rs7405806

Variant names:

• chr17-66435476-C-A
• rs7405806
• NM_002737.3:c.206-60725C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-66435476-C-A
• chr17-66435476-C-G
• chr17-66435476-C-T

Variant summary

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

The NM_002737.3(PRKCA):​c.206-60725C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,998 control chromosomes in the GnomAD database, including 25,493 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 0.55 (25493 hom., cov: 32)
• Consequence: PRKCA NM_002737.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• 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]

ENSG00000289587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKCA	NM_002737.3	MANE Select	c.206-60725C>A		intron	N/A	NP_002728.2	L7RSM7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKCA	ENST00000413366.8	TSL:1 MANE Select	c.206-60725C>A		intron	N/A	ENSP00000408695.3	P17252
	PRKCA	ENST00000578063.5	TSL:1	n.206-60725C>A		intron	N/A	ENSP00000462087.1	J3KRN5
	PRKCA	ENST00000882063.1		c.206-60725C>A		intron	N/A	ENSP00000552122.1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83220 AN: 151880 Hom.: 25489 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.548 AC: 83234 AN: 151998 Hom.: 25493 Cov.: 32 AF XY: 0.547 AC XY: 40677 AN XY: 74302

African (AFR) AF: 0.264 AC: 10919 AN: 41432

American (AMR) AF: 0.495 AC: 7566 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2376 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3161 AN: 5156

South Asian (SAS) AF: 0.614 AC: 2958 AN: 4816

European-Finnish (FIN) AF: 0.662 AC: 6984 AN: 10550

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47348 AN: 67988

Other (OTH) AF: 0.579 AC: 1222 AN: 2110

Alfa AF: 0.630 Hom.: 24650

Bravo AF: 0.520

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		0.39
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7405806; hg19: chr17-64431594;