Help Section
Query types
By variant
Input should be chrom-pos-ref-alt. Genomic positions should be under GRCh38 assembly.
By gene symbols
The symbols should be the HGNC gene symbols and can be only queried one gene at a time
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Results
Results by variant search
A table containing the annotation and effect measure scores of the variant will be given. The threshold set in the website are arbitrary and can be adjusted based on your preference or use case. The page also includes the allele count (AC), allele freqency (AF) and allele number (AN) based on the latest version of gnomAD - v4. Finally, the probability of the variant (Symetrics Score) being deleterious is also included. The suggested threshold is 0.875 but you can opt to use 0.5 as per standard classification threshold. The t = 0.875 is based on the determined threshold at which there is a balance among precision, accuracy, ROC, sensitivity and specificity.
Results by gene
The gene search results will show a table of the Symetrics Z-scores, reflecting the intolerance of that gene to synonymous variation. The suggested threshold for this is +1.96 which is 2 standard deviation away from the expected value. The page also includes a few other intolerance measure acquired from gnomAD.