On the use of Disavow tool / Have I done it correctly, or what's wrong with my perception?

[AMTrends]

On a site I used GSA search engine ranker. Now, I got good links out of it. But, also got 4900 links from one domain. And, I thought according to ahrefs. One link from the one domain is equal to 4900 links from one domain. So, I downloaded links those 4900 and added 4899 links to disavow tool. To disavow, to keep my site stable at rankings and safe from any future penalty. Is that a correct way to try disavow tool? The site rankings are as it is.

[Highland]

Wait, you just saw a bunch of links and disavowed them because... you saw a bunch of links? Did you have any penalties or rank drops? Anything that would lead you to believe these links are actively harming your rankings?

Disavow is a cleanup tool, not a preventative tool. I mean, there's a really good reason why they tell you NOT to use this tool lightly. If i could put this on a giant neon sign I would, but here's what Google says on their help page (emphasis mine)

This is an advanced feature and should only be used with caution. If used incorrectly, this feature can potentially harm your site’s performance in Google’s search results. We recommend that you disavow backlinks only if you believe you have a considerable number of spammy, artificial, or low-quality links pointing to your site, and if you are confident that the links are causing issues for you. In most cases, Google can assess which links to trust without additional guidance, so most normal or typical sites will not need to use this tool.

If I were you, I'd yank the disavow out right now

[RyanPurkey]

Highland's analysis is correct. You should only be using the disavow tool carefully and with a measured approach, and usually in dealing with penalties.