17-56848105-A-G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_003647.3(DGKE):c.888+40A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000174 in 1,148,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000017 ( 0 hom. )
Consequence
DGKE
NM_003647.3 intron
NM_003647.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.171
Publications
4 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]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
Variant 17-56848105-A-G is Pathogenic according to our data. Variant chr17-56848105-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 548648.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKE | ENST00000284061.8 | c.888+40A>G | intron_variant | Intron 5 of 11 | 1 | NM_003647.3 | ENSP00000284061.3 | |||
DGKE | ENST00000572944.1 | c.717+40A>G | intron_variant | Intron 4 of 9 | 1 | ENSP00000458493.1 | ||||
TRIM25 | ENST00000648772.1 | n.*313+3838T>C | intron_variant | Intron 10 of 12 | ENSP00000498158.1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
Cov.:
30
GnomAD4 exome AF: 0.00000174 AC: 2AN: 1148968Hom.: 0 Cov.: 16 AF XY: 0.00000177 AC XY: 1AN XY: 565848 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1148968
Hom.:
Cov.:
16
AF XY:
AC XY:
1
AN XY:
565848
show subpopulations
African (AFR)
AF:
AC:
0
AN:
24582
American (AMR)
AF:
AC:
0
AN:
22146
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17264
East Asian (EAS)
AF:
AC:
0
AN:
30288
South Asian (SAS)
AF:
AC:
0
AN:
45722
European-Finnish (FIN)
AF:
AC:
0
AN:
42654
Middle Eastern (MID)
AF:
AC:
0
AN:
4138
European-Non Finnish (NFE)
AF:
AC:
2
AN:
915556
Other (OTH)
AF:
AC:
0
AN:
46618
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome Cov.: 30
GnomAD4 genome
Cov.:
30
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hemolytic-uremic syndrome Pathogenic:1
Apr 08, 2015
Yale Center for Mendelian Genomics, Yale University
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -1
DS_DL_spliceai
Position offset: -40
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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