Variant 16-24191137-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_002738.7(PRKCB):c.1770C>T(p.Gly590=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,613,202 control chromosomes in the GnomAD database, including 50,312 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 0.25 ( 5032 hom., cov: 31)

Exomes 𝑓: 0.24 ( 45280 hom. )

Consequence

PRKCB
NM_002738.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP7

Synonymous conserved (PhyloP=-1.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PRKCB	NM_002738.7 linkuse as main transcript	c.1770C>T	p.Gly590=	synonymous_variant	16/17	ENST00000643927.1
PRKCB	NM_212535.3 linkuse as main transcript	c.1770C>T	p.Gly590=	synonymous_variant	16/17
PRKCB	XM_047434365.1 linkuse as main transcript	c.1383C>T	p.Gly461=	synonymous_variant	15/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKCB	ENST00000643927.1 linkuse as main transcript	c.1770C>T	p.Gly590=	synonymous_variant	16/17		NM_002738.7	A1	P05771-2
PRKCB	ENST00000321728.12 linkuse as main transcript	c.1770C>T	p.Gly590=	synonymous_variant	16/17	1		P4	P05771-1
PRKCB	ENST00000466124.1 linkuse as main transcript	c.87C>T	p.Gly29=	synonymous_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38148

AN:

151794

Hom.:

5027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.292

Gnomad EAS

AF:

0.0951

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.267

GnomAD3 exomes

AF:

0.232

AC:

58240

AN:

251222

Hom.:

7487

AF XY:

0.240

AC XY:

32581

AN XY:

135764

show subpopulations

Gnomad AFR exome

AF:

0.302

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.279

Gnomad EAS exome

AF:

0.0881

Gnomad SAS exome

AF:

0.337

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.259

GnomAD4 exome

AF:

0.245

AC:

357680

AN:

1461290

Hom.:

45280

Cov.:

AF XY:

0.248

AC XY:

180419

AN XY:

726978

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.155

Gnomad4 ASJ exome

AF:

0.273

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.335

Gnomad4 FIN exome

AF:

0.193

Gnomad4 NFE exome

AF:

0.246

Gnomad4 OTH exome

AF:

0.247

GnomAD4 genome

AF:

0.251

AC:

38181

AN:

151912

Hom.:

5032

Cov.:

AF XY:

0.249

AC XY:

18482

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.215

Gnomad4 ASJ

AF:

0.292

Gnomad4 EAS

AF:

0.0951

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.186

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.266

Alfa

AF:

0.227

Hom.:

2390

Bravo

AF:

0.250

Asia WGS

AF:

0.226

AC:

789

AN:

3478

EpiCase

AF:

0.248

EpiControl

AF:

0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

8.1

DANN

Benign

0.65

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over