chr1-117933344-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006784.3(WDR3):c.25C>T(p.Arg9Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000102 in 1,614,050 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 2 hom. )
Consequence
WDR3
NM_006784.3 missense
NM_006784.3 missense
Scores
6
9
4
Clinical Significance
Conservation
PhyloP100: 5.74
Genes affected
WDR3 (HGNC:12755): (WD repeat domain 3) This gene encodes a nuclear protein containing 10 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, which usually include a trp-asp at the C-terminal end. Proteins belonging to the WD repeat family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR3 | NM_006784.3 | c.25C>T | p.Arg9Cys | missense_variant | 2/27 | ENST00000349139.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR3 | ENST00000349139.6 | c.25C>T | p.Arg9Cys | missense_variant | 2/27 | 1 | NM_006784.3 | P1 | |
WDR3 | ENST00000369441.7 | c.25C>T | p.Arg9Cys | missense_variant | 2/10 | 1 | |||
WDR3 | ENST00000471680.1 | n.207C>T | non_coding_transcript_exon_variant | 2/5 | 5 | ||||
WDR3 | ENST00000487202.5 | n.116C>T | non_coding_transcript_exon_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152188Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000135 AC: 34AN: 251458Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135900
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GnomAD4 exome AF: 0.000105 AC: 154AN: 1461862Hom.: 2 Cov.: 30 AF XY: 0.000151 AC XY: 110AN XY: 727238
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74346
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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 | Aug 02, 2021 | The c.25C>T (p.R9C) alteration is located in exon 2 (coding exon 1) of the WDR3 gene. This alteration results from a C to T substitution at nucleotide position 25, causing the arginine (R) at amino acid position 9 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
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
.;D
Sift4G
Pathogenic
D;D
Polyphen
0.40
.;B
Vest4
MVP
MPC
0.25
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