14-24115649-G-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_025230.5(DCAF11):c.55G>T(p.Gly19Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
DCAF11
NM_025230.5 missense
NM_025230.5 missense
Scores
8
10
Clinical Significance
Conservation
PhyloP100: 3.04
Genes affected
DCAF11 (HGNC:20258): (DDB1 and CUL4 associated factor 11) This gene encodes a WD repeat-containing protein that interacts with the COP9 signalosome, a macromolecular complex that interacts with cullin-RING E3 ligases and regulates their activity by hydrolyzing cullin-Nedd8 conjugates. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.32010972).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.55G>T (p.G19C) alteration is located in exon 2 (coding exon 1) of the DCAF11 gene. This alteration results from a G to T substitution at nucleotide position 55, causing the glycine (G) at amino acid position 19 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
.;T;T;.;.;T;T;T;.;.;T;T;.;T;T;T;T;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;N;.;.;.;N;.;.;.;.;.;.;.;.;.;.;.;.;.;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;N;D;D;N;N;D;D;N;D;N;D;N;N;D;D;D;D;D;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D;D;.;D;D;D;D;.;D;D;D;D;D;D;D;D
Sift4G
Benign
T;T;T;T;T;T;D;T;D;D;T;D;T;T;D;T;T;D;T;D
Polyphen
0.98, 0.96
.;D;.;.;.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;D
Vest4
0.54, 0.41, 0.54
MutPred
Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);Gain of glycosylation at P16 (P = 0.1401);
MVP
MPC
0.38
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.