The most convenient option is to ask your Company to revise its TDS returns so that the amount is reflected in your 26AS and you can very well claim it in your return.
if that doesnt happen then, you can file your Income Tax Return based on the Form 16, but then the Department will send you a Demand Notice and then you will have to produce the Form 16 to them in order to waive the demand.
Trust this clarifies your query.
Feel free to get back/ call back for any further clarifications.
Rohit R Sharma
BCOM, ACA, LLB - GEN, CERT. FAFP