The reason people generally say "it varies" is because it depends on how much you are wanting to have customized, whether or not you want it done by a professional (who will generally charge a lot more) or an amateur (who will usually charge a lot less but may or may not have mastered the quality you want), and whether or not you want full exclusive rights and won't be used by anybody else but you (usually charged at a larger rate).
I guess first you'd need to tell us what you mean by custom. Simply replacing the entire RTP with resources found in the store and free-to-use scripts can still make it custom, but not necessarily unique, since somebody else can use the same resources. There's plenty of audio and graphic packs in the store for very low cost, and replacing the whole RTP with these might only set you back by about $100. As for scripts, Yanfly and Yumi both offer very good scripts that are free for commercial use.
If you want fully custom, unique for your game only, it depends on how much of it you want customized. As Seraph stated, a couple of sprites might set you back $50. Doing a full sheet might cost $200, and doing several of those sheets might cost $1000, and that still doesn't include scripts, tilesets/objects, or audio.
A full custom-made tileset alone (just 5 sheets A-E) might cost you $500 to $1000. Assuming you want more than just 5 sheets, that can easily go up.
I don't know the rate of audio tracks, but I'd speculate it depends on the composer, and can easily go for about $25 a track for the best composer. It depends on the composer, the length of the track, and the style.
Again, it also depends on whether the artist/composer/writer can re-sell their material, how many of each resource you need, and the quality of those resources.
Based on what I heard previously, to fully customize your game from scratch (meaning everything is made specifically for you - no RTP, no store purchases, nothing currently floating around on the net for grabs), I'm going to say a minimum of $5000, and that's probably shooting on the low end.
Edit: I was typing this as Shaz replied. His response is quick and to the point.