Excerpt as meta description problem

My theme needs a specific php shortcode to be placed before my content in the post editor, in order to show a certain template.

I want to do a better onsite SEO by making each post has its own meta description pulled straight from the excerpt of the post.

The problem is that in this way, it will always pull the first lines of the excerpt, as a result my meta description will be shown like this:

“[shortcode] This is a description of the post bla bla…”

Is there any way to exclude certain phrases like this shortcode for my meta description? Or is there any way to pull the excerpt starting from the 5th word (for example)?

Thank you in advance..