NM_003647.3:c.465-211_465-205dupAAAAAAA

Variant names:

• chr17-56843797-C-CAAAAAAA
• rs368992473
• NM_003647.3:c.465-211_465-205dupAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_003647.3(DGKE):​c.465-211_465-205dupAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0015 (5 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: DGKE NM_003647.3 intron
• Clinical Significance: Not reported in ClinVar
• 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKE	NM_003647.3	c.465-211_465-205dupAAAAAAA		intron_variant	Intron 2 of 11	ENST00000284061.8	NP_003638.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DGKE	ENST00000284061.8	c.465-222_465-221insAAAAAAA		intron_variant	Intron 2 of 11	1	NM_003647.3	ENSP00000284061.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 163 AN: 109050 Hom.: 5 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.000898

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00124

Gnomad ASJ AF: 0.00137

Gnomad EAS AF: 0.00153

Gnomad SAS AF: 0.000629

Gnomad FIN AF: 0.000737

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00198

Gnomad OTH AF: 0.00218

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: 0.00149 AC: 162 AN: 109050 Hom.: 5 Cov.: 0 AF XY: 0.00154 AC XY: 78 AN XY: 50598

Gnomad4 AFR AF: 0.000897

Gnomad4 AMR AF: 0.00124

Gnomad4 ASJ AF: 0.00137

Gnomad4 EAS AF: 0.00153

Gnomad4 SAS AF: 0.000317

Gnomad4 FIN AF: 0.000737

Gnomad4 NFE AF: 0.00198

Gnomad4 OTH AF: 0.00216

ClinVar

Not reported in ClinVar

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;