Hopefully you’ll qualify to exclude the gain, anyway (as discussed in this home sale article). But even if you don’t, your transaction should be accurately represented on your return after you go through the TurboTax screens. After you indicate you sold a home (in “Less Common Income” under “Federal Taxes”) and give the address, you’ll see a screen where you enter the selling date and price from the 1099, then a total of all the sales expenses from the settlement statement (there’s a link too, with a long list of examples).
Next you’ll see a screen regarding your purchase, and the “cost basis” amounts should include the original purchase price plus any significant improvements you’ve made (there’s a link elaborating on that also). The program does the math from there, and reports the net gain on form 8949 and Schedule D. (And although you can click a box to leave it off the return if you’re excluding it, you should still report it if there’s a 1099-S.)
I’m not completely clear on the part about your receiving half — if you’re saying you were a joint owner (and the other owner isn’t on your tax return), you’d report only your half of the gross proceeds, your half of the sales expenses, and your half of the basis including improvements (unless you paid more than half of those and are confident about proving it). So the final number for you would be half of the total net gain.
I hope I correctly understood your question, yossiradu56-gmai! If so, the government is aware that the 1099 amount is likely not the actual gain, so you should be fine.
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