3-186116501-T-C

Position:

• chr3-186116501-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447054.5(DGKG):​n.132-10559A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKG	ENST00000447054.5	n.132-10559A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.765

Alfa AF: 0.791 Hom.: 72807

Bravo AF: 0.737

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7647305; hg19: chr3-185834290;