17-56843797-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003647.3(DGKE):c.465-205dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.026 (189 hom., cov: 0)
• Consequence: DGKE NM_003647.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0310

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]

TRIM25 (HGNC:12932): (tripartite motif containing 25) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein is an RNA binding protein, functions as a ubiquitin E3 ligase and is involved in multiple cellular processes, including regulation of antiviral innate immunity. [provided by RefSeq, Sep 2021]

LOC124904036 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-56843797-C-CA is Benign according to our data. Variant chr17-56843797-C-CA is described in ClinVar as [Benign]. Clinvar id is 1292022.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKE	NM_003647.3	c.465-205dup		intron_variant		ENST00000284061.8
LOC124904036	XR_007065857.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DGKE	ENST00000284061.8	c.465-205dup		intron_variant		1	NM_003647.3	P1
DGKE	ENST00000572944.1	c.295-205dup		intron_variant		1
DGKE	ENST00000576869.5	n.613-205dup		intron_variant, non_coding_transcript_variant		1
TRIM25	ENST00000648772.1	c.*314-8_*314-7insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0261 AC: 2855 AN: 109366 Hom.: 188 Cov.: 0

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.00133

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.000682

Gnomad EAS AF: 0.000254

Gnomad SAS AF: 0.00252

Gnomad FIN AF: 0.00271

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000941

Gnomad OTH AF: 0.0188

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

GnomAD4 genome AF: 0.0262 AC: 2863 AN: 109366 Hom.: 189 Cov.: 0 AF XY: 0.0266 AC XY: 1348 AN XY: 50750

Gnomad4 AFR AF: 0.0914

Gnomad4 AMR AF: 0.0112

Gnomad4 ASJ AF: 0.000682

Gnomad4 EAS AF: 0.000255

Gnomad4 SAS AF: 0.00254

Gnomad4 FIN AF: 0.00271

Gnomad4 NFE AF: 0.000941

Gnomad4 OTH AF: 0.0187

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

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs368992473; hg19: chr17-54921158;