rs834092

Variant names:

• chr7-137525969-C-T
• rs834092
• NM_001321708.2:c.2148-4003G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321708.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKI	NM_001321708.2	MANE Select	c.2148-4003G>A		intron	N/A	NP_001308637.1
	DGKI	NM_001388092.1		c.2211-4003G>A		intron	N/A	NP_001375021.1
	DGKI	NM_004717.3		c.2148-4003G>A		intron	N/A	NP_004708.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKI	ENST00000614521.2	TSL:5 MANE Select	c.2148-4003G>A		intron	N/A	ENSP00000479053.2
	DGKI	ENST00000453654.6	TSL:1	c.1248-4003G>A		intron	N/A	ENSP00000392161.1
	DGKI	ENST00000424189.6	TSL:5	c.2211-4003G>A		intron	N/A	ENSP00000396078.2

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

African (AFR) AF: 0.0638 AC: 2629 AN: 41194

American (AMR) AF: 0.0901 AC: 1362 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3464

East Asian (EAS) AF: 0.110 AC: 562 AN: 5096

South Asian (SAS) AF: 0.00546 AC: 26 AN: 4762

European-Finnish (FIN) AF: 0.00211 AC: 22 AN: 10434

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.00215 AC: 146 AN: 67872

Other (OTH) AF: 0.0433 AC: 91 AN: 2104

Alfa AF: 0.0131 Hom.: 96

Bravo AF: 0.0433

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.8
DANN	Benign	0.57
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs834092; hg19: chr7-137210715;