You're going in for a job interview. You tell the employee near the entrance that you have an appointment with the manager. He tells you to wait.
This is a polite formal phrase often used with customers, guests, or patients to ask them to wait. Several different words can be used to mean "soon" in this phrase:
He'll be with you shortly.
I'll be with you soon.
He'll be with you in just a second.
She'll be with you in just a minute.
"Shortly" is a slightly formal way to say "soon" or "in just a few minutes". Use it in sentences like this:
We will begin shortly.
She'll be with you shortly.
We will be departing shortly.