Watching a GoToWebinar, there are no "presenter icon" to mute him/her/it/they/them, neither a way to temporarily mute/quieten the webinar while watching in an office etc.
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I was about to say to just mute the speaker on your computer.
But then I re-read your subject line, and it apears you want to mute the sound coming from the GoToWebinar, yet allow other sounds to continue being heard on your computer. Is this true? If so, whaat other sounds are you trying to hear? Music, message alerts?
What operating system are you using (Mac, Windows, Linux)?
Answering a SKype call, listening to music while the speaker waffles through introductions (especially when I've joined before the starting time, and need a quick mute till the start etc.)
It is possible you might be able to do something like this in the Windows environment, since Windows has a mixer to mix audio from different internal sources. I see no way to do this on a Mac.
I'd like to echo @Chris Droessler's suggestion. If you are using Windows you can right-click the speaker icon, select the volume mixer and adjust the volume of individual applications that are running. If you use a Mac I think there may be 3rd party applications that can give you the same ability.
Which MacOSX 3rd party product to spent money on for only GoToWebinar??
Perhaps have a look at VLC's open sourcce code to see how it's done in there to mute and change volume of an application, instead of not providing that function ;(
Rather than asking why GoTo does not include that feature, you should ask Apple why they choose to not include that feature. Apple could easily buy a company like Sound Control and include their functionality in Mac OS, and then you would have individual volume control over all your applications..