2-74422238-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032118.4(WDR54):c.85C>T(p.Arg29Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,614,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032118.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250534Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135514
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727212
GnomAD4 genome AF: 0.000230 AC: 35AN: 152356Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.85C>T (p.R29C) alteration is located in exon 2 (coding exon 1) of the WDR54 gene. This alteration results from a C to T substitution at nucleotide position 85, causing the arginine (R) at amino acid position 29 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