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I might be missing something, but I did not found a way for setting Mysql variables in my.cnf file in Webmin. The mysql module has a page "MySQL server options" that lists only 8 variables, which do not even reflect the actual settings apart "Maximum number of connections", "Query cache size in bytes" and "Maximum packet size".
Thanks for help and Happy New Year!
Unfortunately Webmin does not have a dedicated edit box for the my.cnf file. You'll need to do that via the File Manager under Others, or directly on the server by logging in via SSH.
After making changes to the file, you'll need to restart MySQL.
This is exactly what I do. Well, though