Table 1 Sequence variants according to the Human Genome Variation Society(HGVS) (http://www.hgvs.org/mutnomen/standards.html)
From: Harmonizing the interpretation of genetic variants across the world: the Malaysian experience
| Variants | Description |
|---|---|
| DNA/RNA |
Conversion = a sequence change where a range of nucleotides are replaced by a sequence from Elsewhere in the genome Deletion = a sequence change where one or more nucleotides are removed (deleted) Deletion/insertion (indel) = a sequence change where one or more nucleotides are replaced by one or More other nucleotides Note: when one nucleotide is replaced by one other nucleotide the change is called a substitution Duplication = a sequence change where a copy of one or more nucleotides are inserted directly 3’- flanking of the original copy Note: when the copied sequence is not inserted directly 3’-flanking of the original copy the change is called an insertion Insertion = a sequence change where one or more nucleotides are inserted between two nucleotides but where the insertion is not a copy of a sequence immediately 5’-flanking (see duplication) Inversion = a sequence change where more than one nucleotide replacing the original sequence are the reverse complement of the original sequence Substitution = a sequence change where one nucleotide is replaced by one other nucleotide Note: a sequence change where one nucleotide is replaced by more than one other nucleotide is a deletion-insertion (indel) Note: a sequence change where more than one nucleotide is replaced by one or more other nucleotide is a deletion-insertion (indel) |
| Characters used: |
(1) Reference sequences c. = coding DNA reference sequence (2) Numbering I. Genomic, mitochondrial, non-coding RNA, RNA and protein reference sequence N = nucleotide N in reference sequence (e.g. 311A > G) II. coding DNA reference sequence N = nucleotide N in protein coding sequence (e.g. 11A > G) N + M = nucleotide M in the intron after (3′ of) position N in the coding DNA reference sequence (e.g. 30 + 4A > G) 3) Specific characters + (plus) − (minus) > (greater than) = changes to (substitution) c.5T > G substitution 4) Others chr = chromosome (e.g. chr19 or chrX) del = deletion dup = duplication ext = extension (e.g. N- or C-terminus of protein) ins = insertion inv = inversion con = (gene) conversion fs = frame shift t = translocation |