Current basic rules in a nutshella
1.
Most
3’ position assigned to be changed. Example: g.5delT (not: g.4delT)
2.
Ranges
of a reference sequence involved in deletions, duplications or inversions are
indicated by their start and end positions separated by an underscore. Example:
g.5_10del
3.
The
location of an insertion is indicated by the consecutive positions of the flanking
nucleotides separated by an underscore. Example: g.5_6insTA
4.
Single
variants in multiple alleles are listed separately between square brackets,
which are separated by a semicolon. Example: g.[5delT];[123A4G]
5.
Multiple
variants in a single allele are listed between square brackets and separated by
a semicolon. Example: g.[1A4T; 7del] (not: g.[7del;1A4T])
6.
Variants
in a single allele are ordered from 5’ to 3’
Extended rules
1.
‘‘Suballeles’’
using nested and composite change formats are preferred to describe changes
within the range of duplications, inversions, insertions, and gene conversions
2.
Nucleotide
numbers or ranges specifying the position of a variant in a suballele refer to
the original reference sequence in its original orientation. They cannot exceed
the range of the duplication, inversion, or gene conversion to which it belongs
3.
Variants
in a suballele are listed between curly braces and separated by a semicolon
4.
When
different levels of nesting are used, variant type hierarchy and order are
evaluated from the deepest suballele level upward
5.
Sequences
inserted in a suballele can be specified by a stretch of nucleotides and/or
their corresponding accession number and version number separated by a
semicolon and ordered from 5’ to 3’ . Examples: g.5_25dup{11_12insAT}, g.5_2500dup{111_112insAB345678.1}
or g.5_2500dup{111_112ins{GC;AB345678.1; AB456789.1;TAC}
6.
Insertions
of sequences between 5’ and 3’ copies of a duplicated sequence (i.e., before
the start of the 30 copy) have no insertion position numbers in the suballele
description. Example: g.5_25dup{insAT}
7.
Multiple
variants in a suballele are ordered from 5’ to 3’
aSee the HGVS
guidelines at http://www.hgvs.org/mutnomen/ for the complete set of abbreviations
and definitions.
Reference:
Taschner,
P.E. & den Dunnen, J.T. Describing structural changes by extending HGVS
sequence variation nomenclature. Hum Mutat 32, 507-11 (2011).
