10-120886823-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_018117.12(WDR11):c.2108G>A(p.Arg703Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018117.12 missense
Scores
Clinical Significance
Conservation
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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 |
---|---|---|---|---|---|---|---|---|---|---|
WDR11 | ENST00000263461.11 | c.2108G>A | p.Arg703Gln | missense_variant | Exon 16 of 29 | 1 | NM_018117.12 | ENSP00000263461.5 | ||
WDR11 | ENST00000497136.6 | n.*627G>A | non_coding_transcript_exon_variant | Exon 14 of 26 | 1 | ENSP00000474595.1 | ||||
WDR11 | ENST00000605543.5 | n.*627G>A | non_coding_transcript_exon_variant | Exon 9 of 22 | 2 | ENSP00000475076.1 | ||||
WDR11 | ENST00000497136.6 | n.*627G>A | 3_prime_UTR_variant | Exon 14 of 26 | 1 | ENSP00000474595.1 | ||||
WDR11 | ENST00000605543.5 | n.*627G>A | 3_prime_UTR_variant | Exon 9 of 22 | 2 | ENSP00000475076.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251182Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135754
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461754Hom.: 0 Cov.: 35 AF XY: 0.0000193 AC XY: 14AN XY: 727168
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74260
ClinVar
Submissions by phenotype
CHARGE syndrome Uncertain:1
We have identified a WDR11 missense mutation, NM_018117.11: c.2108G>A ( p.Arg703Gln), in a two-year-old boy with severe growth retardation, ventricular septal defect, and coloboma symptoms. This variant was not identified in either parent, and 8 of the 11 in silico prediction methods, including PolyPhen-2 (HDIV and HVAR), Mutation Taster, and LRT, used to predict its functional effects revealed that the variant was probably damaging/deleterious. Three-dimensional (3D) structural analysis revealed this variant was mapped onto an evolutionarily conserved region of the homologous protein. In summary, NM_018117.11: c.2108G>A (p.Arg703Gln) variant meets ACMG guidelines to be classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at