Table 1 New symbols and symbol applications in the extended standard human sequence variant nomenclature^a

n

Position number prefix for non-coding DNA positions. Numbering starts at the first nucleotide of the non-coding transcript. Example: n.46G>T

p

Suffix to specify protein isoforms in descriptions using LRG sequences (Locus Reference Genomic) [18]. Example: LRG_1p1

t

Suffix to specify transcript variants in descriptions using LRG sequences. Example: LRG_1t1

u

Upstream. Position number prefix for coding DNA positions upstream (5') of the start of the transcript. Example: c.-110-u256G>T

_i

Gene symbol suffix to specify protein isoforms in protein variant descriptions using genomic reference sequences. Example: DMD_i2

_v

Gene symbol suffix to specify transcript variants in coding DNA variant descriptions using genomic reference sequences. Example: DMD_v2

^

Exclusive or: to combine DNA descriptions, which are derived from protein level descriptions. Example: backtranslation of p.Ser124Arg, where the Ser-124 codon at c.370_372 is AGC. The variant should be described as c.[370A>C^372C>R] to reflect that arginine can be encoded by six possible codons, AGR (AGC and AGT) and CGN (CGA, CGC, CGG and CGT), respectively.

/

Allele separator in mosaic cases. Used in ISCN [5]. Example: c.[=/85C>T]

//

Allele separator in chimaeric cases. Used in ISCN [5]. Example: c.[=//85C>T]

{ }

Curly braces enclose "sub-alleles", changes within the range of duplications, inversions, gene conversions and insertions. Example: c.24_65inv{46G>T} (See [4, 5] for details)

;

Replaces + in SingleAlleleVarSet, MultiAlleleVars and MultiTranscriptVar

(;)

Replaces (+) indicating uncertain phase in UnkAlleleVars. In general, parentheses are used to indicate uncertainty.