rs3760158
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003647.3(DGKE):āc.579A>Cā(p.Thr193Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 1,570,546 control chromosomes in the GnomAD database, including 419,981 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.71 ( 38496 hom., cov: 31)
Exomes š: 0.73 ( 381485 hom. )
Consequence
DGKE
NM_003647.3 synonymous
NM_003647.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.356
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 made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 17-56844133-A-C is Benign according to our data. Variant chr17-56844133-A-C is described in ClinVar as [Benign]. Clinvar id is 259116.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-56844133-A-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.356 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKE | NM_003647.3 | c.579A>C | p.Thr193Thr | synonymous_variant | 3/12 | ENST00000284061.8 | NP_003638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKE | ENST00000284061.8 | c.579A>C | p.Thr193Thr | synonymous_variant | 3/12 | 1 | NM_003647.3 | ENSP00000284061.3 |
Frequencies
GnomAD3 genomes AF: 0.708 AC: 107508AN: 151854Hom.: 38486 Cov.: 31
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GnomAD3 exomes AF: 0.726 AC: 156530AN: 215610Hom.: 57668 AF XY: 0.721 AC XY: 84669AN XY: 117456
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GnomAD4 exome AF: 0.731 AC: 1037347AN: 1418574Hom.: 381485 Cov.: 31 AF XY: 0.728 AC XY: 513891AN XY: 705420
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GnomAD4 genome AF: 0.708 AC: 107564AN: 151972Hom.: 38496 Cov.: 31 AF XY: 0.709 AC XY: 52618AN XY: 74214
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ClinVar
Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 08, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Immunoglobulin-mediated membranoproliferative glomerulonephritis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at