Leg pain when sitting at desk too long- blood clot?

Not likely: My first suspicion would be a herniated disc in your back pinching a nerve. Especially if it happens every day and goes away when you stretch or walk. Get this checked out soon, delaying treatment can result in permanent nerve damage!

Possible but unlikel: Typically, leg pain when sitting for extended periods of time is due to venous pooling in the limbs, which causes an increase in venous pressure, leading to a wide variety of symptoms, such as aching, heaviness, cramping, fatigue ..Etc it is possible to develop superficial blood clots, known as phlebitis, or less likely the more serious dvt, or deep vein thrombosis. See a dr for us to be sure.