If you return the excess contribution by April 15, 2020, you will not be charged the 6% penalty on the excess contribution. If you indicate in Turbo Tax that you intend to withdraw the contribution, IRS will take you on your word. If you are audited however, you will need proof of that check sent to you by your HSA trustee.
This 6% penalty tax has nothing to do with how your tax rate is calculated your return. The tax rate is based from taxable income that is determined by adjusted gross income minus your standard or itemized deductions reported in your return..
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