Variants

When One Letter Changes Everything

A single nucleotide variant (SNV, also called SNP) is a position in the genome where individuals differ by a single DNA letter. The human genome contains roughly 4–5 million such differences between any two people.

Most variants are neutral — they occur in non-functional regions. But some variants, particularly those in regulatory elements or splice sites, can disrupt gene regulation and cause disease.

def apply_variant(seq, position, alt):
    """Replace the base at position with alt."""
    return seq[:position] + alt + seq[position+1:]

def find_differences(ref, alt_seq):
    """Return positions where ref and alt_seq differ."""
    return [i for i in range(min(len(ref), len(alt_seq)))
            if ref[i] != alt_seq[i]]

ref = "ATCGATCG"
mutant = apply_variant(ref, 3, "T")  # G→T at position 3
print(mutant)                          # ATCTATCG
print(find_differences(ref, mutant))   # [3]

This is precisely what AlphaGenome does at scale: given a reference sequence and a variant (position + alternative base), it runs two predictions — one for the reference, one for the mutant — and reports the delta. That delta is the variant's predicted effect on gene regulation.

Your Task

Implement apply_variant(seq, position, alt) and find_differences(ref, alt_seq).