2-233364596-G-A

Variant names:

• chr2-233364596-G-A
• rs838705
• NM_152879.3:c.156+9922G>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.156+9922G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,052 control chromosomes in the GnomAD database, including 29,558 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 0.62 (29558 hom., cov: 32)
• Consequence: DGKD NM_152879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 28 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKD	NM_152879.3	c.156+9922G>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.156+9922G>A		intron_variant	Intron 1 of 29	1	NM_152879.3	ENSP00000264057.2
DGKD	ENST00000442524.4	c.102+9922G>A		intron_variant	Intron 1 of 3	3		ENSP00000485047.1
DGKD	ENST00000427930.5	c.156+9922G>A		intron_variant	Intron 1 of 3	5		ENSP00000407938.1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94406 AN: 151934 Hom.: 29537 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.621 AC: 94466 AN: 152052 Hom.: 29558 Cov.: 32 AF XY: 0.624 AC XY: 46351 AN XY: 74312

African (AFR) AF: 0.615 AC: 25509 AN: 41464

American (AMR) AF: 0.595 AC: 9093 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2451 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3779 AN: 5182

South Asian (SAS) AF: 0.759 AC: 3666 AN: 4828

European-Finnish (FIN) AF: 0.605 AC: 6380 AN: 10538

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41476 AN: 67962

Other (OTH) AF: 0.638 AC: 1347 AN: 2110

Alfa AF: 0.622 Hom.: 127911

Bravo AF: 0.617

Asia WGS AF: 0.750 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.37
PhyloP100		-1.6
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: rs838705; hg19: chr2-234273242;