hgvs_convert
ActiveTool of com.seqbench/workbench
declared in 1.1.0
Parse an HGVS "c." variant description (by gene symbol, RefSeq NM_, or Ensembl ENST accession), convert it to genomic (g.) coordinates via a real, live-fetched Ensembl exon/CDS map (transcripts resolved through the bundled MANE RefSeq<->Ensembl crosswalk), apply 3'-rule normalization to any del/dup/ins, and predict the protein (p.) effect where that is safely computable. Refuses cleanly — rather than guessing — for circular/mitochondrial genomes, RNA-level or protein-level input, uncertain/mosaic syntax, splice-junction-adjacent or inversion protein effects, and non-MANE/non-Ensembl transcripts.
Parameters schema
{
"type": "object",
"required": [
"variant"
],
"properties": {
"variant": {
"type": "string",
"description": "A full HGVS \"c.\" variant description: \"<accession or gene symbol>:c.<edit>\", e.g. \"NM_000546.6:c.215C>G\" or \"TP53:c.215C>G\". Substitution (\">\"), deletion (\"del\"), duplication (\"dup\"), insertion (\"ins\"), delins, and inversion (\"inv\") are supported."
}
},
"additionalProperties": false
}Parent server
com.seqbench/workbench
1/7 registries