hgvs2reference Python API

The hgvs2ref() method retrieves the reference sequence corresponding to an HGVS sequence variant description.

It is intended for applications that require the reference sequence underlying a submitted variant, for example to extract the reference allele or surrounding sequence.

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Importing VariantValidator

from VariantValidator import Validator

Create a validator instance:

vv = Validator()

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Basic usage

Call hgvs2ref() with an HGVS sequence variant description.

result = vv.hgvs2ref("NM_000088.4:c.589G>T")

The method returns a dictionary containing the retrieved reference sequence and associated metadata.

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Return value

The returned dictionary contains the following fields.

Field	Description
variant	The submitted HGVS sequence variant description.
start_position	The HGVS start position.
end_position	The HGVS end position.
sequence	The reference sequence corresponding to the variant coordinates.
warning	Any non-fatal warning generated during processing.
error	Error message if sequence retrieval failed.

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Supported input

hgvs2ref() accepts the HGVS sequence variant types described in the Supported Input Formats guide.

RNA (r.), protein (p.), and mitochondrial (m.) sequence variants are not currently supported.

Fully intronic transcript variants cannot currently be resolved because HGVS transcript descriptions do not explicitly define the genomic reference sequence used for transcript alignment. A future HGVS nomenclature update is expected to address this limitation.

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Example

from VariantValidator import Validator

vv = Validator()

result = vv.hgvs2ref("NC_000017.11:g.50198002C>A")

print(result["sequence"])

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Errors and warnings

If the submitted variant cannot be parsed or the reference sequence cannot be retrieved, an error message is returned in the error field.

Warnings are returned in the warning field where sequence retrieval is only partially possible, such as transcript variants spanning intron boundaries.