First step is to check if the disk space usage is reported the same from backend.
If you see a difference in disk space usage then login todu *-sch /home/username
If that reports a lot of disk space usage under the field "Others" you may need to find all the files owned by that user. For that execute the command after entering / :cPanel >> Disk Space Usage.
Now open the file and check.cd /
find . -user YOU_USERNAME > owner.txt
Most probably there can be files owned by the user in mailman, antivirus quarantine folder, extracted/incremental backups.
Clamscan quarantine folder