chr5-111092379-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_139281.3(WDR36):c.-78C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000352 in 1,614,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_139281.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710 | c.-78C>A | 5_prime_UTR_variant | Exon 1 of 23 | 1 | NM_139281.3 | ENSP00000424628.3 | |||
WDR36 | ENST00000505303.5 | n.59C>A | non_coding_transcript_exon_variant | Exon 1 of 15 | 5 | |||||
WDR36 | ENST00000515784.1 | n.33C>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000259 AC: 65AN: 251316Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135886
GnomAD4 exome AF: 0.000363 AC: 531AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.000360 AC XY: 262AN XY: 727238
GnomAD4 genome AF: 0.000249 AC: 38AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74500
ClinVar
Submissions by phenotype
not provided Uncertain:2
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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This missense change has been observed in individual(s) with glaucoma (PMID: 17563723, 18172102). This variant is present in population databases (rs148041801, gnomAD 0.05%). This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 31 of the WDR36 protein (p.Pro31Thr). -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at