I believe the answer is no.

Not in this software.  Would have to be mailed.

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@jeanmarc wrote:

I ask because the IRS instructions specifically say "select the Superseded Return checkbox in the software or the return will reject as a duplicate filing".

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I assume this is a corporate or partnership return?

Individual

I'd just efile an amended return when that becomes available.  As long as it's filed before the due date it counts as a superseded return.

As was noted above, a 1040X filed by the due date *IS* a Superseded return. 

For a 1040, there is no such thing as being able to e-file a specific "superseded" return other than using a 1040X.  The citation you referenced is NOT for 1040s.