17-56834568-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003647.3(DGKE):c.-18-210G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,874 control chromosomes in the GnomAD database, including 31,852 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.64 (31852 hom., cov: 33)
• Consequence: DGKE NM_003647.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0130

Genes affected

DGKE (HGNC:2852): (diacylglycerol kinase epsilon) Diacylglycerol kinases are thought to be involved mainly in the regeneration of phosphatidylinositol (PI) from diacylglycerol in the PI-cycle during cell signal transduction. When expressed in mammalian cells, DGK-epsilon shows specificity for arachidonyl-containing diacylglycerol. DGK-epsilon is expressed predominantly in testis. [provided by RefSeq, Jul 2008]

C17orf67 (HGNC:27900): (chromosome 17 open reading frame 67) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 17-56834568-G-A is Benign according to our data. Variant chr17-56834568-G-A is described in ClinVar as [Benign]. Clinvar id is 1249672.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKE	NM_003647.3	c.-18-210G>A		intron_variant		ENST00000284061.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKE	ENST00000284061.8	c.-18-210G>A		intron_variant		1	NM_003647.3	P1
DGKE	ENST00000572810.1	c.-18-210G>A		intron_variant		1
DGKE	ENST00000576869.5	n.131-210G>A		intron_variant, non_coding_transcript_variant		1
C17orf67	ENST00000487705.1	n.285+3921C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97663 AN: 151756 Hom.: 31853 Cov.: 33

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.643 AC: 97701 AN: 151874 Hom.: 31852 Cov.: 33 AF XY: 0.644 AC XY: 47828 AN XY: 74230

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.659

Alfa AF: 0.637 Hom.: 4450

Bravo AF: 0.651

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	5.6
Dann	Benign	0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.16		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: rs2235092; hg19: chr17-54911929;