rs834063

chr7-137542798-A-G

Variant summary

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

The NM_001321708.2(DGKI):c.2147+9571T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,188 control chromosomes in the GnomAD database, including 2,414 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 0.14 (2414 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKI	NM_001321708.2	c.2147+9571T>C		intron_variant		ENST00000614521.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKI	ENST00000614521.2	c.2147+9571T>C		intron_variant		5	NM_001321708.2	P3

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21118 AN: 152070 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.139 AC: 21189 AN: 152188 Hom.: 2414 Cov.: 32 AF XY: 0.137 AC XY: 10198 AN XY: 74414

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.0746

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0852 Hom.: 1063

Bravo AF: 0.146

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.8
Dann	Benign	0.48

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: rs834063; hg19: chr7-137227544;