rs1358446

Variant names:

• chr7-137521168-A-C
• rs1358446
• NM_001321708.2:c.2248+698T>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+698T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,048 control chromosomes in the GnomAD database, including 1,396 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 0.092 (1396 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKI	NM_001321708.2	c.2248+698T>G		intron_variant	Intron 21 of 32	ENST00000614521.2	NP_001308637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKI	ENST00000614521.2	c.2248+698T>G		intron_variant	Intron 21 of 32	5	NM_001321708.2	ENSP00000479053.2

Frequencies

GnomAD3 genomes AF: 0.0920 AC: 13977 AN: 151930 Hom.: 1397 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00527

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0920 AC: 13991 AN: 152048 Hom.: 1396 Cov.: 32 AF XY: 0.0925 AC XY: 6876 AN XY: 74316

African (AFR) AF: 0.240 AC: 9932 AN: 41450

American (AMR) AF: 0.116 AC: 1775 AN: 15242

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

East Asian (EAS) AF: 0.135 AC: 696 AN: 5148

South Asian (SAS) AF: 0.110 AC: 532 AN: 4820

European-Finnish (FIN) AF: 0.00527 AC: 56 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0110 AC: 751 AN: 67980

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0623 Hom.: 138

Bravo AF: 0.108

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		1.9
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: rs1358446; hg19: chr7-137205914;