One of a set of sequence features known to exist at a particular genomic location.
An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).
A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations , where such variations don't neccessarily impact a gene. To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.  https://isogg.org/wiki/Allele (retrieved 2018-03-17)  http://semanticscience.org/resource/allele (retrieved 2018-03-17)  https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)  https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)  http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)  http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) [6a] https://www.ncbi.nlm.nih.gov/mesh/68000483  https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)  https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)  http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)  http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)  http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)