You may want to add offsetTop and scrollTop value in case You are animating not the whole page , but rather some nested content.
e.g :
var itemTop= $('.letter[name="'+id+'"]').offset().top;
var offsetTop = $someWrapper.offset().top;
var scrollTop = $someWrapper.scrollTop();
var y = scrollTop + letterTop - offsetTop
this.manage_list_wrap.animate({
scrollTop: y
}, 1000);