9-124855705-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001045476.3(WDR38):c.262C>T(p.Arg88Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,613,256 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001045476.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR38 | ENST00000373574.2 | c.262C>T | p.Arg88Cys | missense_variant | Exon 3 of 9 | 1 | NM_001045476.3 | ENSP00000362677.1 | ||
WDR38 | ENST00000613760.4 | c.262C>T | p.Arg88Cys | missense_variant | Exon 3 of 9 | 1 | ENSP00000483312.1 | |||
WDR38 | ENST00000618744.4 | c.97-92C>T | intron_variant | Intron 2 of 7 | 1 | ENSP00000483432.1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 248956Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135146
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461056Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 726876
GnomAD4 genome AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.262C>T (p.R88C) alteration is located in exon 3 (coding exon 3) of the WDR38 gene. This alteration results from a C to T substitution at nucleotide position 262, causing the arginine (R) at amino acid position 88 to be replaced by a cysteine (C). 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