rs3890137

Variant names:

• chr17-66730709-G-A
• rs3890137
• NM_002737.3:c.919-1979G>A

Variant summary

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

The NM_002737.3(PRKCA):​c.919-1979G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,114 control chromosomes in the GnomAD database, including 35,882 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 0.69 (35882 hom., cov: 32)
• Consequence: PRKCA NM_002737.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• 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]

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 (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002737.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKCA	NM_002737.3	MANE Select	c.919-1979G>A		intron	N/A	NP_002728.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKCA	ENST00000413366.8	TSL:1 MANE Select	c.919-1979G>A		intron	N/A	ENSP00000408695.3
	PRKCA	ENST00000284384.6	TSL:5	n.*521-1979G>A		intron	N/A	ENSP00000284384.6

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104102 AN: 151996 Hom.: 35824 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.685 AC: 104219 AN: 152114 Hom.: 35882 Cov.: 32 AF XY: 0.688 AC XY: 51165 AN XY: 74354

African (AFR) AF: 0.723 AC: 30017 AN: 41494

American (AMR) AF: 0.660 AC: 10097 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2423 AN: 3468

East Asian (EAS) AF: 0.712 AC: 3681 AN: 5168

South Asian (SAS) AF: 0.674 AC: 3246 AN: 4816

European-Finnish (FIN) AF: 0.713 AC: 7553 AN: 10586

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44929 AN: 67976

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.667 Hom.: 4191

Bravo AF: 0.683

Asia WGS AF: 0.698 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.23
PhyloP100		-0.57
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: rs3890137; hg19: chr17-64726827; COSMIC: COSV52597618;