Deleteriousness versus pathogenicity
What’s the difference between deleteriousness and pathogenicity? Box 1 from the article “Guidelines for investigating causality of sequence variants in human disease” has the following definitions:
Incidental findings using GEMINI
The American College of Medical Genetics and Genomics (ACMG) have recommended that genetic variants that may be pathogenic or likely pathogenic in certain genes should be reported back to the patient. The latest list of genes can be found here. How do I assess whether a variant is pathogenic or likely pathogenic? Use this tool,…
Summary plots from GEMINI
I’m a fan of GEMINI and have been using it for for a year and a half for various exome projects. I have written two scripts that can generate variant summaries from a GEMINI database. I prefer bar plots over the pie charts created by VEP. A summary pie chart created by VEP.