X-48601844-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001347217.2(WDR13):c.892G>T(p.Gly298Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,202,565 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 47 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001347217.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR13 | ENST00000376729.10 | c.892G>T | p.Gly298Trp | missense_variant | Exon 7 of 10 | 5 | NM_001347217.2 | ENSP00000365919.5 | ||
WDR13 | ENST00000218056.9 | c.892G>T | p.Gly298Trp | missense_variant | Exon 6 of 9 | 1 | ENSP00000218056.5 | |||
WDR13 | ENST00000479279.5 | n.1759G>T | non_coding_transcript_exon_variant | Exon 5 of 8 | 1 | |||||
WDR13 | ENST00000482760.3 | c.136G>T | p.Gly46Trp | missense_variant | Exon 2 of 5 | 3 | ENSP00000483191.1 |
Frequencies
GnomAD3 genomes AF: 0.0000887 AC: 10AN: 112735Hom.: 0 Cov.: 24 AF XY: 0.0000860 AC XY: 3AN XY: 34887
GnomAD3 exomes AF: 0.000116 AC: 20AN: 172041Hom.: 0 AF XY: 0.000138 AC XY: 8AN XY: 57995
GnomAD4 exome AF: 0.0000982 AC: 107AN: 1089830Hom.: 0 Cov.: 31 AF XY: 0.000123 AC XY: 44AN XY: 356856
GnomAD4 genome AF: 0.0000887 AC: 10AN: 112735Hom.: 0 Cov.: 24 AF XY: 0.0000860 AC XY: 3AN XY: 34887
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
WDR13: PP2, BS2 -
- -
- -
not specified Uncertain:1
The c.892G>T (p.G298W) alteration is located in exon 6 (coding exon 6) of the WDR13 gene. This alteration results from a G to T substitution at nucleotide position 892, causing the glycine (G) at amino acid position 298 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at