chr17-66555697-C-G

Variant names:

• chr17-66555697-C-G
• rs2078153
• NM_002737.3:c.288+59414C>G

Variant summary

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

The NM_002737.3(PRKCA):​c.288+59414C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,890 control chromosomes in the GnomAD database, including 4,432 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 0.24 (4432 hom., cov: 31)
• Consequence: PRKCA NM_002737.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 5 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKCA	NM_002737.3	c.288+59414C>G		intron_variant	Intron 3 of 16	ENST00000413366.8	NP_002728.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKCA	ENST00000413366.8	c.288+59414C>G		intron_variant	Intron 3 of 16	1	NM_002737.3	ENSP00000408695.3
PRKCA	ENST00000578063.5	n.288+59414C>G		intron_variant	Intron 3 of 9	1		ENSP00000462087.1
PRKCA	ENST00000284384.6	n.340+1118C>G		intron_variant	Intron 4 of 14	5		ENSP00000284384.6

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36307 AN: 151772 Hom.: 4423 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.239 AC: 36342 AN: 151890 Hom.: 4432 Cov.: 31 AF XY: 0.239 AC XY: 17761 AN XY: 74248

African (AFR) AF: 0.220 AC: 9108 AN: 41410

American (AMR) AF: 0.233 AC: 3558 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5172

South Asian (SAS) AF: 0.350 AC: 1679 AN: 4794

European-Finnish (FIN) AF: 0.219 AC: 2302 AN: 10530

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16660 AN: 67962

Other (OTH) AF: 0.259 AC: 544 AN: 2102

Alfa AF: 0.232 Hom.: 520

Bravo AF: 0.238

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.71
PhyloP100		-0.19
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: rs2078153; hg19: chr17-64551815;