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GeneBe

3-186224531-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001346.3(DGKG):c.1827-12646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,258 control chromosomes in the GnomAD database, including 66,739 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 0.94 ( 66739 hom., cov: 31)

Consequence

DGKG
NM_001346.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.230
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DGKGNM_001346.3 linkuse as main transcriptc.1827-12646T>C intron_variant ENST00000265022.8
DGKGNM_001080744.2 linkuse as main transcriptc.1752-12646T>C intron_variant
DGKGNM_001080745.2 linkuse as main transcriptc.1710-12646T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DGKGENST00000265022.8 linkuse as main transcriptc.1827-12646T>C intron_variant 1 NM_001346.3 P1P49619-1

Frequencies

GnomAD3 genomes
AF:
0.936
AC:
142376
AN:
152140
Hom.:
66697
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.892
Gnomad AMI
AF:
0.984
Gnomad AMR
AF:
0.961
Gnomad ASJ
AF:
0.933
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.918
Gnomad FIN
AF:
0.963
Gnomad MID
AF:
0.892
Gnomad NFE
AF:
0.948
Gnomad OTH
AF:
0.946
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.936
AC:
142477
AN:
152258
Hom.:
66739
Cov.:
31
AF XY:
0.938
AC XY:
69824
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.892
Gnomad4 AMR
AF:
0.961
Gnomad4 ASJ
AF:
0.933
Gnomad4 EAS
AF:
0.997
Gnomad4 SAS
AF:
0.918
Gnomad4 FIN
AF:
0.963
Gnomad4 NFE
AF:
0.948
Gnomad4 OTH
AF:
0.945
Alfa
AF:
0.937
Hom.:
15076
Bravo
AF:
0.936
Asia WGS
AF:
0.951
AC:
3308
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
3.6
Dann
Benign
0.74

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7620841; hg19: chr3-185942320; API