The coherent electron transport along zigzag and metallic armchair graphene nanoribbons in the presence of one or two vacancies is investigated. Having in mind atomic scale tunability of the conductance fingerprints, the primary focus is on the effect of the distance to the edges and inter vacancies spacing. An involved interplay of vacancies sublattice location and nanoribbon edge termination, together with the spacing parameters lead to a wide conductance resonance line shape modification. Turning on a magnetic field introduces a new length scale that unveils counter-intuitive aspects of the interplay between purely geometric aspects of the system and the underlying atomic scale nature of graphene. Comment: 9 pages, 8 figures, figure and references added