Most of organization scans their servers with System Center Endpoint Protection. In an effort to improve our security and reduce our risk of an infection on various servers in organization. SCCM, the tool that manages the Anti-malware environment, is set up to search for servers with SharePoint Server installed
Mostly quick scans will scheduled daily and should complete within approximately 15 minutes. This will help ensure the scan is completed before working hours. The Quick scan only scans resident memory and critical OS files. Also, All incoming files will be scanned automatically to protect systems after the full scan is completed and to compliment the Quick scans.
To minimize performance impacts mostly Microsoft and vendors recommends some file and folder exception. As SharePoint Administrator, IT team might ask you to provide certain folders that may have to be excluded from antivirus scanning when you use file-level antivirus software in SharePoint.
More information can be found at below link for SharePoint Servers. Refer below article and prepare the List of folders for each farm admin account and Search Index folder on Search Servers.
https://support.microsoft.com/en-us/help/952167/certain-folders-may-have-to-be-excluded-from-antivirus-scanning-when-y
