rs2971871

Variant names:

• chr2-233470440-C-T
• rs2971871
• ENST00000430834.1:n.*2360C>T

Variant summary

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

The ENST00000430834.1(DGKD):​n.*2360C>T variant causes a non coding transcript exon 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 ENST00000430834.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 8 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]

ENSG00000302812 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DGKD	NM_152879.3	c.*980C>T		3_prime_UTR_variant	Exon 30 of 30	ENST00000264057.7	NP_690618.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKD	ENST00000264057.7	c.*980C>T		3_prime_UTR_variant	Exon 30 of 30	1	NM_152879.3	ENSP00000264057.2

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

African (AFR) AF: 0.250 AC: 3 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.179 AC: 14 AN: 78

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.357 AC: 5 AN: 14

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.226 AC: 52 AN: 230

Other (OTH) AF: 0.375 AC: 6 AN: 16

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

African (AFR) AF: 0.159 AC: 6615 AN: 41526

American (AMR) AF: 0.144 AC: 2201 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3462

East Asian (EAS) AF: 0.0959 AC: 496 AN: 5172

South Asian (SAS) AF: 0.133 AC: 644 AN: 4828

European-Finnish (FIN) AF: 0.259 AC: 2732 AN: 10556

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13751 AN: 67928

Other (OTH) AF: 0.173 AC: 366 AN: 2112

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
PhyloP100		0.53
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: rs2971871; hg19: chr2-234379086;