7-137447847-C-G

Position:

• chr7-137447847-C-G

Variant summary

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

The NM_001321708.2(DGKI):​c.2736-3745G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,186 control chromosomes in the GnomAD database, including 54,164 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 0.84 (54164 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

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 (SAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKI	NM_001321708.2	c.2736-3745G>C		intron_variant		ENST00000614521.2	NP_001308637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKI	ENST00000614521.2	c.2736-3745G>C		intron_variant		5	NM_001321708.2	ENSP00000479053	P3

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127818 AN: 152070 Hom.: 54159 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.840 AC: 127873 AN: 152186 Hom.: 54164 Cov.: 32 AF XY: 0.840 AC XY: 62519 AN XY: 74410

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.856

Alfa AF: 0.865 Hom.: 7092

Bravo AF: 0.831

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.79

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: rs7804771; hg19: chr7-137132593;