Variant chr2-233354616-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_152879.3(DGKD):c.98C>T(p.Pro33Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,129,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000082 ( 0 hom., cov: 30)

Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

DGKD
NM_152879.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0300

Variant links:

Genes affected

DGKD (HGNC:2851): (diacylglycerol kinase delta) This gene encodes a cytoplasmic enzyme that phosphorylates diacylglycerol to produce phosphatidic acid. Diacylglycerol and phosphatidic acid are two lipids that act as second messengers in signaling cascades. Their cellular concentrations are regulated by the encoded protein, and so it is thought to play an important role in cellular signal transduction. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

DGKD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.16455957).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKD	NM_152879.3 linkuse as main transcript	c.98C>T	p.Pro33Leu	missense_variant	1/30	ENST00000264057.7	NP_690618.2	Q16760-1
DGKD	XM_047446097.1 linkuse as main transcript	c.98C>T	p.Pro33Leu	missense_variant	1/29		XP_047302053.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DGKD	ENST00000264057.7 linkuse as main transcript	c.98C>T	p.Pro33Leu	missense_variant	1/30	1	NM_152879.3	ENSP00000264057.2	Q16760-1
DGKD	ENST00000442524.4 linkuse as main transcript	c.44C>T	p.Pro15Leu	missense_variant	1/4	3		ENSP00000485047.1	A0A096LNI6
DGKD	ENST00000427930.5 linkuse as main transcript	c.98C>T	p.Pro33Leu	missense_variant	1/4	5		ENSP00000407938.1	C9JY42

Frequencies

GnomAD3 genomes

AF:

0.0000821

AC:

AN:

146102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000490

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000678

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000137

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000568

AC:

AN:

88028

Hom.:

AF XY:

0.0000582

AC XY:

AN XY:

51532

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000394

Gnomad NFE exome

AF:

0.0000773

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000106

AC:

104

AN:

982914

Hom.:

Cov.:

AF XY:

0.000109

AC XY:

AN XY:

478084

show subpopulations

Gnomad4 AFR exome

AF:

0.0000520

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000155

Gnomad4 NFE exome

AF:

0.000114

Gnomad4 OTH exome

AF:

0.000180

GnomAD4 genome

AF:

0.0000821

AC:

AN:

146102

Hom.:

Cov.:

AF XY:

0.0000422

AC XY:

AN XY:

71040

show subpopulations

Gnomad4 AFR

AF:

0.0000490

Gnomad4 AMR

AF:

0.0000678

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000137

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000680

ExAC

AF:

0.0000375

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 02, 2023

The c.98C>T (p.P33L) alteration is located in exon 1 (coding exon 1) of the DGKD gene. This alteration results from a C to T substitution at nucleotide position 98, causing the proline (P) at amino acid position 33 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.20

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.19

T;T

Eigen

Benign

-0.23

Eigen_PC

Benign

-0.42

FATHMM_MKL

Benign

0.20

M_CAP

Pathogenic

0.96

MetaRNN

Benign

0.16

T;T

MetaSVM

Uncertain

0.27

MutationAssessor

Benign

0.81

L;.

PrimateAI

Uncertain

0.76

PROVEAN

Benign

-1.6

N;N

REVEL

Uncertain

0.32

Sift

Uncertain

0.0080

D;D

Sift4G

Uncertain

0.020

D;T

Polyphen

0.99

D;.

Vest4

0.12

MutPred

0.23

Loss of loop (P = 9e-04);Loss of loop (P = 9e-04);

MVP

0.76

MPC

0.50

ClinPred

0.11

GERP RS

1.3

Varity_R

0.084

gMVP

0.43

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