No. It does not affect your rep at all.  But, you can get badges for upvoted comments: 

>**[Commentator][1]**: Left 10 comments. 


and 

>**[Pundit][2]** Left 10 comments with score of 5 or more.  


  [1]: https://superuser.com/badges/31/commentator
  [2]: https://superuser.com/badges/40/pundit