chr14-102139930-A-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144574.4(WDR20):āc.7A>Gā(p.Thr3Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000862 in 1,612,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000039 ( 0 hom., cov: 32)
Exomes š: 0.000091 ( 0 hom. )
Consequence
WDR20
NM_144574.4 missense
NM_144574.4 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 6.78
Genes affected
WDR20 (HGNC:19667): (WD repeat domain 20) This gene encodes a WD repeat-containing protein that functions to preserve and regulate the activity of the USP12-UAF1 deubiquitinating enzyme complex. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.042661577).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDR20 | NM_144574.4 | c.7A>G | p.Thr3Ala | missense_variant | 1/3 | ENST00000342702.8 | NP_653175.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR20 | ENST00000342702.8 | c.7A>G | p.Thr3Ala | missense_variant | 1/3 | 1 | NM_144574.4 | ENSP00000341037 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251180Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135746
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GnomAD4 exome AF: 0.0000911 AC: 133AN: 1459932Hom.: 0 Cov.: 31 AF XY: 0.0000854 AC XY: 62AN XY: 725784
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
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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 | Jun 04, 2024 | The c.7A>G (p.T3A) alteration is located in exon 1 (coding exon 1) of the WDR20 gene. This alteration results from a A to G substitution at nucleotide position 7, causing the threonine (T) at amino acid position 3 to be replaced by an alanine (A). 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
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;.;.;T;.;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N;N;N;.;N;N;N
MutationTaster
Benign
D;D;D;D;D;D;D;D;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;.;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T;T
Polyphen
B;.;.;B;.;.;.;.;.
Vest4
MutPred
Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);Loss of methylation at K8 (P = 0.0803);
MVP
MPC
0.47
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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