**Core Concept**
The commonest congenital anomaly seen in pregnancies with diabetes mellitus is related to the teratogenic effects of hyperglycemia on fetal development. This is primarily due to the increased glucose levels in the maternal bloodstream, which can lead to excessive glucose crossing the placenta and affecting fetal organogenesis.

**Why the Correct Answer is Right**
The correct answer is neural tube defects (NTDs). Hyperglycemia in diabetic pregnancies leads to an increase in the levels of glucose in the fetal bloodstream. High glucose levels can disrupt normal neural tube closure, leading to NTDs such as anencephaly and spina bifida. This is because glucose can inhibit the activity of enzymes required for neural tube closure, such as folate-dependent enzymes.

**Why Each Wrong Option is Incorrect**
* **Option A:** Sacral agenesis is a rare congenital anomaly that can occur in diabetic pregnancies, but it is not the commonest anomaly.
* **Option B:** Omphalocele is a type of gastroschisis, but it is not the most common congenital anomaly seen in diabetic pregnancies.
* **Option C:** Congenital heart defects can occur in diabetic pregnancies, but they are not the most common anomaly.

**Clinical Pearl / High-Yield Fact**
It is essential to note that women with pre-existing diabetes mellitus have a higher risk of congenital anomalies, and early folic acid supplementation is recommended to reduce this risk.

**Correct Answer: C. Neural tube defects (NTDs).**