Genetic Variant DGKE:c.465-209_465-205dupAAAAA (chr17-56843797-C-CAAAAA) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_003647.3(DGKE):c.465-209_465-205dupAAAAA 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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0310

Publications

0 publications found

Variant links:

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]

DGKE links:

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]

TRIM25 links:

LOC124904036 (HGNC:):

LOC124904036 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 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 VariationId is 1243279.Status of the report is criteria_provided_single_submitter, 1 stars.

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.465-209_465-205dupAAAAA		intron	N/A	NP_003638.1	A1L4Q0

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

61189

AN:

108168

Hom.:

17602

Cov.:

show subpopulations

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.:

AF XY:

0.569

AC XY:

28531

AN XY:

50160

show subpopulations

African (AFR)

AF:

0.544

AC:

15558

AN:

28590

American (AMR)

AF:

0.675

AC:

6457

AN:

9570

Ashkenazi Jewish (ASJ)

AF:

0.550

AC:

1607

AN:

2922

East Asian (EAS)

AF:

0.890

AC:

3478

AN:

3906

South Asian (SAS)

AF:

0.505

AC:

1573

AN:

3112

European-Finnish (FIN)

AF:

0.489

AC:

1920

AN:

3926

Middle Eastern (MID)

AF:

0.595

AC:

113

AN:

190

European-Non Finnish (NFE)

AF:

0.543

AC:

29249

AN:

53826

Other (OTH)

AF:

0.584

AC:

802

AN:

1374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

964

1928

2892

3856

4820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.031

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over