rs1525047

Variant names:

• chr7-137554067-G-A
• rs1525047
• NM_001321708.2:c.1948-1499C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-137554067-G-A
• chr7-137554067-G-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.1948-1499C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,112 control chromosomes in the GnomAD database, including 2,055 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 (2055 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKI	NM_001321708.2	c.1948-1499C>T		intron_variant	Intron 19 of 32	ENST00000614521.2	NP_001308637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKI	ENST00000614521.2	c.1948-1499C>T		intron_variant	Intron 19 of 32	5	NM_001321708.2	ENSP00000479053.2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16611 AN: 151992 Hom.: 2054 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.109 AC: 16635 AN: 152112 Hom.: 2055 Cov.: 32 AF XY: 0.110 AC XY: 8178 AN XY: 74362

African (AFR) AF: 0.298 AC: 12351 AN: 41424

American (AMR) AF: 0.128 AC: 1962 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5174

South Asian (SAS) AF: 0.110 AC: 530 AN: 4816

European-Finnish (FIN) AF: 0.00528 AC: 56 AN: 10604

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

European-Non Finnish (NFE) AF: 0.0115 AC: 784 AN: 68016

Other (OTH) AF: 0.0923 AC: 195 AN: 2112

Alfa AF: 0.0297 Hom.: 74

Bravo AF: 0.128

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.32
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1525047; hg19: chr7-137238813; COSMIC: COSV55968150;