rs834092

chr7-137525969-C-T

Variant summary

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

The NM_001321708.2(DGKI):c.2148-4003G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 151,252 control chromosomes in the GnomAD database, including 217 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 0.032 (217 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKI	NM_001321708.2	c.2148-4003G>A		intron_variant		ENST00000614521.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKI	ENST00000614521.2	c.2148-4003G>A		intron_variant		5	NM_001321708.2	P3

Frequencies

GnomAD3 genomes AF: 0.0321 AC: 4845 AN: 151136 Hom.: 217 Cov.: 32

Gnomad AFR AF: 0.0639

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.00566

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.0128

Gnomad NFE AF: 0.00215

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0321 AC: 4848 AN: 151252 Hom.: 217 Cov.: 32 AF XY: 0.0330 AC XY: 2434 AN XY: 73856

Gnomad4 AFR AF: 0.0638

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.00546

Gnomad4 FIN AF: 0.00211

Gnomad4 NFE AF: 0.00215

Gnomad4 OTH AF: 0.0433

Alfa AF: 0.00889 Hom.: 47

Bravo AF: 0.0433

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	6.8
Dann	Benign	0.57

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: rs834092; hg19: chr7-137210715;