rs1525047

chr7-137554067-G-Achr7-137554067-G-T

Variant summary

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

The NM_001321708.2(DGKI):c.1948-1499C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,112 control chromosomes in the GnomAD database, including 2,055 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 (2055 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKI	NM_001321708.2	c.1948-1499C>T		intron_variant		ENST00000614521.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKI	ENST00000614521.2	c.1948-1499C>T		intron_variant		5	NM_001321708.2	P3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16611 AN: 151992 Hom.: 2054 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.109 AC: 16635 AN: 152112 Hom.: 2055 Cov.: 32 AF XY: 0.110 AC XY: 8178 AN XY: 74362

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.00528

Gnomad4 NFE AF: 0.0115

Gnomad4 OTH AF: 0.0923

Alfa AF: 0.0165 Hom.: 32

Bravo AF: 0.128

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.9
Dann	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1525047; hg19: chr7-137238813; COSMIC: COSV55968150;