A lack of self-confidence quite often indicates a deep-seated fear that was the result of a single experience in your early life.
As adults we have different ways of responding to situations and we can choose the most appropriate response. For example, when someone threatens you today, you could feel fear or get angry or just shrug it off or even laugh it off, depending on your judgment of the situation and your life experience.
However, if the same situation happens to a small child, the child may react with fear, and then continue to react with fear to any similar situation even as an adult, because of the very strong impact of that one experience.
How do you get to the bottom of your lack of confidence? You could try hypnosis or therapy, or you could keep a journal in a very specific way.
The good news is that you can get to the bottom of this and then accept and use the talents that you have without feeling inferior to anyone.
It is also possible that you are in the right job but in the wrong company. If lacking self-confidence is the only thing your seniors criticize you about, then they must be satisfied with the quality of your work.
Now that you have both the qualifications and some work experience, maybe you should put out your CV. What if you get a job where you can use your skills and where people appreciate you for who you are, rather than try and change you? You will not know unless you make the move.