7-137519073-G-C

Variant names:

• chr7-137519073-G-C
• rs6467710
• NM_001321708.2:c.2248+2793C>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.2248+2793C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 152,040 control chromosomes in the GnomAD database, including 483 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 0.060 (483 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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.2248+2793C>G		intron	N/A	NP_001308637.1
	DGKI	NM_001388092.1		c.2311+2793C>G		intron	N/A	NP_001375021.1
	DGKI	NM_004717.3		c.2248+2793C>G		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.2248+2793C>G		intron	N/A	ENSP00000479053.2
	DGKI	ENST00000453654.6	TSL:1	c.1348+2793C>G		intron	N/A	ENSP00000392161.1
	DGKI	ENST00000424189.6	TSL:5	c.2311+2793C>G		intron	N/A	ENSP00000396078.2

Frequencies

GnomAD3 genomes AF: 0.0599 AC: 9098 AN: 151922 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0599 AC: 9102 AN: 152040 Hom.: 483 Cov.: 32 AF XY: 0.0607 AC XY: 4508 AN XY: 74320

African (AFR) AF: 0.117 AC: 4855 AN: 41496

American (AMR) AF: 0.107 AC: 1622 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.110 AC: 568 AN: 5168

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4820

European-Finnish (FIN) AF: 0.0109 AC: 115 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0191 AC: 1298 AN: 67952

Other (OTH) AF: 0.0668 AC: 141 AN: 2110

Alfa AF: 0.0219 Hom.: 58

Bravo AF: 0.0713

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		-0.44
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: rs6467710; hg19: chr7-137203819;