3-186116710-A-T

Variant names:

• chr3-186116710-A-T
• rs9816226
• ENST00000447054.5:n.132-10768T>A

Variant summary

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

The ENST00000447054.5(DGKG):​n.132-10768T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,178 control chromosomes in the GnomAD database, including 51,768 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 0.82 (51768 hom., cov: 32)
• Consequence: DGKG ENST00000447054.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 123 publications found

Genes affected

DGKG (HGNC:2853): (diacylglycerol kinase gamma) This gene encodes an enzyme that is a member of the type I subfamily of diacylglycerol kinases, which are involved in lipid metabolism. These enzymes generate phosphatidic acid by catalyzing the phosphorylation of diacylglycerol, a fundamental lipid second messenger that activates numerous proteins, including protein kinase C isoforms, Ras guanyl nucleotide-releasing proteins and some transient receptor potential channels. Diacylglycerol kinase gamma has been implicated in cell cycle regulation and in the negative regulation of macrophage differentiation in leukemia cells. Multiple transcript variants encoding different isoforms have been found for this gene. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447054.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKG	ENST00000447054.5	TSL:3	n.132-10768T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125280 AN: 152060 Hom.: 51731 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.824 AC: 125372 AN: 152178 Hom.: 51768 Cov.: 32 AF XY: 0.827 AC XY: 61545 AN XY: 74384

African (AFR) AF: 0.801 AC: 33251 AN: 41486

American (AMR) AF: 0.860 AC: 13160 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2837 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4920 AN: 5190

South Asian (SAS) AF: 0.805 AC: 3884 AN: 4824

European-Finnish (FIN) AF: 0.847 AC: 8951 AN: 10574

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55560 AN: 68014

Other (OTH) AF: 0.835 AC: 1764 AN: 2112

Alfa AF: 0.825 Hom.: 28744

Bravo AF: 0.825

Asia WGS AF: 0.879 AC: 3056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9816226; hg19: chr3-185834499;