Very slow queries selecting @@ session variables.
Sometimes things like this happen because of other things going on at the same time.  Can you spot such in the slowlog?
The probably will probably be solved in version 8.0, when a number of things get turned into real InnoDB tables.
Some 3rd party products issue an awful number of seemingly spurious and redundant information queries.  Let's see the output from SHOW GLOBAL STATUS LIKE 'Com%';
Set long_query_time = 0.1 and see if you catch a lot more of these queries, plus other things.