Don't believe those online calculators, unless you want a spec home which you clearly don't.

Permits depend on your county. We paid ~$1500.

Utilities depends on your utility company and if there is a feed closeby. We spend ~$2500 although we already have services available at the lot.

The 10-20% GC fee does not include subcontractors or any other labor (like, if you're GC do some digging himself, he would charge a labor for that).

Of course, there's also another option where you get a contract price, where everything is included. The GC just gives you the total cost to build, and that's it. But if you do a change after the contract is signed, that may cost you dearly. Change orders are expensive.

Hey, I'm not sure which one you used. But there's one I found that is actually pretty accurate. You choose the size, levels of quality for different things, where you're building, and the price includes everything including the contractor markup. So here's the link, if you want to try it: http://building-cost.net/CornersType.asp
Good luck!

I've used building-cost before and just retried it. Came out pretty close for me again.

I built twice recently and 1 house was $12k in permits and one was $7k in permits. Permitting is one area where city's can assess an impact fee even if they call it something different. The $7k was $1000 for the permit and then there was $4500 for water impact fee based on number of bedrooms(4). Then there were assorted other fees.

Utilities are another variable that don't get included in those calculators. Septic just cost me 7% of total build cost - this is not normal but nothing about utilities is - often people pay $10k to get "hooked up" and others pay nothing.

might as well give everyone the link

Here is a link that might be useful: Building - Cost calculator

It sounds like you are in the 'education' stage of building. I recently bought the book, "What Your Contractor Can't Tell You" by Amy Johnston. I've only read about 2 or 3 chapters but I have learned so much and I consider myself pretty knowledgeable about building. She breaks down the process of building into easily understood parts and not only explains the details but gives you things to think about.

I thought about this forum as I read the chapter on architects. She explained the process, the contract types, even the personality/work styles of architects and I can see many people on this forum could benefit from her expertise.

A home is likely the biggest purchase of your life so $22 for this book will be the best money you're ever likely to spend.