Genetic Variant PRKCB:p.Pro202Pro (chr16-24092867-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_002738.7(PRKCB):c.606C>T(p.Pro202Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 1,614,006 control chromosomes in the GnomAD database, including 1,490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.036 ( 131 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1359 hom. )

Consequence

PRKCB
NM_002738.7 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.17

Variant links:

Genes affected

PRKCB (HGNC:9395): (protein kinase C beta) Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and second messenger diacylglycerol. PKC family members phosphorylate a wide variety of protein targets and are known to be involved in diverse cellular signaling pathways. PKC family members also serve as major receptors for phorbol esters, a class of tumor promoters. Each member of the PKC family has a specific expression profile and is believed to play a distinct role in cells. The protein encoded by this gene is one of the PKC family members. This protein kinase has been reported to be involved in many different cellular functions, such as B cell activation, apoptosis induction, endothelial cell proliferation, and intestinal sugar absorption. Studies in mice also suggest that this kinase may also regulate neuronal functions and correlate fear-induced conflict behavior after stress. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

PRKCB 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=-0.3).

BP6

Variant 16-24092867-C-T is Benign according to our data. Variant chr16-24092867-C-T is described in ClinVar as [Benign]. Clinvar id is 3055721.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.17 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKCB	NM_002738.7 link	c.606C>T	p.Pro202Pro	synonymous_variant	Exon 6 of 17	ENST00000643927.1	NP_002729.2	P05771-2
PRKCB	NM_212535.3 link	c.606C>T	p.Pro202Pro	synonymous_variant	Exon 6 of 17		NP_997700.1	P05771-1
PRKCB	XM_047434365.1 link	c.219C>T	p.Pro73Pro	synonymous_variant	Exon 5 of 16		XP_047290321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKCB	ENST00000643927.1 link	c.606C>T	p.Pro202Pro	synonymous_variant	Exon 6 of 17		NM_002738.7	ENSP00000496129.1		P05771-2

Frequencies

GnomAD3 genomes

AF:

0.0365

AC:

5546

AN:

152110

Hom.:

132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0268

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0185

Gnomad ASJ

AF:

0.0271

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.0622

Gnomad FIN

AF:

0.0427

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0375

Gnomad OTH

AF:

0.0330

GnomAD3 exomes

AF:

0.0418

AC:

10507

AN:

251374

Hom.:

338

AF XY:

0.0420

AC XY:

5705

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.0255

Gnomad AMR exome

AF:

0.0159

Gnomad ASJ exome

AF:

0.0296

Gnomad EAS exome

AF:

0.117

Gnomad SAS exome

AF:

0.0521

Gnomad FIN exome

AF:

0.0436

Gnomad NFE exome

AF:

0.0380

Gnomad OTH exome

AF:

0.0384

GnomAD4 exome

AF:

0.0405

AC:

59174

AN:

1461778

Hom.:

1359

Cov.:

AF XY:

0.0405

AC XY:

29445

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.0260

Gnomad4 AMR exome

AF:

0.0170

Gnomad4 ASJ exome

AF:

0.0295

Gnomad4 EAS exome

AF:

0.0874

Gnomad4 SAS exome

AF:

0.0520

Gnomad4 FIN exome

AF:

0.0456

Gnomad4 NFE exome

AF:

0.0393

Gnomad4 OTH exome

AF:

0.0423

GnomAD4 genome

AF:

0.0364

AC:

5543

AN:

152228

Hom.:

131

Cov.:

AF XY:

0.0365

AC XY:

2718

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0267

Gnomad4 AMR

AF:

0.0184

Gnomad4 ASJ

AF:

0.0271

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.0620

Gnomad4 FIN

AF:

0.0427

Gnomad4 NFE

AF:

0.0375

Gnomad4 OTH

AF:

0.0326

Alfa

AF:

0.0356

Hom.:

Bravo

AF:

0.0350

Asia WGS

AF:

0.0780

AC:

271

AN:

3478

EpiCase

AF:

0.0364

EpiControl

AF:

0.0360

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PRKCB-related disorder

Benign:1

Sep 04, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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