rs6808013

Variant names:

• chr3-186232440-G-A
• rs6808013
• NM_001346.3:c.1826+10064C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001346.3. 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
	DGKG	NM_001346.3	MANE Select	c.1826+10064C>T		intron	N/A	NP_001337.2
	DGKG	NM_001080744.2		c.1751+10064C>T		intron	N/A	NP_001074213.1
	DGKG	NM_001080745.2		c.1709+10064C>T		intron	N/A	NP_001074214.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKG	ENST00000265022.8	TSL:1 MANE Select	c.1826+10064C>T		intron	N/A	ENSP00000265022.3
	DGKG	ENST00000344484.8	TSL:1	c.1751+10064C>T		intron	N/A	ENSP00000339777.4
	DGKG	ENST00000480809.5	TSL:1	n.2089+10064C>T		intron	N/A

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

African (AFR) AF: 0.482 AC: 19948 AN: 41392

American (AMR) AF: 0.806 AC: 12323 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2740 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5060 AN: 5194

South Asian (SAS) AF: 0.885 AC: 4269 AN: 4824

European-Finnish (FIN) AF: 0.796 AC: 8418 AN: 10582

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53626 AN: 67988

Other (OTH) AF: 0.731 AC: 1541 AN: 2108

Alfa AF: 0.764 Hom.: 32336

Bravo AF: 0.707

Asia WGS AF: 0.879 AC: 3048 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.58
PhyloP100		-0.084
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6808013; hg19: chr3-185950229;