chr5-111092567-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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WDR36 | NM_139281.3 | c.111G>T | p.Lys37Asn | missense_variant | 1/23 | ENST00000513710.4 | |
WDR36 | XM_047416729.1 | c.111G>T | p.Lys37Asn | missense_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710.4 | c.111G>T | p.Lys37Asn | missense_variant | 1/23 | 1 | NM_139281.3 | P1 | |
WDR36 | ENST00000505303.5 | n.247G>T | non_coding_transcript_exon_variant | 1/15 | 5 | ||||
WDR36 | ENST00000515784.1 | n.221G>T | non_coding_transcript_exon_variant | 1/2 | 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:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 12, 2022 | 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. ClinVar contains an entry for this variant (Variation ID: 623421). This variant has not been reported in the literature in individuals affected with WDR36-related conditions. This variant is present in population databases (rs200337257, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. 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). - |
High myopia Uncertain:1
Uncertain significance, no assertion criteria provided | research | Institute of Human Genetics, Polish Academy of Sciences | Dec 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at