-101856756-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001352913.2(PPP2R5C):c.330T>C(p.Phe110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0453 in 1,614,032 control chromosomes in the GnomAD database, including 1,930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.054 ( 299 hom., cov: 33)

Exomes 𝑓: 0.044 ( 1631 hom. )

Consequence

PPP2R5C
NM_001352913.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.505

Variant links:

Genes affected

PPP2R5C (HGNC:9311): (protein phosphatase 2 regulatory subunit B'gamma) The product of 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 a gamma isoform of the regulatory subunit B56 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

PPP2R5C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 14-101856756-T-C is Benign according to our data. Variant chr14-101856756-T-C is described in ClinVar as [Benign]. Clinvar id is 1602207.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.505 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.089 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP2R5C	NM_001352913.2 linkuse as main transcript	c.330T>C	p.Phe110=	synonymous_variant	4/16	ENST00000694906.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP2R5C	ENST00000694906.1 linkuse as main transcript	c.330T>C	p.Phe110=	synonymous_variant	4/16		NM_001352913.2	P3

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8235

AN:

152236

Hom.:

299

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0915

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0327

Gnomad ASJ

AF:

0.0461

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0265

Gnomad FIN

AF:

0.0320

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0469

Gnomad OTH

AF:

0.0540

GnomAD3 exomes

AF:

0.0386

AC:

9702

AN:

251448

Hom.:

266

AF XY:

0.0385

AC XY:

5238

AN XY:

135900

show subpopulations

Gnomad AFR exome

AF:

0.0894

Gnomad AMR exome

AF:

0.0202

Gnomad ASJ exome

AF:

0.0437

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.0309

Gnomad FIN exome

AF:

0.0312

Gnomad NFE exome

AF:

0.0462

Gnomad OTH exome

AF:

0.0375

GnomAD4 exome

AF:

0.0444

AC:

64878

AN:

1461678

Hom.:

1631

Cov.:

AF XY:

0.0438

AC XY:

31846

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.0942

Gnomad4 AMR exome

AF:

0.0220

Gnomad4 ASJ exome

AF:

0.0450

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0309

Gnomad4 FIN exome

AF:

0.0324

Gnomad4 NFE exome

AF:

0.0472

Gnomad4 OTH exome

AF:

0.0419

GnomAD4 genome

AF:

0.0541

AC:

8247

AN:

152354

Hom.:

299

Cov.:

AF XY:

0.0522

AC XY:

3890

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.0914

Gnomad4 AMR

AF:

0.0327

Gnomad4 ASJ

AF:

0.0461

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0267

Gnomad4 FIN

AF:

0.0320

Gnomad4 NFE

AF:

0.0469

Gnomad4 OTH

AF:

0.0539

Alfa

AF:

0.0506

Hom.:

111

Bravo

AF:

0.0552

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0467

EpiControl

AF:

0.0481

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

5.6

DANN

Benign

0.51

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over