Technically, he doesn't need to file a tax return as 6100 +3500 + 1300 = less than the $12,550 filing requirement.
Unfortunately, income on a 1099-Misc may be red flagged by the IRS as unearned income, which means a lower filing threshold and smaller standard deduction (and actual tax). You could just not file and hope to explain it if you hear from the IRS. Filing may head off an IRS inquiry. But, there's still some risk, as the correct way to file does not put the income on the line, where the IRS expects a 1099-Misc to be reported.
The college should not have used a 1099-Misc. They shoulda added the stipend to box 5 of the 1098-T or used a W-2. That said, it's still common practice, and is handled as follows:
In TurboTax, do not enter at the 1099-Misc place. Instead, after entering the 1098-T, in the education interview, you will eventually reach a screen asking if he had any additional scholarships. It's there that you enter the $6100. That puts it on line 1 of form 1040 with the notation SCH to the left.
