17-56843797-C-CA

Variant names:

• chr17-56843797-C-CA
• rs368992473
• NM_003647.3:c.465-205dupA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003647.3(DGKE):​c.465-205dupA 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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003647.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKE	NM_003647.3	MANE Select	c.465-205dupA		intron	N/A	NP_003638.1	A1L4Q0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGKE	ENST00000284061.8	TSL:1 MANE Select	c.465-222_465-221insA		intron	N/A	ENSP00000284061.3	P52429-1
	DGKE	ENST00000572944.1	TSL:1	c.294-222_294-221insA		intron	N/A	ENSP00000458493.1	I3L112
	DGKE	ENST00000576869.5	TSL:1	n.613-222_613-221insA		intron	N/A

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

African (AFR) AF: 0.0914 AC: 2654 AN: 29030

American (AMR) AF: 0.0112 AC: 109 AN: 9706

Ashkenazi Jewish (ASJ) AF: 0.000682 AC: 2 AN: 2934

East Asian (EAS) AF: 0.000255 AC: 1 AN: 3920

South Asian (SAS) AF: 0.00254 AC: 8 AN: 3154

European-Finnish (FIN) AF: 0.00271 AC: 11 AN: 4066

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 196

European-Non Finnish (NFE) AF: 0.000941 AC: 51 AN: 54216

Other (OTH) AF: 0.0187 AC: 26 AN: 1392

Alfa AF: 0.00210 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.031
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs368992473; hg19: chr17-54921158;