Create a new branch with just that change:
# If you haven't set up your remote yet, run this line:
# git remote add upstream https://github.com/konradjk/exac_browser.git
git fetch --all # Get the latest code
git checkout -b my-single-change upstream/master # Create new branch based on upstream/master
git cherry-pick b50b2e7 # Cherry pick the commit you want
git push -u origin my-single-change # Push your changes to the remote branch
Then create the PR from that branch.