Thank you for your answer but my question is: if for example i have 20 backlinks and in Webmaster tools there are only 5 links, does this means 5 links will be taken in consideration when it comes to my website rankings.To me backlink checkers in general all have a gray area. I have a site that had an infographic page shared on pintrest about 15k times and google used to show me those as links in webmaster tools. I have built some links to my sites before and experience a rank increase but they never show in webmaster tools either. Best thing to do is make sure the link url is still alive and search the url in google exactly as it shows in the search bar. If the url comes up then the link is indexed in my openion. So yes, links may sometimes NOT show up in wmt even though they are alive.
Regardless, I swear they program it to intentionally mess with you.
I noticed Google webmaster tools removed several backlinks for one of my sites recently.