10-6530263-C-T

Variant names:

• chr10-6530263-C-T
• rs11259403
• NM_006257.5:c.-9-15119G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006257.5(PRKCQ):​c.-9-15119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,972 control chromosomes in the GnomAD database, including 23,908 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 0.51 (23908 hom., cov: 31)
• Consequence: PRKCQ NM_006257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 16 publications found

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]

ENSG00000302067 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKCQ	NM_006257.5	c.-9-15119G>A		intron_variant	Intron 1 of 17	ENST00000263125.10	NP_006248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKCQ	ENST00000263125.10	c.-9-15119G>A		intron_variant	Intron 1 of 17	1	NM_006257.5	ENSP00000263125.5
PRKCQ	ENST00000397176.6	c.-9-15119G>A		intron_variant	Intron 1 of 16	5		ENSP00000380361.2
PRKCQ	ENST00000539722.5	c.-323-15119G>A		intron_variant	Intron 1 of 16	2		ENSP00000441752.1
ENSG00000302067	ENST00000783835.1	n.382-7150C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77194 AN: 151854 Hom.: 23894 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.567

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.508 AC: 77218 AN: 151972 Hom.: 23908 Cov.: 31 AF XY: 0.512 AC XY: 38045 AN XY: 74278

African (AFR) AF: 0.132 AC: 5454 AN: 41456

American (AMR) AF: 0.665 AC: 10160 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2557 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4818

European-Finnish (FIN) AF: 0.658 AC: 6923 AN: 10528

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45186 AN: 67966

Other (OTH) AF: 0.569 AC: 1198 AN: 2104

Alfa AF: 0.621 Hom.: 99142

Bravo AF: 0.490

Asia WGS AF: 0.516 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.69
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11259403; hg19: chr10-6572225;