Initially entered the US as a nonresident alien for tax purposes and now a resident alien (since the substancial presence test was passed) on an F-1 visa (visa status remained unchanged). Form W-9 has been submitted to IRS by employer and for the first $9,000 for 2018, tax was not withheld. In publication 519, it says that if the income is exempt from U.S. tax, it does not need to be reported on form 1040. Is that the case?
As the income is included in your W-2, you will need to subtract the $9,000 in another area of your tax return.