2-233376098-C-A

Variant names:

• chr2-233376098-C-A
• rs838709
• NM_152879.3:c.157-12159C>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.157-12159C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 151,942 control chromosomes in the GnomAD database, including 42,448 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 0.74 (42448 hom., cov: 30)
• Consequence: DGKD NM_152879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKD	NM_152879.3	c.157-12159C>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.157-12159C>A		intron_variant	Intron 1 of 29	1	NM_152879.3	ENSP00000264057.2
DGKD	ENST00000442524.4	c.103-12159C>A		intron_variant	Intron 1 of 3	3		ENSP00000485047.1
DGKD	ENST00000427930.5	c.156+21424C>A		intron_variant	Intron 1 of 3	5		ENSP00000407938.1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112513 AN: 151824 Hom.: 42396 Cov.: 30

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.741 AC: 112616 AN: 151942 Hom.: 42448 Cov.: 30 AF XY: 0.739 AC XY: 54881 AN XY: 74222

African (AFR) AF: 0.872 AC: 36154 AN: 41456

American (AMR) AF: 0.657 AC: 10042 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2785 AN: 3472

East Asian (EAS) AF: 0.748 AC: 3866 AN: 5166

South Asian (SAS) AF: 0.857 AC: 4103 AN: 4790

European-Finnish (FIN) AF: 0.635 AC: 6687 AN: 10532

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46495 AN: 67934

Other (OTH) AF: 0.739 AC: 1561 AN: 2112

Alfa AF: 0.706 Hom.: 160781

Bravo AF: 0.745

Asia WGS AF: 0.820 AC: 2851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.040
DANN	Benign	0.55
PhyloP100		-1.9
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: rs838709; hg19: chr2-234284744;