rs16960228

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000413366.8(PRKCA):​c.1854+3730G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,288 control chromosomes in the GnomAD database, including 2,327 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 0.13 ( 2327 hom., cov: 32)

Consequence

PRKCA
ENST00000413366.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRKCANM_002737.3 linkuse as main transcriptc.1854+3730G>A intron_variant ENST00000413366.8 NP_002728.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRKCAENST00000413366.8 linkuse as main transcriptc.1854+3730G>A intron_variant 1 NM_002737.3 ENSP00000408695 P1

Frequencies

GnomAD3 genomes
AF:
0.128
AC:
19506
AN:
152170
Hom.:
2317
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.309
Gnomad AMI
AF:
0.0285
Gnomad AMR
AF:
0.109
Gnomad ASJ
AF:
0.0478
Gnomad EAS
AF:
0.182
Gnomad SAS
AF:
0.0393
Gnomad FIN
AF:
0.0282
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0463
Gnomad OTH
AF:
0.112
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.128
AC:
19555
AN:
152288
Hom.:
2327
Cov.:
32
AF XY:
0.126
AC XY:
9396
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.310
Gnomad4 AMR
AF:
0.109
Gnomad4 ASJ
AF:
0.0478
Gnomad4 EAS
AF:
0.181
Gnomad4 SAS
AF:
0.0389
Gnomad4 FIN
AF:
0.0282
Gnomad4 NFE
AF:
0.0463
Gnomad4 OTH
AF:
0.110
Alfa
AF:
0.0589
Hom.:
901
Bravo
AF:
0.144
Asia WGS
AF:
0.124
AC:
431
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.0030
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16960228; hg19: chr17-64788827; API