Myvariant Queries

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

Audit 0.4.1 · source sha c8c1fc3a2b13 · 19 Oct 2026Report an issue or request a re-scan

• PublisherGPTomics GitHub organizationOwner of the repository this skill is read from
• Source folderGPTomics/bioSkills/clinical-databases/myvariant-queriesThe exact folder we audited
• LicenceMITAs the repository states it
• Commit pinned for this verdictc8c1fc3a2b13A new audit runs when the source changes
• Repository statusArchivedLast push 65 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases…

---
name: bio-clinical-databases-myvariant-queries
description: Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.
tool_type: python
primary_tool: myvariant
---

## Version Compatibility

Reference examples tested with: myvariant 1.0.0+, requests 2.31+, pandas 2.2+. myvariant.info aggregates >=21 sources; the operative version of each source is queryable via the `_meta` field and the `/v1/metadata` endpoint.

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. dbNSFP version drift is the dominant staleness vector: AlphaMissense was added to dbNSFP v4.4 (~2024); querying `dbnsfp.alphamissense.score` returns whatever version of dbNSFP is currently loaded; check `_meta.src.dbnsfp.version`.

# MyVariant.info Queries; Aggregated Annotation

**'Annotate my variants with ClinVar + gnomAD + CADD + AlphaMissense in one batch'** -> Query the BioThings myvariant.info aggregator with field selection and version tracking, then parse nested responses.

- Python: `myvariant.MyVariantInfo().getvariant(hgvs_or_rsid, fields=['clinvar', 'gnomad_exome', 'dbnsfp'])`
- Python (batch): `mv.getvariants(ids_list, fields=...)`; up to 1000 IDs per request
- Python (search): `mv.query('clinvar.gene.symbol:BRCA1 AND clinvar.clinical_significance:Pathogenic')`
- REST: `GET https://myvariant.info/v1/variant/{hgvs_or_id}?fields=...`
- Bulk: `POST https://myvariant.info/v1/variant` with comma-separated IDs

## BioThings Architecture (Lelong 2022 *Bioinformatics*)

myvariant.info is one of three flagship BioThings APIs (with MyGene.info and MyChem.info). All three share the BioThings SDK, which auto-deploys an Elasticsearch index from heterogeneous source files via per-source dataloaders. The 2022 paper formalized the SDK; the architecture itself is older (Xin 2016 *Genome Biol*).

- Elasticsearch-backed: queries use Lucene operators (AND, OR, NOT, range like `dbnsfp.cadd.phred:>20`)
- Dotted-field-name syntax for nested JSON
- The `_id` field is canonical HGVS-g per record (e.g., `chr7:g.117199644G>A`)

## Aggregated Sources: ~21 and Counting

| Source | What | Notes |
|--------|------|-------|
| ClinVar | Pathogenicity | Weekly refresh |
| gnomAD v4 exomes + genomes | Population AF | grpmax_faf95 surfaced |
| dbSNP Build 156 | rsID + alleles | RsMergeArch resolved |
| dbNSFP v4.x | Meta-aggregator of 40+ in silico predictors | Includes AlphaMissense, REVEL, BayesDel |
| CADD | Deleteriousness | Genome-wide |
| CIViC | Cancer interpretation | Per-disease |
| COSMIC | Somatic variants | Catalogue of Somatic Mutations |
| EVS | Exome Variant Server | Legacy (deprecated by gnomAD) |
| ExAC | ExAC frequencies | Legacy (superseded by gnomAD) |
| GRASP | GWAS associations | -- |
| GWAS Catalog | Curated GWAS | -- |
| Wellderly | Disease-resistant elderly cohort | -- |
| EMV | -- | -- |
| DOCM | Database of Curated Mutations | -- |
| ICGC | International cancer | -- |
| MutDB | -- | -- |
| GO | Gene Ontology | -- |
| Snpeff | snpEff annotations | -- |
| GeneReviews | Disease/gene reviews | -- |
| MutPred | Functional impact | -- |

**dbNSFP is itself an aggregator.** Querying `dbnsfp.alphamissense.score` returns the version that dbNSFP loaded, not AlphaMissense direct. The lag from publication (Cheng 2023 *Science*) to integration into myvariant.info is typically 6-18 months via dbNSFP.

## Scopes and Query Forms

| Endpoint | Method | Use |
|----------|--------|-----|
| `/v1/variant/{id}` | GET | Single canonical-ID lookup |
| `/v1/variant` | POST (batched IDs) | Batch lookup, up to 1000 IDs |
| `/v1/query?q={lucene}` | GET | Flexible Elasticsearch search |
| `/v1/metadata` | GET | Per-source versions |

**Scopes** (the `scopes` parameter on `/v1/query` POST) specifies which fields to match an input ID against: `hgvs`, `rsid`, `dbsnp.rsid`, `dbnsfp.genename`, `chrom`, `_id`. The `_id` is canonical HGVS-g.

## Reproducibility: The `_meta` Field

Every record carries `_meta.src` showing per-source version:

```python
mv = myvariant.MyVariantInfo()
record = mv.getvariant('chr7:g.140453136A>T', fields=['_meta', 'clinvar', 'dbnsfp.alphamissense'])
print(record['_meta']['src']['dbnsfp']['version'])  # e.g., '4.7a'
print(record['_meta']['src']['clinvar']['version'])  # e.g., '20250901'
```

For reproducibility, record per-source versions in analysis output alongside results.

## Comparison to Alternatives

| Tool | Approach | When to use |
|------|----------|-------------|
| **myvariant.info** | Cloud aggregator, ES-backed | Quick batch annotation, no local setup |
| **OpenCRAVAT** (Pagel 2020 *JCO Clin Cancer Inform*) | Local install, modular annotators | Offline / PHI-sensitive |
| **VarSome** (Kopanos 2019 *Bioinformatics* 35:1978; commercial) | Hosted, 22 sources | 82% ACMG criteria auto-application (highest); clinical labs |
| **Franklin / Genoox** | Commercial hosted | 59 data sources; family/cohort analysis |
| **GeneBe.net** (Stawiński 2024 *Clin Genet*) | Open-source web + API | Free Tavtigian-point-system-based ACMG; comparable to VarSome |
| **ANNOVAR / VEP / snpEff** | Local annotation tools | Pipeline integration, batch annotation, no ACMG |

**myvariant.info does NOT produce ACMG calls**; it is purely an annotation aggregator. Pair with InterVar, GeneBe, or the `acmg-classification` skill for classification.

## Decision Tree by Query Scenario

| Scenario | Recommended path | Why |
|----------|------------------|-----|
| Single variant batch annotation | `getva

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

pip install myvariant requests pandas

git clone https://github.com/GPTomics/bioSkills
git -C bioSkills checkout c8c1fc3a2b13

Works in

1. 2026-10-19
   ✓SAFE B 89 / 100

   first audit · source c8c1fc3a2b13

Questions about Myvariant Queries

• github.com/GPTomics/bioSkills/tree/main/clinical-databases/myvar — the audited source at commit c8c1fc3a2b13 and every finding aboveObserved · 19 Oct 2026

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