A method for identifying in a patient sample, with a variant annotation module on at least one data processor, variants from at least one medical variant reference database, a variant v being defined by a start coordinate s(v), an end coordinate e(v) and a string alt(v) of a genomic variation relative to a human genome reference string R, characterized in that the method comprises the steps of: - acquiring variant calling information of next generation sequencing data of a patient biological sample, the variant calling information comprising a set V* of genomic variants in at least one genomic region to be analyzed; - identifying, in the at least one medical variant reference database, a subset D = { d 1, d 2,..., d | D |} of variant entries defined on the reference string R; - selecting, for each variant database entry d ∈ D, a subset V = { v 1, v 2,..., v | V |}, V ⊆ V*, of patient variants defined on the reference string R and on the same coordinate system as the variant database entry d; - selecting an extended genomic region coordinate range a.. b, the start and end coordinate boundaries a and b being defined such that they at least include the start and end coordinates from all the patient variants in the subset V, as well as the start and end coordinates of the variant database entry d; - reconstructing over the extended genomic region coordinate range a.. b the database variant haplotype string h a..b (d) for the reference variant entry d as the concatenation of three genomic information strings RP left + alt ( d) + RP right, wherein alt ( d)is the alternative string characterizing the variant d, RP left is a string corresponding to extended genomic region on the left of the variant alt ( d) in the reference human genome R and RP right is a string corresponding to extended genomic region on the right of the variant alt ( d) in the reference human genome R; - reconstructing over the extended genomic region coordinate range a.. b the patient variant haplotype string h a..b, X being a subset of the selected region variant calling information V comprising at least one selected patient variant v j; - identifying that the variant calling information of the patient sample includes the medical variant database entry d if the length of the reconstructed database variant haplotype string h a..b ( d) equals the length of the reconstructed patient variant haplotype string h a..b, the reconstructed patient variant haplotype string h a..b differs from the reconstructed database variant haplotype string h a..b ( d) by at least one mismatch in either the RP left string or the RP right string of the reconstructed database variant haplotype string h a..b ( d), and every variant in the subset X of patient sample variants overlap by at least one symbol the location defined by the start and the end coordinates of the database variant entry d. - acquiring variant calling information of next generation sequencing data of a patient biological sample, the variant calling information comprising a set V* of genomic variants in at least one genomic region to be analyzed; - identifying, in the at least one medical variant reference database, a subset D = { d 1, d 2,..., d | D |} of variant entries defined on the reference string R; - selecting, for each variant database entry d ∈ D, a subset V = { v 1, v 2,..., v | V |}, V ⊆ V*, of patient variants defined on the reference string R and on the same coordinate system as the variant database entry d; - selecting an extended genomic region coordinate range a.. b, the start and end coordinate boundaries a and b being defined such that they at least include the start and end coordinates from all the patient variants in the subset V, as well as the start and end coordinates of the variant database entry d; - reconstructing over the extended genomic region coordinate range a.. b the database variant haplotype string h a..b (d) for the reference variant entry d as the concatenation of three genomic information strings RP left + alt ( d) + RP right, wherein alt ( d)is the alternative string characterizing the variant d, RP left is a string corresponding to extended genomic region on the left of the variant alt ( d) in the reference human genome R and RP right is a string corresponding to extended genomic region on the right of the variant alt ( d) in the reference human genome R; - reconstructing over the extended genomic region coordinate range a.. b the patient variant haplotype string h a..b, X being a subset of the selected region variant calling information V comprising at least one selected patient variant v j; - identifying that the variant calling information of the patient sample includes the medical variant database entry d if the length of the reconstructed database variant haplotype string h a..b ( d) equals the length of the reconstructed patient variant haplotype string h a..b, the reconstructed patient variant haplotype string h a..b differs from the reconstructed database variant haplotype string h a..b ( d) by at least one mismatch in either the RP left string or the RP right string of the reconstructed database variant haplotype string h a..b ( d), and every variant in the subset X of patient sample variants overlap by at least one symbol the location defined by the start and the end coordinates of the database variant entry d.