Genetic Variant PRKCQ:c.118+426G>A (chr10-6514592-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006257.5(PRKCQ):c.118+426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,192 control chromosomes in the GnomAD database, including 43,178 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 0.75 ( 43178 hom., cov: 33)

Consequence

PRKCQ
NM_006257.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

8 publications found

Variant links:

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]

PRKCQ links:

ENSG00000302067 (HGNC:):

ENSG00000302067 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKCQ	NM_006257.5 link	c.118+426G>A		intron_variant	Intron 2 of 17	ENST00000263125.10	NP_006248.1	Q04759-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PRKCQ	ENST00000263125.10 link	c.118+426G>A	intron_variant	Intron 2 of 17	1	NM_006257.5	ENSP00000263125.5	Q04759-1
PRKCQ	ENST00000397176.6 link	c.118+426G>A	intron_variant	Intron 2 of 16	5		ENSP00000380361.2	Q04759-2
PRKCQ	ENST00000539722.5 link	c.-197+426G>A	intron_variant	Intron 2 of 16	2		ENSP00000441752.1	Q04759-3
ENSG00000302067	ENST00000783835.1 link	n.382-22821C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.747

AC:

113601

AN:

152074

Hom.:

43147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.605

Gnomad AMI

AF:

0.859

Gnomad AMR

AF:

0.847

Gnomad ASJ

AF:

0.781

Gnomad EAS

AF:

0.662

Gnomad SAS

AF:

0.728

Gnomad FIN

AF:

0.796

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.807

Gnomad OTH

AF:

0.764

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

GnomAD4 genome

AF:

0.747

AC:

113682

AN:

152192

Hom.:

43178

Cov.:

AF XY:

0.747

AC XY:

55539

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.605

AC:

25127

AN:

41504

American (AMR)

AF:

0.847

AC:

12953

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.781

AC:

2713

AN:

3472

East Asian (EAS)

AF:

0.662

AC:

3428

AN:

5178

South Asian (SAS)

AF:

0.728

AC:

3507

AN:

4818

European-Finnish (FIN)

AF:

0.796

AC:

8434

AN:

10590

Middle Eastern (MID)

AF:

0.813

AC:

239

AN:

294

European-Non Finnish (NFE)

AF:

0.807

AC:

54895

AN:

68022

Other (OTH)

AF:

0.758

AC:

1603

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1456

2912

4369

5825

7281

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

854

1708

2562

3416

4270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.790

Hom.:

200912

Bravo

AF:

0.743

Asia WGS

AF:

0.670

AC:

2332

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.16

(source)

DANN

Benign

0.65

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over