NM_002737.3:c.206-49783T>C

Variant names:

• chr17-66446418-T-C
• rs172939
• NM_002737.3:c.206-49783T>C

Variant summary

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

The NM_002737.3(PRKCA):​c.206-49783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,086 control chromosomes in the GnomAD database, including 35,712 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 0.68 (35712 hom., cov: 32)
• Consequence: PRKCA NM_002737.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

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]

ENSG00000289587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKCA	NM_002737.3	c.206-49783T>C		intron_variant	Intron 2 of 16	ENST00000413366.8	NP_002728.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKCA	ENST00000413366.8	c.206-49783T>C		intron_variant	Intron 2 of 16	1	NM_002737.3	ENSP00000408695.3

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103958 AN: 151968 Hom.: 35679 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.684 AC: 104049 AN: 152086 Hom.: 35712 Cov.: 32 AF XY: 0.685 AC XY: 50902 AN XY: 74306

African (AFR) AF: 0.692 AC: 28697 AN: 41490

American (AMR) AF: 0.712 AC: 10886 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2340 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3678 AN: 5156

South Asian (SAS) AF: 0.533 AC: 2567 AN: 4816

European-Finnish (FIN) AF: 0.705 AC: 7443 AN: 10556

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46122 AN: 67994

Other (OTH) AF: 0.715 AC: 1508 AN: 2108

Alfa AF: 0.684 Hom.: 6904

Bravo AF: 0.691

Asia WGS AF: 0.615 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.59
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: rs172939; hg19: chr17-64442536;