10-6430929-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_006257.5(PRKCQ):c.1846C>A(p.Arg616=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,613,574 control chromosomes in the GnomAD database, including 36,221 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 0.18 (2742 hom., cov: 32)
  • Exomes 𝑓: 0.21 (33479 hom.)
• Consequence: PRKCQ NM_006257.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

PRKCQ (HGNC:9410): (protein kinase C theta) Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and the 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. The protein encoded by this gene is one of the PKC family members. It is a calcium-independent and phospholipid-dependent protein kinase. This kinase is important for T-cell activation. It is required for the activation of the transcription factors NF-kappaB and AP-1, and may link the T cell receptor (TCR) signaling complex to the activation of the transcription factors. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BP7: Synonymous conserved (PhyloP=1.09 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKCQ	NM_006257.5	c.1846C>A	p.Arg616=	synonymous_variant	17/18	ENST00000263125.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKCQ	ENST00000263125.10	c.1846C>A	p.Arg616=	synonymous_variant	17/18	1	NM_006257.5	P1
PRKCQ	ENST00000397176.6	c.1657C>A	p.Arg553=	synonymous_variant	16/17	5
PRKCQ	ENST00000539722.5	c.1471C>A	p.Arg491=	synonymous_variant	16/17	2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27775 AN: 152016 Hom.: 2739 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.171

GnomAD3 exomes AF: 0.174 AC: 43605 AN: 250646 Hom.: 4339 AF XY: 0.178 AC XY: 24081 AN XY: 135472

Gnomad AFR exome AF: 0.146

Gnomad AMR exome AF: 0.0825

Gnomad ASJ exome AF: 0.153

Gnomad EAS exome AF: 0.0350

Gnomad SAS exome AF: 0.141

Gnomad FIN exome AF: 0.254

Gnomad NFE exome AF: 0.223

Gnomad OTH exome AF: 0.186

GnomAD4 exome AF: 0.207 AC: 302011 AN: 1461440 Hom.: 33479 Cov.: 33 AF XY: 0.205 AC XY: 148819 AN XY: 727024

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.0867

Gnomad4 ASJ exome AF: 0.161

Gnomad4 EAS exome AF: 0.0202

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.258

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.183 AC: 27777 AN: 152134 Hom.: 2742 Cov.: 32 AF XY: 0.181 AC XY: 13445 AN XY: 74386

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.168

Alfa AF: 0.194 Hom.: 5988

Bravo AF: 0.172

Asia WGS AF: 0.0830 AC: 291 AN: 3478

EpiCase AF: 0.207

EpiControl AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
Cadd	Benign	7.5
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs11258747; hg19: chr10-6472891; COSMIC: COSV54107502;