1. Your capital gain is the difference between the selling price and the purchase price or cost basis.
Suppose you bought the home for $100,000 and sold for $200,000. You only got $48,000 cash because in the past, you took out an HELOC. Your gain is still $100,000, it's just that you took some of the gain out early through the HELOC.
2. You can include some closing costs in your basis as adjustments, see publication 523.
https://www.irs.gov/pub/irs-pdf/p523.pdf
3. If you owned the home for at least 2 years, and lived in the home for at least 2 years in the past 5 years as your main home, you can exclude (not pay tax on) up to $250,000 of capital gains if you are single or $500,000 if you are married filing jointly.
Using as your main home for 2 of the past 5 years means 730 days out of the 1825 days before the sale, the days do not have to be consecutive.
4. If your gain is less than $250,000 (or $500,000) and you qualify for the exclusion, and you did not get a form 1099-S at the sale, you don't even have to report the sale on your tax return.
If you got a 1099-S, you must report the sale even if you can exclude the gain.
5. If your gain is more than your exclusion or you don't qualify for the exclusion, your gain is a long term capital gain taxed at 15% (sometimes 20%) on your federal return, and at your regular state income tax rates on your state income tax return. You can make estimated payments to the IRS and the state now. If you overpay your estimate, the overpayment will come back to you in your tax refund.
