Google docs uses the ⌘-, shortcut, I can't type this in Safari because it opens Safari's preferences.
How can I work around this?
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Unfortunately, ⌘Cmd, is almost universally the default keyboard shortcut in Mac apps for Preferences.
As I could not find any simple way of reassigning or customizing keyboard shortcuts for Google Docs, the best workaround is to override the system shortcut for Preferences instead, to avoid the conflict. Thankfully this can be done easily in OS X:
Preferences...exactly, including the 3 dots.
Once you've added the new shortcut for Preferences, you can use ⌘Cmd, for formatting subscripts in Google Docs!