rs13035837

Positions:

• chr2-233358196-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152879.3(DGKD):​c.156+3522C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,220 control chromosomes in the GnomAD database, including 1,202 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 0.11 (1202 hom., cov: 33)
• Consequence: DGKD NM_152879.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKD	NM_152879.3	c.156+3522C>T		intron_variant		ENST00000264057.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKD	ENST00000264057.7	c.156+3522C>T		intron_variant		1	NM_152879.3
DGKD	ENST00000427930.5	c.156+3522C>T		intron_variant		5
DGKD	ENST00000442524.4	c.103+3522C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16735 AN: 152102 Hom.: 1204 Cov.: 33

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.110 AC: 16739 AN: 152220 Hom.: 1202 Cov.: 33 AF XY: 0.113 AC XY: 8416 AN XY: 74442

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.120

Alfa AF: 0.132 Hom.: 2932

Bravo AF: 0.106

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.56

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

Other links and lift over

dbSNP: rs13035837; hg19: chr2-234266842;