Not to be redundant, but rather supportive, from quake 2 server doc:
set (command)
syntax: set [variable] [string]
Sets the value of a valid cvar or a user-created variable.
seta (command)
syntax: set [variable] [string]
Sets the value of a valid cvar or a user-created variable. It will also archive the variable and its current setting in CONFIG.CFG (not user-created ones though).