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Good afternoon. You will report any gain on the sale of your stock on your Form 1040. Then, the gift should not generate any tax. Each donor can give $13,000 per year per person under the annual gift exclusion. In addition to that, each person has a $5,000,000 lifetime exemption....which means a person can give a cumulative amount of up to $5,000,000 in gifts without incurring gift tax....the donor must file a gift tax return (Form 709) to let the IRS know how much of the lifetime exemption is being used, but there will be no gift tax until cumulative gifts have exceeded the $5,000,000.
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The 1099R only reports the amount of the total proceeds. Your gain is the proceeds less your cost basis in those stocks. You have to figure that amount and the difference is your gain or loss. Then, you will need to file the Form 709 in the amount of the total gift to your son in excess of $13,000...the first $13,000 will qualify under the annual gift exclusion.
The Form 709 has nothing to do with the 1099R..the 1099R only relates to your personal income tax. The Form 709 only relates to the amount you give your son.
On Form 8949 and Schedule D, you show the total proceeds (as evidenced by the 1099R) and your basis, and the net is subject to capital gains tax.