rs12535157

Variant names:

• chr7-137422201-C-A
• rs12535157
• NM_001321708.2:c.2762-9994G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-137422201-C-A
• chr7-137422201-C-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.2762-9994G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,028 control chromosomes in the GnomAD database, including 8,240 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 0.30 (8240 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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.2762-9994G>T		intron	N/A	NP_001308637.1
	DGKI	NM_001388092.1		c.2825-9994G>T		intron	N/A	NP_001375021.1
	DGKI	NM_004717.3		c.2786-9994G>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.2762-9994G>T		intron	N/A	ENSP00000479053.2
	DGKI	ENST00000453654.6	TSL:1	c.1793-9994G>T		intron	N/A	ENSP00000392161.1
	DGKI	ENST00000424189.6	TSL:5	c.2825-9994G>T		intron	N/A	ENSP00000396078.2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45781 AN: 151910 Hom.: 8232 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.301 AC: 45801 AN: 152028 Hom.: 8240 Cov.: 32 AF XY: 0.309 AC XY: 22986 AN XY: 74316

African (AFR) AF: 0.119 AC: 4938 AN: 41494

American (AMR) AF: 0.451 AC: 6892 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3351 AN: 5166

South Asian (SAS) AF: 0.486 AC: 2336 AN: 4804

European-Finnish (FIN) AF: 0.299 AC: 3159 AN: 10574

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22766 AN: 67942

Other (OTH) AF: 0.326 AC: 683 AN: 2098

Alfa AF: 0.315 Hom.: 1743

Bravo AF: 0.305

Asia WGS AF: 0.538 AC: 1874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.72
PhyloP100		0.27
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: rs12535157; hg19: chr7-137106947;