Yes you can still file as MFS. If filing as Married Filing Separately, you will divide everything equally including the exclusion. Total exclusion for each of you will be $250,000.
Since the total exclusion of gain is $500,000 and if you file as MFS then each of you can take $250,000 of exclusion.
So if you want to file as MFS, you can split everything 50/50 including the 1099-S which you would have received.
To include the 1099-S that you should have received from the sale of your home follow these steps:
Please follow the steps below to include your 1099-S on your tax return:
• Go to Federal Taxes
• Select Wages & Income
• Click I'll choose what I work on
• Scroll down toward the bottom and find the "Less Common Income" section
• Select Start next to Sale of Home
• Go through this section and include your 1099-S information.
