Table 1

New symbols and symbol applications in the extended standard human sequence variant nomenclaturea

d

Downstream. Position number prefix for coding DNA positions following the end (3') of the transcript. Example: c.*405+d256G>T


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.


a See http://www.hgvs.org/mutnomen webcite for a full list of symbols and their use.

Laros et al. BMC Bioinformatics 2011 12(Suppl 4):S5   doi:10.1186/1471-2105-12-S4-S5

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