3-186115970-C-A

Position:

• chr3-186115970-C-A

Variant summary

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

The ENST00000447054.5(DGKG):​n.132-10028G>T 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 0.658 in 151,956 control chromosomes in the GnomAD database, including 34,096 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 0.66 (34096 hom., cov: 31)
• Consequence: DGKG ENST00000447054.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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.132-10028G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99953 AN: 151838 Hom.: 34098 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.658 AC: 99968 AN: 151956 Hom.: 34096 Cov.: 31 AF XY: 0.655 AC XY: 48687 AN XY: 74278

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.677

Alfa AF: 0.739 Hom.: 81526

Bravo AF: 0.640

Asia WGS AF: 0.542 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7635103; hg19: chr3-185833759;