rs4561502

chr17-66400862-C-Achr17-66400862-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002737.3(PRKCA):c.205+94735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,030 control chromosomes in the GnomAD database, including 26,221 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 0.58 (26221 hom., cov: 32)
• Consequence: PRKCA NM_002737.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

PRKCA (HGNC:9393): (protein kinase C alpha) 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 in cells. The protein encoded by this gene is one of the PKC family members. This kinase has been reported to play roles in many different cellular processes, such as cell adhesion, cell transformation, cell cycle checkpoint, and cell volume control. Knockout studies in mice suggest that this kinase may be a fundamental regulator of cardiac contractility and Ca(2+) handling in myocytes. [provided by RefSeq, Jul 2008]

PRKCA-AS1 (HGNC:51347): (PRKCA antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKCA	NM_002737.3	c.205+94735C>A		intron_variant		ENST00000413366.8
PRKCA-AS1	NR_110822.1	n.1207-2644G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKCA	ENST00000413366.8	c.205+94735C>A		intron_variant		1	NM_002737.3	P1
PRKCA	ENST00000578063.5	c.205+94735C>A		intron_variant, NMD_transcript_variant		1
PRKCA-AS1	ENST00000584715.5	n.1964-2644G>T		intron_variant, non_coding_transcript_variant		2
PRKCA	ENST00000284384.6	c.197+94735C>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88395 AN: 151912 Hom.: 26203 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.582 AC: 88456 AN: 152030 Hom.: 26221 Cov.: 32 AF XY: 0.581 AC XY: 43154 AN XY: 74320

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.601

Alfa AF: 0.621 Hom.: 11870

Bravo AF: 0.568

Asia WGS AF: 0.503 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.34
Dann	Benign	0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4561502; hg19: chr17-64396980;