chr5-111092611-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_139281.3(WDR36):c.155C>T(p.Thr52Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000917 in 1,613,168 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710.4 | c.155C>T | p.Thr52Ile | missense_variant | Exon 1 of 23 | 1 | NM_139281.3 | ENSP00000424628.3 | ||
WDR36 | ENST00000505303.5 | n.291C>T | non_coding_transcript_exon_variant | Exon 1 of 15 | 5 | |||||
WDR36 | ENST00000515784.1 | n.265C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000102 AC: 25AN: 246114Hom.: 1 AF XY: 0.0000825 AC XY: 11AN XY: 133352
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1460904Hom.: 1 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 726728
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.323C>T (p.T108I) alteration is located in exon 1 (coding exon 1) of the WDR36 gene. This alteration results from a C to T substitution at nucleotide position 323, causing the threonine (T) at amino acid position 108 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 108 of the WDR36 protein (p.Thr108Ile). This variant is present in population databases (rs753451887, gnomAD 0.04%). 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: 1433828). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at