By all means, if you have most of the qualifications, go for it! But. . . read the job announcement very carefully! It usually will distinguish between "required" and "preferred" qualifications. Employers HATE when you apply for jobs if you do not meet the "required" qualifications. They think you are being disrespectful of their time, and, they may not hire you for any subsequent position if you do something like this!
Also, pay attention to the salary, if posted. If a job pays very well, the company will likely get enough highly qualified applicants to choose from. But, if it pays less, they are going to have to be willing to be flexible.
While it is true you can learn some skills on the job, sometimes companies need someone who can hit the ground running. Also, if it is a basic skill, you really should already possess it - you would not expect an Administrative Assistant to not know MS Word, for example!
I read somewhere, (I can't remember where, or I'd give credit!) that Men will apply for jobs if they match 60% of the qualifications, but Women look for that 100% match. I have seen it happen!! A lady was the ideal candidate for a position, except for one minor thing. (something like replacing the bottled water). And she tried to talk herself out of it! By all means, don't do that!
Some employers are more concerned that the candidate will be a good fit with the rest of the team, and are willing to train. Sometimes it just depends on why they have the vacancy and how much time they have to do that training. What I recommend is that you try to take a truly objective look at your qualifications, and the position, and, ask yourself if you were the employer, if you would interview you!
If it is a position you truly want, you should write a really good cover letter to go with it, to address any concerns they might have.
hope this helps!