---
title: "Variant Annotator"
method: POST
path: "/variant_annotate"
tags: ["Alignment & variants"]
---

# Variant Annotator

`POST /variant_annotate`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/variant_annotate`
- Auth: none required

One-box variant lookup against MyVariant.info: accepts an rsID, chrom:pos:ref:alt (colon- or hyphen-separated), genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" / "TP53:c.215C>G", bridged via the hgvs_convert tool). Returns a ClinVar significance summary, gnomAD exome/genome allele frequencies, and CADD/SIFT/PolyPhen2/REVEL pathogenicity predictor scores — each section explicitly null when that source has no data, never silently omitted. See the result's own "caveats" for real data-freshness limits (frozen gnomAD/CADD snapshots, periodic ClinVar snapshot).

Batchable via `POST /batch`.

## Request body

- object
  - `variant` string, required: An rsID ("rs1042522"), chrom:pos:ref:alt with either separator ("17:7676154:G:C" or "17-7676154-G-C", single-base substitutions only), genomic HGVS ("chr17:g.7676154G>C" or "17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" or "TP53:c.215C>G").
  - `assembly` 'hg19' | 'hg38': Genome build for rsID/chrom-pos-ref-alt/genomic-HGVS lookups (MyVariant.info's native default is hg19). Ignored for transcript "c." input, which is always bridged via GRCh38/hg38 (hgvs_convert's own coordinate space).

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)