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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