rs73728712

Variant names:

• chr7-137555667-G-A
• rs73728712
• NM_001321708.2:c.1948-3099C>T

Variant summary

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

The NM_001321708.2(DGKI):​c.1948-3099C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 151,964 control chromosomes in the GnomAD database, including 2,165 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 0.11 (2165 hom., cov: 31)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 0 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 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.1948-3099C>T		intron	N/A	NP_001308637.1
	DGKI	NM_001388092.1		c.1948-3099C>T		intron	N/A	NP_001375021.1
	DGKI	NM_004717.3		c.1948-3099C>T		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.1948-3099C>T		intron	N/A	ENSP00000479053.2
	DGKI	ENST00000453654.6	TSL:1	c.1048-3099C>T		intron	N/A	ENSP00000392161.1
	DGKI	ENST00000424189.6	TSL:5	c.1948-3099C>T		intron	N/A	ENSP00000396078.2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16963 AN: 151846 Hom.: 2164 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.00924

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.00521

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.112 AC: 16988 AN: 151964 Hom.: 2165 Cov.: 31 AF XY: 0.112 AC XY: 8336 AN XY: 74284

African (AFR) AF: 0.306 AC: 12673 AN: 41374

American (AMR) AF: 0.129 AC: 1978 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00924 AC: 32 AN: 3464

East Asian (EAS) AF: 0.133 AC: 687 AN: 5168

South Asian (SAS) AF: 0.110 AC: 529 AN: 4814

European-Finnish (FIN) AF: 0.00521 AC: 55 AN: 10550

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 796 AN: 67992

Other (OTH) AF: 0.0949 AC: 200 AN: 2108

Alfa AF: 0.0444 Hom.: 966

Bravo AF: 0.131

Asia WGS AF: 0.100 AC: 347 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.52
PhyloP100		-0.026
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: rs73728712; hg19: chr7-137240413;