THREE.JS - Change Loaded Mesh's Vertex Coordinate Absolutely (Distort Mesh) and Use That Vertex

Question

I want to change my loaded mesh's vertices in absolute way. For example, this is a vertex from original mesh (loaded mesh): original vertex

That vertex has to be like this: changed vertex

As you can see y coordinate changed (specifically y), but there is a problem. I cannot see that on viewport and use for positioning. In other word, I want to distort my mesh by changing vertex coordinate values, after distortion process I want to make manipulation on it.

To do that I used this: codes , so I made y coordinate subtracted with 5.5;

console.log(vector) shows expected vertex, but there is no change on viewport(screen) and if I try to use that vertex, it reverts back to its original value.

Note: I also used .updateMatrixWorld(); and .needsUpdate = true; but no luck.

Help me, please. Thank you.