5-111092567-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_139281.3(WDR36):c.111G>T(p.Lys37Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,614,208 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_139281.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710.4 | c.111G>T | p.Lys37Asn | missense_variant | Exon 1 of 23 | 1 | NM_139281.3 | ENSP00000424628.3 | ||
WDR36 | ENST00000505303.5 | n.247G>T | non_coding_transcript_exon_variant | Exon 1 of 15 | 5 | |||||
WDR36 | ENST00000515784.1 | n.221G>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152276Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000229 AC: 57AN: 249372Hom.: 1 AF XY: 0.000267 AC XY: 36AN XY: 134840
GnomAD4 exome AF: 0.000251 AC: 367AN: 1461814Hom.: 1 Cov.: 31 AF XY: 0.000275 AC XY: 200AN XY: 727194
GnomAD4 genome AF: 0.000217 AC: 33AN: 152394Hom.: 1 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74520
ClinVar
Submissions by phenotype
not provided Uncertain:2
This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 93 of the WDR36 protein (p.Lys93Asn). This variant is present in population databases (rs200337257, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with WDR36-related conditions. ClinVar contains an entry for this variant (Variation ID: 623421). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt WDR36 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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High myopia Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at