chr7-137536546-A-G

Variant names:

• chr7-137536546-A-G
• rs834067
• NM_001321708.2:c.2148-14580T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321708.2(DGKI):​c.2148-14580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,054 control chromosomes in the GnomAD database, including 6,411 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 0.22 (6411 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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.2148-14580T>C		intron	N/A	NP_001308637.1
	DGKI	NM_001388092.1		c.2210+9354T>C		intron	N/A	NP_001375021.1
	DGKI	NM_004717.3		c.2148-14580T>C		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.2148-14580T>C		intron	N/A	ENSP00000479053.2
	DGKI	ENST00000453654.6	TSL:1	c.1248-14580T>C		intron	N/A	ENSP00000392161.1
	DGKI	ENST00000424189.6	TSL:5	c.2210+9354T>C		intron	N/A	ENSP00000396078.2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33283 AN: 151936 Hom.: 6384 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.219 AC: 33359 AN: 152054 Hom.: 6411 Cov.: 32 AF XY: 0.218 AC XY: 16206 AN XY: 74310

African (AFR) AF: 0.514 AC: 21293 AN: 41406

American (AMR) AF: 0.187 AC: 2857 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0995 AC: 345 AN: 3468

East Asian (EAS) AF: 0.135 AC: 699 AN: 5184

South Asian (SAS) AF: 0.276 AC: 1329 AN: 4820

European-Finnish (FIN) AF: 0.0594 AC: 630 AN: 10602

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0827 AC: 5623 AN: 67998

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.129 Hom.: 1892

Bravo AF: 0.241

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.31
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: rs834067; hg19: chr7-137221292;