3-53178163-C-T

Position:

• chr3-53178163-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006254.4(PRKCD):​c.-19-241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0881 in 152,126 control chromosomes in the GnomAD database, including 1,116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.088 (1116 hom., cov: 31)
• Consequence: PRKCD NM_006254.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.484

Genes affected

PRKCD (HGNC:9399): (protein kinase C delta) The protein encoded by this gene is a member of the protein kinase C family of serine- and threonine-specific protein kinases. The encoded protein is activated by diacylglycerol and is both a tumor suppressor and a positive regulator of cell cycle progression. Also, this protein can positively or negatively regulate apoptosis. Defects in this gene are a cause of autoimmune lymphoproliferative syndrome. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 3-53178163-C-T is Benign according to our data. Variant chr3-53178163-C-T is described in ClinVar as [Benign]. Clinvar id is 1233848.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKCD	NM_006254.4	c.-19-241C>T		intron_variant		ENST00000330452.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKCD	ENST00000330452.8	c.-19-241C>T		intron_variant		1	NM_006254.4	P1

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13377 AN: 152008 Hom.: 1113 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0385

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0881 AC: 13397 AN: 152126 Hom.: 1116 Cov.: 31 AF XY: 0.0854 AC XY: 6351 AN XY: 74376

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0384

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0724 Hom.: 106

Bravo AF: 0.0966

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.34

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: rs56972966; hg19: chr3-53212179;