X-49076729-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001029896.2(WDR45):c.257G>A(p.Arg86Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000034 in 1,204,606 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R86W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001029896.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR45 | NM_001029896.2 | c.257G>A | p.Arg86Gln | missense_variant | 5/11 | ENST00000376372.9 | |
WDR45 | NM_007075.4 | c.260G>A | p.Arg87Gln | missense_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR45 | ENST00000376372.9 | c.257G>A | p.Arg86Gln | missense_variant | 5/11 | 1 | NM_001029896.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112238Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34402
GnomAD3 exomes AF: 0.0000587 AC: 10AN: 170223Hom.: 0 AF XY: 0.0000177 AC XY: 1AN XY: 56617
GnomAD4 exome AF: 0.0000357 AC: 39AN: 1092368Hom.: 0 Cov.: 31 AF XY: 0.0000307 AC XY: 11AN XY: 358424
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112238Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34402
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2019 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2017 | The p.R87Q variant (also known as c.260G>A), located in coding exon 4 of the WDR45 gene, results from a G to A substitution at nucleotide position 260. The arginine at codon 87 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Neurodegeneration with brain iron accumulation 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at