2-233356202-C-G

Variant names:

• chr2-233356202-C-G
• rs1550532
• NM_152879.3:c.156+1528C>G

Variant summary

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

The NM_152879.3(DGKD):​c.156+1528C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,212 control chromosomes in the GnomAD database, including 43,119 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 0.75 (43119 hom., cov: 33)
• Consequence: DGKD NM_152879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 44 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152879.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKD	NM_152879.3	MANE Select	c.156+1528C>G		intron	N/A	NP_690618.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKD	ENST00000264057.7	TSL:1 MANE Select	c.156+1528C>G		intron	N/A	ENSP00000264057.2
	DGKD	ENST00000442524.4	TSL:3	c.102+1528C>G		intron	N/A	ENSP00000485047.1
	DGKD	ENST00000427930.5	TSL:5	c.156+1528C>G		intron	N/A	ENSP00000407938.1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113564 AN: 152094 Hom.: 43069 Cov.: 33

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.747 AC: 113665 AN: 152212 Hom.: 43119 Cov.: 33 AF XY: 0.747 AC XY: 55576 AN XY: 74418

African (AFR) AF: 0.877 AC: 36440 AN: 41544

American (AMR) AF: 0.659 AC: 10078 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2777 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3882 AN: 5176

South Asian (SAS) AF: 0.858 AC: 4144 AN: 4830

European-Finnish (FIN) AF: 0.679 AC: 7189 AN: 10588

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46669 AN: 67996

Other (OTH) AF: 0.741 AC: 1566 AN: 2112

Alfa AF: 0.724 Hom.: 5006

Bravo AF: 0.746

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0030
DANN	Benign	0.65
PhyloP100		-2.7
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: rs1550532; hg19: chr2-234264848;