Did you know that you can see canonical SPDI notation – SPDI notation expressed on the GRCh38 chromosomal sequence – in ClinVar?
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 firstname.lastname@example.org with any feedback or questions about this new feature.