2-233470440-C-T

Position:

• chr2-233470440-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.*980C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,444 control chromosomes in the GnomAD database, including 2,593 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 0.18 (2583 hom., cov: 33)
  • Exomes 𝑓: 0.22 (10 hom.)
• Consequence: DGKD NM_152879.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKD	NM_152879.3	c.*980C>T		3_prime_UTR_variant	30/30	ENST00000264057.7	NP_690618.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKD	ENST00000264057.7	c.*980C>T		3_prime_UTR_variant	30/30	1	NM_152879.3	ENSP00000264057.2
DGKD	ENST00000409813.7	c.*980C>T		3_prime_UTR_variant	29/29	1		ENSP00000386455.3
DGKD	ENST00000430834.1	n.*2360C>T		non_coding_transcript_exon_variant	23/23	1		ENSP00000390970.1
DGKD	ENST00000430834.1	n.*2360C>T		3_prime_UTR_variant	23/23	1		ENSP00000390970.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27813 AN: 151966 Hom.: 2581 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0961

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.222 AC: 80 AN: 360 Hom.: 10 Cov.: 0 AF XY: 0.243 AC XY: 55 AN XY: 226

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.357

Gnomad4 NFE exome AF: 0.226

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.183 AC: 27811 AN: 152084 Hom.: 2583 Cov.: 33 AF XY: 0.183 AC XY: 13577 AN XY: 74324

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0959

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.173

Alfa AF: 0.198 Hom.: 481

Bravo AF: 0.173

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.46

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: rs2971871; hg19: chr2-234379086;