NM_003647.3:c.465-210_465-205dupAAAAAA

Variant names:

• chr17-56843797-C-CAAAAAA
• rs368992473
• NM_003647.3:c.465-210_465-205dupAAAAAA

Variant summary

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

The NM_003647.3(DGKE):​c.465-210_465-205dupAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1378 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-CAAAAAA is Benign according to our data. Variant chr17-56843797-C-CAAAAAA is described in ClinVar as [Benign]. Clinvar id is 1238428.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DGKE	NM_003647.3	c.465-210_465-205dupAAAAAA		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_465-221insAAAAAA		intron_variant	Intron 2 of 11	1	NM_003647.3	ENSP00000284061.3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 12589 AN: 108732 Hom.: 1378 Cov.: 0

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00459

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.116 AC: 12585 AN: 108734 Hom.: 1378 Cov.: 0 AF XY: 0.109 AC XY: 5502 AN XY: 50458

Gnomad4 AFR AF: 0.0422

Gnomad4 AMR AF: 0.0757

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.00461

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.0874

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.103

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 29, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;