Short Answer: As long as you're honest, there usually aren't any negative consequences, though you'll likely not get the job.
Coming from someone who's applied to many, many jobs he's not qualified for, the most likely response you'll get is no response, or the "thanks but no thanks" email 3 months later.
Hiring managers have a general sense of what kind of skills and experience they're looking for on a candidate's resume, and will only get back to you if you seem to match what they're looking for. The interview comes next, which can further weed out candidates who wouldn't be a good fit for the team.
My point is that if they don't think that you would be a good fit for the role, either technically or professionally, they will likely not extend you an offer. If they do extend you an offer, they think that you do, in fact, know enough technical knowledge to satisfactorily perform within the job.
This is, of course, assuming that you're being honest with the hiring manager and the company you're applying to. All in all, the only negative consequence that can result from applying for a job you aren't qualified for is if you are being dishonest about your skills or experience, both of which will be verified anyway. After all, reputation means quite a lot when searching for jobs, and the last thing you want to be known for is being dishonest.