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Oh yes! Your FICO score will outshine the sun!!!
Actually, I don't think the amount you deposit on a secured credit card will make any kind of impression on FICO whatsoever. The idea behind having a large credit line is so that down the line when you app for prime cards, that are unsecured, the banks will see that you already have a large limit and they will hopefully be more inclined to grant you a larger limit to start out with.
Score will not depend on the size of the deposit. Future CL may be bigger with bigger deposit. It was with me (1/2 of the time).
A higher credit line will not affect your score directly. It'll make it easier to manage the utilization on the card - if you have $300 CL, having a 1-9% util means leaving $3-27 balance on the statement. If you have $3000, you can leave $30-270. A lot easier to manage the larger numbers, in my opinion. But above and beyond that, it doesn't do anything.
It might help with future credit card applications if the creditor bases your credit limit on your existing limits. But not everyone does so it's not a guaranteed benefit. Of course, with BofA you'll most likely keep your CL when the card graduates, so it might be worth having a higher limit for that.
If you can afford having the money set aside as a security deposit for a year, go for it. I'm not sure about all the way to $4.9k, but $1-3k should be sufficient for most purposes.