rs2059320

Variant names:

• chr7-137740025-C-T
• rs2059320
• NM_001321708.2:c.402-50023G>A

Variant summary

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

The NM_001321708.2(DGKI):​c.402-50023G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,072 control chromosomes in the GnomAD database, including 6,954 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 0.23 (6954 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 4 publications found

Genes affected

DGKI (HGNC:2855): (diacylglycerol kinase iota) This gene is a member of the type IV diacylglycerol kinase subfamily. Diacylglycerol kinases regulate the intracellular concentration of diacylglycerol through its phosphorylation, producing phosphatidic acid. The specific role of the enzyme encoded by this gene is undetermined, however, it may play a crucial role in the production of phosphatidic acid in the retina or in recessive forms of retinal degeneration. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKI	NM_001321708.2	c.402-50023G>A		intron_variant	Intron 1 of 32	ENST00000614521.2	NP_001308637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKI	ENST00000614521.2	c.402-50023G>A		intron_variant	Intron 1 of 32	5	NM_001321708.2	ENSP00000479053.2

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34127 AN: 151954 Hom.: 6921 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.225 AC: 34225 AN: 152072 Hom.: 6954 Cov.: 32 AF XY: 0.226 AC XY: 16838 AN XY: 74352

African (AFR) AF: 0.536 AC: 22206 AN: 41442

American (AMR) AF: 0.232 AC: 3549 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1186 AN: 5140

South Asian (SAS) AF: 0.205 AC: 985 AN: 4816

European-Finnish (FIN) AF: 0.108 AC: 1143 AN: 10608

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4302 AN: 68002

Other (OTH) AF: 0.189 AC: 398 AN: 2108

Alfa AF: 0.109 Hom.: 1411

Bravo AF: 0.249

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.58
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: rs2059320; hg19: chr7-137424771;