Donating appreciated stock is not “tax exempt.” It is a tax deduction, which means something different. The stock donation is listed on schedule A as a charitable contribution and the details are reported on form 8283. You only get an actual tax benefit if the total itemized deductions on schedule A is more than your standard deduction.

just one of the many odd tax laws. assuming that you donate a security held long term with a FMV of $5,000 and a tax basis of $3,000, you get a $5,000 deduction on schedule A without getting taxed on the $2,000 gain. it is properly not reflected on line 2a.   for some calculations the amount on line 2a is used to calculate Modified Adjusted Gross income.