Canonical SPDI notation now in ClinVar

Did you know that you can see canonical SPDI notation – SPDI notation expressed on the GRCh38 chromosomal sequence – in ClinVar?

Figure 1. The canonical SPDI is provided within the “Variant details” tab. This is just one of many ways to see the notation.

This allows you to easily make connections between output from NCBI’s Variation Services and ClinVar data.

The canonical SPDI is available from ClinVar in several ways:

  • In the VCV XML, ClinVarVariationRelease, as: VariationArchive/InterpretedRecord/SimpleAllele/CanonicalSPDI/
  • In the RCV XML, ClinVarFullRelease, as: ClinVarSet/MeasureSet/CanonicalSPDI/
  • In the download for search results
  • On Variation pages (Figure 1)
  • By search, e.g. NC_000010.11:87925523:C:G[Canonical SPDI]

Check out some other examples of SPDI notation for different types of variants: 

NCBI’s SPDI notation describes variants as a sequence of four attributes: sequence, position, deletion and insertion (Holmes et al., 2019). It is a valuable format for bioinformatics as it provides an unambiguous representation of a variant and removes the over-precision that is often used for variants in repetitive regions.

Please contact the ClinVar Team at with any feedback or questions about this new feature.

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