7-137531768-T-C

Variant names:

• chr7-137531768-T-C
• rs834082
• NM_001321708.2:c.2148-9802A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321708.2(DGKI):​c.2148-9802A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0368 in 152,202 control chromosomes in the GnomAD database, including 262 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 0.037 (262 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• 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=-0.89).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKI	NM_001321708.2	MANE Select	c.2148-9802A>G		intron	N/A	NP_001308637.1	O75912-2
	DGKI	NM_001388092.1		c.2211-9802A>G		intron	N/A	NP_001375021.1	E7EWQ4
	DGKI	NM_004717.3		c.2148-9802A>G		intron	N/A	NP_004708.1	O75912-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKI	ENST00000614521.2	TSL:5 MANE Select	c.2148-9802A>G		intron	N/A	ENSP00000479053.2	O75912-2
	DGKI	ENST00000453654.6	TSL:1	c.1248-9802A>G		intron	N/A	ENSP00000392161.1	E9PFX6
	DGKI	ENST00000424189.6	TSL:5	c.2211-9802A>G		intron	N/A	ENSP00000396078.2	E7EWQ4

Frequencies

GnomAD3 genomes AF: 0.0368 AC: 5600 AN: 152084 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00219

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0368 AC: 5607 AN: 152202 Hom.: 262 Cov.: 32 AF XY: 0.0376 AC XY: 2800 AN XY: 74396

African (AFR) AF: 0.0804 AC: 3338 AN: 41532

American (AMR) AF: 0.0913 AC: 1395 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3468

East Asian (EAS) AF: 0.110 AC: 571 AN: 5170

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4824

European-Finnish (FIN) AF: 0.00207 AC: 22 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00219 AC: 149 AN: 68010

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0110 Hom.: 53

Bravo AF: 0.0483

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.24
PhyloP100		-0.51
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: rs834082; hg19: chr7-137216514;