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That's all good and well, but why doesn't Turbo Tax permit you to indicate royalty income should be treated as a capital gain and avoid all of the nonsense. That would provide direct linkage between the income and how it is to be treated and not the offsetting kluges offered up.
How SHOULD the EMPLOYER report this? Should it go on 1099-Misc as Other Income?
Yes, reporting patent income on a 1099-Misc as Other Income is appropriate.
Unfortunately, you still have to go through the exercise of reporting the income, backing it out with a negative entry, and reporting it in the Investments section in TurboTax to take advantage of a lower Capital Gain tax rate (if that applies to you).
What does one do for the Net Investment Income Tax? If the inventor assigned the patent to the employer/university but still receives a portion of the royalty due to the Bayh-Dole Act, , does it escape NIIT under the trade or business exception?
No. In general, net investment income includes, but is not limited to: interest, dividends, capital gains, rental and royalty income, and non-qualified annuities.
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