chrX-48599387-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001347217.2(WDR13):c.317G>A(p.Arg106His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,207,018 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001347217.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000442 AC: 5AN: 113076Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35204
GnomAD3 exomes AF: 0.0000290 AC: 5AN: 172703Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 59223
GnomAD4 exome AF: 0.0000229 AC: 25AN: 1093942Hom.: 0 Cov.: 31 AF XY: 0.0000278 AC XY: 10AN XY: 360072
GnomAD4 genome AF: 0.0000442 AC: 5AN: 113076Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35204
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.317G>A (p.R106H) alteration is located in exon 3 (coding exon 3) of the WDR13 gene. This alteration results from a G to A substitution at nucleotide position 317, causing the arginine (R) at amino acid position 106 to be replaced by a histidine (H). 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