Many people don't like to use all of one stat for there runes but for all ability power runes it might lead you (playing as Annie) to first blood or an early kill against other teams which can lead you to a major advantage with extra gold and to gain more experience point this is why I use these runes.

These masteries are the average 9/0/21 for Annie that everyone knows. The 9 points in offense leading up to the magic penetration. The other 21 points are in utility because it can decrease Annie's cooldown for her flash which can prevent a death or can give you a kill same with ignite. Also it can improve mana regeneration along with health regeneration.

I found out that the boots of speed and 2 health and 1 mana potion are the best for me. If you don't like Mejia's Soulstealer or you are new to Annie than you can replace that with any item you like but in any Annie game the Soulstealer can make or break the quality of how you play. A lot of ranged casters buy the rod of ages which is always good in the beginning and its a decent items cause it gives mana health and ability power which gets stronger each minute. Rabadon's Deathcap is obvious just for the major ability power boost Archangel Staff helps with mana and the 3% of mana converted to ability power can go along way. NOTE you may buy void staff anytime in the order if the other team is stacking up on magic resistance.

Many people may disagree with my choices with not getting molten shield for Annie's passive stuns but if you are smart enough you can time it with out wasting a point for the shield. But if you must you can substitute a spell with the shield.

The obvious choices for Annie would be ignite for sure but for your second ability I choose Flash because it can help you get a spell or avoid a death but like the spell sequence you can substitute and of the summoner spells with another that you like.