Variant 3-53178367-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006254.4(PRKCD):c.-19-37C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,468,282 control chromosomes in the GnomAD database, including 19,225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1324 hom., cov: 32)

Exomes 𝑓: 0.16 ( 17901 hom. )

Consequence

PRKCD
NM_006254.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.504

Variant links:

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]

PRKCD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 3-53178367-C-T is Benign according to our data. Variant chr3-53178367-C-T is described in ClinVar as [Benign]. Clinvar id is 1275121.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKCD	NM_006254.4 linkuse as main transcript	c.-19-37C>T		intron_variant		ENST00000330452.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKCD	ENST00000330452.8 linkuse as main transcript	c.-19-37C>T		intron_variant		1	NM_006254.4	P1	Q05655-1

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18112

AN:

152174

Hom.:

1323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.0179

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.121

GnomAD4 exome

AF:

0.159

AC:

208695

AN:

1315988

Hom.:

17901

Cov.:

AF XY:

0.159

AC XY:

104630

AN XY:

657154

show subpopulations

Gnomad4 AFR exome

AF:

0.0458

Gnomad4 AMR exome

AF:

0.0714

Gnomad4 ASJ exome

AF:

0.148

Gnomad4 EAS exome

AF:

0.0135

Gnomad4 SAS exome

AF:

0.159

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.119

AC:

18109

AN:

152294

Hom.:

1324

Cov.:

AF XY:

0.117

AC XY:

8702

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0496

Gnomad4 AMR

AF:

0.0999

Gnomad4 ASJ

AF:

0.147

Gnomad4 EAS

AF:

0.0177

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.150

Hom.:

217

Bravo

AF:

0.112

Asia WGS

AF:

0.0740

AC:

258

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Nov 12, 2023

This variant is classified as Benign based on local population frequency. This variant was detected in 23% of patients studied by a panel of primary immunodeficiencies. Number of patients: 22. Only high quality variants are reported. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over