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If you are a US citizen or US resident and your spouse does not have a Social Security number or an ITIN and you are not applying for an ITIN with the tax return then you can only file your tax return as Married Filing Separately. Where asked to enter the spouse's Social Security number enter 999-88-9999. You can only print and mail your tax return, it cannot be e-filed. When you print the tax return erase the Social Security number for your spouse and manually enter NRA for non-resident alien.
See this TurboTax support FAQ for the procedure to print and mail a tax return using the online editions - https://ttlc.intuit.com/questions/1944348-how-do-i-print-and-mail-my-return-in-turbotax-online
If you are going to get the SS# for the spouse then do NOT NOT NOT file until you get the number ... put the return on extension if needed and wait to file when the number is issued.
The Protecting Americans from Tax Hikes or PATH Act made several changes to the tax law, including preventing retroactive claims of the EITC and CTC by amending a return or filing an original return for any earlier year in which the individual or anyone listed on the return did not have a SSN valid for employment. You can't claim EITC or CTC unless the Social Security number for you, your spouse (if married filing a joint return) or a qualifying child is issued before the due date of the return including any valid extensions.
http://www.thetaxadviser.com/newsletters/2016/jan/congress-makes-changes-to-popular-tax-credits.html
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