Though we do not have any reference of DBAgent overhead , but it could be very minimal in terms of either cpu or memory.
Weight %, The percentage of the total time consumed by the query for the selected time duration.
The reason for currentOp() command showing top because it will be executed by the agent at every minute to get the current statistics for the running queries. It could be the case that there is not much activity on the mongo caused in showing it as top query.
So, as far as I know there should not be much impact on the database for execution of this query by the agent.
You can further drill down down to the queries windows sections to see the complete details about the query execution.
Please do let us know if there are any further clarifications required.
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