7-137844832-G-A

Position:

• chr7-137844832-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321708.2(DGKI):​c.401+1630C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,140 control chromosomes in the GnomAD database, including 10,894 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 0.24 (10894 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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]

DGKI (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKI	NM_001321708.2	c.401+1630C>T		intron_variant		ENST00000614521.2	NP_001308637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKI	ENST00000614521.2	c.401+1630C>T		intron_variant		5	NM_001321708.2	ENSP00000479053.2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36547 AN: 152020 Hom.: 10848 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.241 AC: 36652 AN: 152140 Hom.: 10894 Cov.: 32 AF XY: 0.233 AC XY: 17359 AN XY: 74376

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.188

Alfa AF: 0.0870 Hom.: 1950

Bravo AF: 0.269

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs6978230; hg19: chr7-137529578;