15-84643509-CAG-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_032856.5(WDR73):c.1096_1097delCT(p.Leu366AlafsTer23) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000211 in 1,424,534 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_032856.5 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000515 AC: 1AN: 194106Hom.: 0 AF XY: 0.00000964 AC XY: 1AN XY: 103686
GnomAD4 exome AF: 0.00000211 AC: 3AN: 1424534Hom.: 0 AF XY: 0.00000284 AC XY: 2AN XY: 705028
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Galloway-Mowat syndrome 1 Pathogenic:2
- -
The c.1096_1097del;p.(Leu366Alafs*23) is a null frameshift variant (NMD) in the WDR73 gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevant exon to the transcript - PVS1_strong. This variant is not present in population databases (rs768820873- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br.) - PM2. In summary, the currently available evidence indicates that the variant is likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at