rs7647305

Variant names:

• chr3-186116501-T-C
• rs7647305
• ENST00000447054.5:n.132-10559A>G

Variant summary

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

The ENST00000447054.5(DGKG):​n.132-10559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,174 control chromosomes in the GnomAD database, including 42,783 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 0.74 (42783 hom., cov: 32)
• Consequence: DGKG ENST00000447054.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 148 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKG	ENST00000447054.5	TSL:3	n.132-10559A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113091 AN: 152056 Hom.: 42777 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.743 AC: 113127 AN: 152174 Hom.: 42783 Cov.: 32 AF XY: 0.749 AC XY: 55687 AN XY: 74394

African (AFR) AF: 0.591 AC: 24493 AN: 41460

American (AMR) AF: 0.811 AC: 12397 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2754 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4811 AN: 5186

South Asian (SAS) AF: 0.760 AC: 3664 AN: 4824

European-Finnish (FIN) AF: 0.822 AC: 8710 AN: 10602

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53686 AN: 68030

Other (OTH) AF: 0.765 AC: 1615 AN: 2110

Alfa AF: 0.781 Hom.: 157479

Bravo AF: 0.737

Asia WGS AF: 0.842 AC: 2928 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	5.7
DANN	Benign	0.49
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7647305; hg19: chr3-185834290;