Genes Evaluated
The HCI variant dictionary contains many cancer predisposition genes (CPGs). These are genes that can cause a moderate to high increase in risk for cancer when mutated in the germline. This made ClinVar a natural choice for external knowledge about records in the collection since ClinVar contains mostly germline variants (more than half a million). However, the number of somatic entries to ClinVar is rising (>4000 as of January 2020) and this trend will make ClinVar a more flexible knowledge source20. The nature of CPGs also leaves them more likely to have multiple classifications and subsequent conflicts as they are more often the subject of expert review panels (more so than other gene types)21. There are also a number of nonclinical variants in the dictionary from research studies conducted by HCI. These variants are not likely to have annotations in ClinVar. Future work to mature this tool could include separate suggestion types and annotation gathering for nonclinical variants. A full list of genes (clinical and non-clinical) in the HCI variant dictionary is included as Supplementary Table 1.