A target with total cover is completely concealed by the cover. There is no visibility in or out.
"A target with total cover can't be targeted directly by an attack or a spell, although some spells can reach such a target by including it in an area of effect. A target has total cover if it is completely concealed by an obstacle."
"A spell's effect expands in straight lines from the point of origin. If no unblocked straight line extends from the point of origin to a location within the area of effect, that location isn't included in the spell's area. To block one of these imaginary lines, an obstruction must provide total cover, as explained in chapter 9."
If the caster of silence is behind total cover, the imaginary line to where the silence is to be cost is blocked.