Preheat the oven to 400 degrees and line a 12-count muffin pan with cupcake liners (or spray with non-stick spray).
In a large bowl, whisk together the flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Set aside.
In a medium-sized mixing bowl, whisk together the brown sugar, milk, yogurt, vegetable oil, molasses, egg, and vanilla extract until fully combined. Pour the wet ingredients into the dry ingredients and fold together using a silicone spatula (stop when you see no more white flour).
Fill the cupcake liners 2/3 of the way full (about 1 1/2 tablespoons of batter) evenly and bake for 15-18 minutes. Use a toothpick to check for doneness (the toothpick should come out clean or crumbly, not wet with batter).
Allow the muffins to cool for 5 minutes in the pan and then transfer them over to a wire baking rack.
Vanilla Glaze: As the muffins are cooling in the pan, make the vanilla icing. Mix all of the ingredients together and drizzle over the top of the warm muffins ( I do this once the muffins are on the wire rack). You can either pipe on the glaze (like I did) or use a spoon or whisk. Store any leftover muffins in an airtight container on the counter for up to 3 days or in the refrigerator for 5 days.