NM_152879.3:c.157-4219G>A

Variant names:

• chr2-233384038-G-A
• rs838715
• NM_152879.3:c.157-4219G>A

Variant summary

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

The NM_152879.3(DGKD):​c.157-4219G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,630 control chromosomes in the GnomAD database, including 9,074 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 0.33 (9074 hom., cov: 31)
• Consequence: DGKD NM_152879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 9 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKD	NM_152879.3	c.157-4219G>A		intron_variant	Intron 1 of 29	ENST00000264057.7	NP_690618.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKD	ENST00000264057.7	c.157-4219G>A		intron_variant	Intron 1 of 29	1	NM_152879.3	ENSP00000264057.2
DGKD	ENST00000442524.4	c.103-4219G>A		intron_variant	Intron 1 of 3	3		ENSP00000485047.1
DGKD	ENST00000427930.5	c.156+29364G>A		intron_variant	Intron 1 of 3	5		ENSP00000407938.1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50383 AN: 151514 Hom.: 9071 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.332 AC: 50395 AN: 151630 Hom.: 9074 Cov.: 31 AF XY: 0.332 AC XY: 24628 AN XY: 74112

African (AFR) AF: 0.187 AC: 7686 AN: 41138

American (AMR) AF: 0.380 AC: 5792 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3466

East Asian (EAS) AF: 0.370 AC: 1906 AN: 5152

South Asian (SAS) AF: 0.264 AC: 1270 AN: 4814

European-Finnish (FIN) AF: 0.382 AC: 4018 AN: 10532

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26866 AN: 67970

Other (OTH) AF: 0.362 AC: 764 AN: 2108

Alfa AF: 0.372 Hom.: 29439

Bravo AF: 0.328

Asia WGS AF: 0.354 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.66
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs838715; hg19: chr2-234292684; COSMIC: COSV107248787; COSMIC: COSV107248787;