chr7-137544682-G-T

Variant names:

• chr7-137544682-G-T
• rs864434
• NM_001321708.2:c.2147+7687C>A

Variant summary

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

The NM_001321708.2(DGKI):​c.2147+7687C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,920 control chromosomes in the GnomAD database, including 3,152 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 0.16 (3152 hom., cov: 32)
• Consequence: DGKI NM_001321708.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• 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 = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKI	NM_001321708.2	c.2147+7687C>A		intron_variant	Intron 20 of 32	ENST00000614521.2	NP_001308637.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKI	ENST00000614521.2	c.2147+7687C>A		intron_variant	Intron 20 of 32	5	NM_001321708.2	ENSP00000479053.2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24629 AN: 151802 Hom.: 3124 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.163 AC: 24702 AN: 151920 Hom.: 3152 Cov.: 32 AF XY: 0.162 AC XY: 11996 AN XY: 74242

African (AFR) AF: 0.348 AC: 14397 AN: 41364

American (AMR) AF: 0.165 AC: 2521 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3472

East Asian (EAS) AF: 0.108 AC: 559 AN: 5178

South Asian (SAS) AF: 0.169 AC: 812 AN: 4806

European-Finnish (FIN) AF: 0.0562 AC: 595 AN: 10584

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0739 AC: 5022 AN: 67930

Other (OTH) AF: 0.154 AC: 324 AN: 2106

Alfa AF: 0.103 Hom.: 672

Bravo AF: 0.179

Asia WGS AF: 0.127 AC: 442 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.29
PhyloP100		-0.057
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: rs864434; hg19: chr7-137229428;