17-66551412-C-T

Position:

• chr17-66551412-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.288+55129C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,158 control chromosomes in the GnomAD database, including 9,305 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 0.34 (9305 hom., cov: 33)
• Consequence: PRKCA NM_002737.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKCA	NM_002737.3	c.288+55129C>T		intron_variant		ENST00000413366.8	NP_002728.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKCA	ENST00000413366.8	c.288+55129C>T		intron_variant		1	NM_002737.3	ENSP00000408695	P1
PRKCA	ENST00000578063.5	c.288+55129C>T		intron_variant, NMD_transcript_variant		1		ENSP00000462087
PRKCA	ENST00000284384.6	c.281-3107C>T		intron_variant, NMD_transcript_variant		5		ENSP00000284384

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51864 AN: 152040 Hom.: 9284 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.341 AC: 51936 AN: 152158 Hom.: 9305 Cov.: 33 AF XY: 0.344 AC XY: 25573 AN XY: 74402

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.334

Alfa AF: 0.320 Hom.: 1658

Bravo AF: 0.351

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.63
DANN	Benign	0.78

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: rs759118; hg19: chr17-64547530;