/shaip/variantvalidator-ensembl

Purpose

Full HGVS validation using the Ensembl transcript set.

Supports:

• cDNA HGVS
• Genomic HGVS
• Protein HGVS
• Intronic variants
• Allele expressions

This endpoint performs the same validation, correction and mapping operations as /shaip/variantvalidator, but uses Ensembl transcripts instead of RefSeq transcripts.

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Method

POST

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Path

/shaip/variantvalidator-ensembl

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Input

Parameter	Type	Required	Description
variant_description	string or array	Yes	HGVS, VCF or pseudo-VCF variant description(s).
genome_build	string	Yes	Reference genome build (GRCh37 or GRCh38).
select_transcripts	string or array	Yes	Transcript selection mode or transcript accession(s). See transcript_selection.md.
liftover_level	string or bool	No	Controls genomic liftover. True performs full liftover, primary excludes alternative scaffolds, and False disables liftover. Defaults to True.

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Example

[
  {
    "variant_description": "ENST00000269305.4:c.215C>G",
    "genome_build": "GRCh38",
    "select_transcripts": "mane_select",
    "liftover_level": "True"
  }
]

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Behaviour

• Validates HGVS, VCF and pseudo-VCF syntax and structure
• Performs correction of minor, unambiguous errors where possible
• Maps variants to transcript and predicted protein consequences
• Returns genomic, transcript and protein representations
• Performs liftover according to the liftover_level setting
• Reports warnings, corrections and sequence mismatches
• Uses the Ensembl transcript set

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Notes

• Multiple inputs
• "17-50198002-C-A|17-50197802-G-T" pipe-delimited string
• ["17-50198002-C-A", "17-50198002-C-T"]
• Maximum of 10 variants per request
• Transcript selection behaviour is defined in Transcript Selection
• liftover_level controls whether additional genome assembly mappings are returned:
• True (default) — perform full liftover to alternative genome assemblies
• primary — perform liftover but exclude alternative scaffold mappings
• False — disable liftover and return only the requested genome assembly
• Uses the Ensembl transcript set only
• Prefer mane_select, mane, or explicit transcript IDs for improved performance
• Avoid all and raw unless full transcript enumeration is required
• For RefSeq-based validation, use /VariantValidator