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Background  Polymorphic  Alu  elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest  AluY  subfamilies, and most structural variant discovery efforts have focused on identifying  Alu  polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older  AluS  subfamily, whose peak activity was tens of millions of years ago. We annotate the  AluS  polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome.    Results  Of 52 previously reported polymorphic  AluS  elements ascertained for this study, 48 were confirmed to belong to the  AluS  subfamily using high stringency subfamily classification criteria. Of these, the majority (77%, 37/48) appear to be deletion polymorphisms. Two polymorphic  AluS  elements (4%) have features of non-classical  Alu  insertions and one polymorphic  AluS  element (2%) likely inserted by a mechanism involving internal priming. Seven  AluS  polymorphisms (15%) appear to have arisen by the classical target-primed reverse transcription (TPRT) retrotransposition mechanism. These seven TPRT products are 3′ intact with 3′ poly-A tails, and are flanked by target site duplications; L1 ORF2p endonuclease cleavage sites were also observed, providing additional evidence that these are L1 ORF2p endonuclease-mediated TPRT insertions. Further sequence analysis showed strong conservation of both the RNA polymerase III promoter and SRP9/14 binding sites, important for mediating transcription and interaction with retrotransposition machinery, respectively. This conservation of functional features implies that some of these are fairly recent insertions since they have not diverged significantly from their respective retrotranspositionally competent source elements.    Conclusions  Of the polymorphic  AluS  elements evaluated in this report, 15% (7/48) have features consistent with TPRT-mediated insertion, thus suggesting that some  AluS  elements have been more active recently than previously thought, or that fixation of  AluS  insertion alleles remains incomplete. These data expand the potential significance of polymorphic  AluS  elements in contributing to structural variation in the human genome. Future discovery efforts focusing on polymorphic  AluS  elements are likely to identify more such polymorphisms, and approaches tailored to identify deletion alleles may be warranted.    Electronic supplementary material  The online version of this article (doi:10.1186/s13100-017-0089-9) contains supplementary material, which is available to authorized users.

Insertion and deletion polymorphisms of the ancient AluS family in the human genome