rs864434

chr7-137544682-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.2147+7687C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,920 control chromosomes in the GnomAD database, including 3,152 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 0.16 (3152 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKI	NM_001321708.2	c.2147+7687C>A		intron_variant		ENST00000614521.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKI	ENST00000614521.2	c.2147+7687C>A		intron_variant		5	NM_001321708.2	P3

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24629 AN: 151802 Hom.: 3124 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.163 AC: 24702 AN: 151920 Hom.: 3152 Cov.: 32 AF XY: 0.162 AC XY: 11996 AN XY: 74242

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0939

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0562

Gnomad4 NFE AF: 0.0739

Gnomad4 OTH AF: 0.154

Alfa AF: 0.102 Hom.: 581

Bravo AF: 0.179

Asia WGS AF: 0.127 AC: 442 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.15
Dann	Benign	0.29

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: rs864434; hg19: chr7-137229428;