/shaip/hgvs2reference

Purpose

Return the reference genomic sequence corresponding to an HGVS description.

This endpoint is intended for:

• Extracting reference bases for a HGVS description
• Verifying reference bases prior to variant processing
• Supporting workflows that require explicit reference sequence lookup

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Method

POST

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Path

/shaip/hgvs2reference

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Input

Parameter	Type	Required
hgvs_description	string	Yes

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Parameter Notes

• hgvs_description must be a valid genomic or coding HGVS expression
• Examples include:
• Genomic: NC_000017.11:g.50198002C>A
• Coding: NM_000088.3:c.589del

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Example Request

{
  "hgvs_description": "NM_000088.3:c.589del"
}

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Example Response

{
  "variant": "NM_000088.3:c.589del",
  "start_position": "589",
  "end_position": "589",
  "warning": "",
  "sequence": "G",
  "error": ""
}

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Behaviour

• Interprets the HGVS description
• Resolves the corresponding reference coordinate
• Returns the reference base or sequence
• Does not perform transcript mapping or consequence prediction

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When to Use

Use this endpoint when:

• You need the reference allele for an HGVS description
• Preparing or validating variant inputs for downstream analysis
• Performing sequence-level checks without full validation

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Notes

• Minimal HGVS validation or correction is performed
• Intronic HGVS expressions are not supported
• Only inputs that resolve to explicit reference coordinates are valid
• For full validation and consequence prediction, use /shaip/VariantValidator