NM_001321708.2:c.401+1630C>T

Variant names:

• chr7-137844832-G-A
• rs6978230
• NM_001321708.2:c.401+1630C>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.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
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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.401+1630C>T		intron	N/A	NP_001308637.1
	DGKI	NM_001388092.1		c.401+1630C>T		intron	N/A	NP_001375021.1
	DGKI	NM_004717.3		c.401+1630C>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.401+1630C>T		intron	N/A	ENSP00000479053.2
	DGKI	ENST00000453654.6	TSL:1	c.-465-1370C>T		intron	N/A	ENSP00000392161.1
	DGKI	ENST00000424189.6	TSL:5	c.401+1630C>T		intron	N/A	ENSP00000396078.2

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

African (AFR) AF: 0.713 AC: 29579 AN: 41476

American (AMR) AF: 0.138 AC: 2104 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.0533 AC: 276 AN: 5174

South Asian (SAS) AF: 0.0466 AC: 225 AN: 4826

European-Finnish (FIN) AF: 0.0426 AC: 451 AN: 10586

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0481 AC: 3273 AN: 68004

Other (OTH) AF: 0.188 AC: 397 AN: 2110

Alfa AF: 0.160 Hom.: 10004

Bravo AF: 0.269

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.54
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: rs6978230; hg19: chr7-137529578;