Preheat the oven to 350℉. Sift the flours, baking powder, baking soda, and salt into a bowl. Prepare the cupcake trays by lining with cupcake papers or parchment squares.
To a mixing bowl or the bowl of a stand mixer add the butter. Cream the butter .Add the sugar and beat until creamy. Add the egg and vanilla and mix in until smooth.
Add the milk, yogurt, and vinegar to the bowl and mix. Next add the dry ingredients on low speed. Mix for a minute until combined.
For the mocha batter: Heat the chocolate chips and the cream together in a bowl in the microwave for 20 seconds. Stir to combine. Add the coffee extract (or omit for the vanilla and chocolate swirl cupcakes). Add a pinch or two of cinnamon, if desired. Add 1 cup of the vanilla batter into the chocolate bowl and stir to combine.
Spoon into the papers, half vanilla on one side of the cupcake paper hole, and mocha (or chocolate batter) on the other side. Use a knife to drag through the batter to swirl.
Bake for 14-16 minutes or until the cupcake springs back when gently pressed. Or insert a toothpick to the center of a cupcake. It should come out clean when done. Remove the tray from the oven. Let sit for 10 minutes on a wire rack in the tray before removing the cupcakes to the wire rack to finish cooling. When completely cool, frost the cupcakes.