17-56843797-C-CAAAAA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_003647.3(DGKE):c.465-209_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 0.57 (17593 hom., cov: 0)
  • Failed GnomAD Quality Control
• 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 17-56843797-C-CAAAAA is Benign according to our data. Variant chr17-56843797-C-CAAAAA is described in ClinVar as [Benign]. Clinvar id is 1243279.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 17602 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DGKE	NM_003647.3	c.465-209_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.465-209_465-205dup		intron_variant		1	NM_003647.3	P1
DGKE	ENST00000572944.1	c.295-209_295-205dup		intron_variant		1
DGKE	ENST00000576869.5	n.613-209_613-205dup		intron_variant, non_coding_transcript_variant		1
TRIM25	ENST00000648772.1	c.*314-8_*314-7insTTTTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.566 AC: 61189 AN: 108168 Hom.: 17602 Cov.: 0

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.590

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.587

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.566 AC: 61175 AN: 108168 Hom.: 17593 Cov.: 0 AF XY: 0.569 AC XY: 28531 AN XY: 50160

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.584

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

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;