Hello Student

No not  at all, it will affect on your JAM examination. Students before the completion of his third year can  appear for IIT JAM examination. If the candidate succeed in this IIT JAM then his or her admission in MSc will be conditional.  Candidate wish to join MSc through IIT JAM then his or her 3rd year final result will be satisfactory and complete before the admission in MSC course. Before admission in MSC through IIT JAM candidate has to show the final year result  and marksheet to the respective authority for scrutiny of candidate's candidature .

Hope this will help.