After you file

Penalties: IRS says:
Subtract any penalty from the amount you owe reported on original 1040.
Don't try to include, but ignore, any new or changed penalty.
IRS will calculate your new penalty on their own and will bill you.

 

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if you already sent an amount that included some penalty,

include that all on Line 16.

Note: 1040-X doesn't have a line for penalty.

 

 

@TaxHacks