rs6808013

Positions:

• chr3-186232440-G-A

Variant summary

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

The NM_001346.3(DGKG):​c.1826+10064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,052 control chromosomes in the GnomAD database, including 40,741 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 0.72 (40741 hom., cov: 33)
• Consequence: DGKG NM_001346.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DGKG	NM_001346.3	c.1826+10064C>T		intron_variant		ENST00000265022.8	NP_001337.2
DGKG	NM_001080744.2	c.1751+10064C>T		intron_variant			NP_001074213.1
DGKG	NM_001080745.2	c.1709+10064C>T		intron_variant			NP_001074214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DGKG	ENST00000265022.8	c.1826+10064C>T		intron_variant		1	NM_001346.3	ENSP00000265022	P1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108893 AN: 151934 Hom.: 40733 Cov.: 33

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.716 AC: 108926 AN: 152052 Hom.: 40741 Cov.: 33 AF XY: 0.722 AC XY: 53649 AN XY: 74340

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.731

Alfa AF: 0.765 Hom.: 22325

Bravo AF: 0.707

Asia WGS AF: 0.879 AC: 3048 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs6808013; hg19: chr3-185950229;