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ClinVar-GKM is distributed as monthly and weekly full bundles plus weekly deltas (JSON), with one typed Parquet dataset of the latest release, free from Cloudflare R2 — no authentication, no egress fees. The layout follows NCBI's ClinVar FTP site. New here? See How Releases Work.

1.1.0 moved every download URL

1.1.0 (released 2026-10-22) moved every download URL to v1/1.1/ and renamed the proposition sections — see the changelog migration notes.

Before you use or share the data

These files carry ClinVar data from NCBI. ClinVar's disclaimer applies: the data is not for direct diagnostic use or medical decision-making without review by a genetics professional. Attribute ClinVar as the data source, cite ClinVar-GKM, and carry the attribution and disclaimer with any copy you redistribute. The CC0 dedication covers ClinGen's transformation only. See Data Use and Citation.

Latest Release

Monthly full or weekly full?

clinvar-gkm_00-latest.json.gz is the newest official monthly: it reflects the last release of the previous month — e.g. the 2026-10 monthly is built from the 2026-09-28 release, the last one before ClinVar's October monthly cut. For the current week, download weekly/clinvar-gkm_00-latest_weekly.json.gz, a full bundle of the newest release. See Weekly Full Bundles.

Browse history and archives: Monthly Full Bundles · Weekly Full Bundles · Weekly Deltas · Parquet Files.

Directory Structure

Versioned layout

The root index.json is a thin version manifest that lists the release lines and points to each line's index. Each line has its own folder, v{major}/{major}.{minor}/. The current line is 1.1, served under v1/1.1/, with its release index at v1/1.1/index.json. PATCH releases (1.1.x) add to the same folder; a new MINOR starts v1/1.2/ and a new MAJOR starts v2/2.0/. A replaced line is frozen and kept indefinitely: its files stay, unchanged. The 1.0.1 generation is the frozen line v1/1.0/.

index.json                                    version manifest (each line -> its index)
v1/
  1.1/                                        current line
    index.json                                release index for the line
    feed.xml                                  Atom feed of the line's releases
    README.txt                                plain-text guide to the line
    clinvar-gkm_00-latest.json.gz             newest official monthly full (stable URL)
    clinvar-gkm_YYYY-MM.json.gz               official monthly fulls, current year
    weekly/
      clinvar-gkm_00-latest_weekly.json.gz    newest weekly full (stable URL)
      clinvar-gkm_YYYY-MMDD.json.gz           weekly fulls, CURRENT MONTH ONLY
    deltas/
      clinvar-gkm-delta_YYYY-MMDD.json.gz     current month's weekly deltas
      clinvar-gkm-delta_YYYY-MMDD.manifest.json
      YYYY-MM/                                earlier months of the current year
    archive/
      YYYY/
        clinvar-gkm_YYYY-MM.json.gz           monthly fulls from prior years
        deltas/YYYY-MM/                       deltas from prior years
    parquet/
      {section}.parquet                       ONE Parquet dataset, the latest (derived; overwritten every release)
      manifest.json                           build date, source release, builder, per-file sha256
  1.0/                                        frozen line: the 1.0.1 generation (bundles, delta manifests, MANIFEST.json; no Parquet)

Every bundle has a <file>.sha256 sidecar (sha256sum -c format), like NCBI's .md5 files.

When files move

  • New month. When the first release of a new month is published, the finished month's deltas move from deltas/ into deltas/YYYY-MM/, and the finished month's weekly fulls are deleted. The newest of them is kept until the new month's official monthly is published, because that monthly is normally a copy of it, and is deleted as soon as the monthly is up. A past week is rebuilt from a monthly plus deltas; see Rebuild a past week.
  • New year. When the first release of a new year is published, the finished year's monthlies move into archive/YYYY/ and its delta folders into archive/YYYY/deltas/YYYY-MM/.
  • A move never changes a file's bytes, name or checksum, only its folder. Scripts that need a dated file should look up its current path in the line's index.json.

How the layout mirrors NCBI

The bundles are built from ClinVar's XML releases, so the layout follows NCBI's ClinVar XML folder:

NCBI ClinVar XML ClinVar-GKM v1/1.1/
xml/ — monthly releases and ClinVarVCVRelease_00-latest.xml.gz top level — official monthlies and clinvar-gkm_00-latest.json.gz
xml/weekly_release/ — the current month's weekly releases and 00-latest_weekly weekly/ — the current month's weekly fulls and clinvar-gkm_00-latest_weekly.json.gz
xml/archive/YYYY/ — monthly releases of prior years archive/YYYY/ — monthlies of prior years
.md5 sidecars .sha256 sidecars
— deltas/ — weekly deltas (ClinVar-GKM only)
— parquet/ — one derived Parquet dataset (ClinVar-GKM only)

Each ClinVar-GKM monthly clinvar-gkm_YYYY-MM lines up with ClinVar's ClinVarVCVRelease_YYYY-MM, and each weekly full or delta with the ClinVar weekly release of the same date.

Troubleshooting

  • HTTP 403. The CDN serves only the root index.json and paths under /v1/; a path allowlist answers every other path with 403, not 404. A 403 usually means a URL from before the current layout, such as a bucket-root datasets/… path. Look up the file's current path in the line's index.json.
  • HTTP 404 under /v1/. The file is not there: a weekly full deleted at month end, a delta moved to deltas/YYYY-MM/, or a monthly moved to archive/YYYY/. See When files move.
  • HTTP 429. Requests are rate-limited. Download whole files and query them locally rather than issuing many small range requests.

Feedback

This project is in active development and we welcome community feedback. If you encounter data quality issues, have questions about the output format, or want to suggest improvements:

  • Open an issue on GitHub
  • Include the release date and specific records involved