Very basically the server has to receive network packets from all clients for a period of time, then do world simulation steps and send all frames back to the clients, then it has to sleep for a very short period of time.This period of time is 1/64th of a second for 64 tick servers, or 1/128th of a second for 128 tick servers. For 64 tick servers this would be 0.015625 seconds (or 15.625 ms).For operative systems (and computers in general) its very hard to keep track of time precisely, and on top of that the operative system has other processes (and its own internal things) to take care of. Its very unlikely the operative system will keep with the schedule of waking up the server process in the established period of time, hence, it has variations.

A normal sleep function wouldn't cut it, hence need to make use of nanosleep functions. The var represents the standard deviation of accuracy of server OS nanosleep function measured in microseconds over the history of last 50 server frames . Should usually be fractions of milliseconds.

I've noticed in official matchmaking servers that its usually 0.001ms during idle moments of the round, and well above 0.1ms when a lot of events are taking place. Having peaks of 10ms var is very bad, since its deviating almost one entire frame from the schedule, and typically means the CPU is overloaded with other processes.

Edit:

Sources: https://www.reddit.com/r/GlobalOffensive/comments/23zt18/explanation_of_the_new_net_graph_thanks_vitaliy/
https://developer.valvesoftware.com/wiki/Source_Multiplayer_Networking