chr4-961139-G-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001347.4(DGKQ):c.2637C>A(p.Val879=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,607,148 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 Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
DGKQ
NM_001347.4 synonymous
NM_001347.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
Genes affected
DGKQ (HGNC:2856): (diacylglycerol kinase theta) The protein encoded by this gene contains three cysteine-rich domains, a proline-rich region, and a pleckstrin homology domain with an overlapping Ras-associating domain. It is localized in the speckle domains of the nucleus, and mediates the regeneration of phosphatidylinositol (PI) from diacylglycerol in the PI-cycle during cell signal transduction. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 4-961139-G-T is Benign according to our data. Variant chr4-961139-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3033599.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.21 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGKQ | NM_001347.4 | c.2637C>A | p.Val879= | synonymous_variant | 22/23 | ENST00000273814.8 | NP_001338.2 | |
DGKQ | XM_047449687.1 | c.2724C>A | p.Val908= | synonymous_variant | 22/23 | XP_047305643.1 | ||
DGKQ | XM_011513411.2 | c.2637C>A | p.Val879= | synonymous_variant | 22/23 | XP_011511713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGKQ | ENST00000273814.8 | c.2637C>A | p.Val879= | synonymous_variant | 22/23 | 1 | NM_001347.4 | ENSP00000273814 | P1 | |
DGKQ | ENST00000509465.5 | c.2439C>A | p.Val813= | synonymous_variant | 21/22 | 5 | ENSP00000425862 | |||
DGKQ | ENST00000515182.1 | c.282C>A | p.Val94= | synonymous_variant | 4/5 | 5 | ENSP00000421756 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000835 AC: 2AN: 239412Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130448
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GnomAD4 exome AF: 0.0000241 AC: 35AN: 1454972Hom.: 0 Cov.: 35 AF XY: 0.0000262 AC XY: 19AN XY: 723932
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74338
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
DGKQ-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 19, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at