Skip to content

feat(variant): show gnomAD population frequency on the variant page - #710

Merged
bencap merged 2 commits into
feature/bencap/variant-level-csv-downloadfrom
feature/bencap/447/gnomad-allele-frequency
Aug 12, 2026
Merged

feat(variant): show gnomAD population frequency on the variant page#710
bencap merged 2 commits into
feature/bencap/variant-level-csv-downloadfrom
feature/bencap/447/gnomad-allele-frequency

Conversation

@bencap

@bencap bencap commented Aug 10, 2026

Copy link
Copy Markdown
Collaborator

Fills the annotations card's "Population Frequency" column, until now a "Data coming soon" placeholder. gnomAD is linked to a single mapped variant by ClinGen allele ID, so the frequency is a direct assertion about the measured allele rather than an aggregate over related variants.

  • Add MvGnomadSummary: AF with the AC/AN behind it, FAF95 with the genetic ancestry group attaining it, and a deep link to the gnomAD variant page, bottom-aligned so provenance lines up across the card's columns.
  • Read the record from the score set's variant data CSV via gnomadFromVariantRow, which normalises the namespace's NA sentinels. A variant absent from gnomAD reports as having no record, not zero frequency.
  • Derive GnomadFrequency from the generated OpenAPI schema, so renaming or retyping a field on the API model breaks compilation here.
  • Split HISTOGRAM_VARIANT_DATA_NAMESPACES into SCORE_SET_CHART_NAMESPACES and VARIANT_PAGE_NAMESPACES. One list fed two screens under a name describing neither, and only the variant page reads gnomAD, so the score set charts no longer fetch seven unused columns on every row.

Requires the widened gnomad CSV namespace in the API, see VariantEffect/mavedb-api#836.

@coveralls

coveralls commented Aug 10, 2026

Copy link
Copy Markdown

Coverage Status

Coverage is 10.159%feature/bencap/447/gnomad-allele-frequency into feature/bencap/variant-level-csv-download. No base build found for feature/bencap/variant-level-csv-download.

@bencap bencap linked an issue Aug 10, 2026 that may be closed by this pull request
@bencap
bencap force-pushed the feature/bencap/447/gnomad-allele-frequency branch from e9d93a7 to 38894c6 Compare August 11, 2026 00:04
@bencap
bencap force-pushed the feature/bencap/447/gnomad-allele-frequency branch from 3bfb73b to 7ffaa12 Compare August 11, 2026 16:27
bencap added 2 commits August 12, 2026 11:39
Fills the annotations card's "Population Frequency" column, until now a
"Data coming soon" placeholder. gnomAD is linked to a single mapped variant
by ClinGen allele ID, so the frequency is a direct assertion about the
measured allele rather than an aggregate over related variants.

- Add MvGnomadSummary: AF with the AC/AN behind it, FAF95 with the genetic
  ancestry group attaining it, and a deep link to the gnomAD variant page,
  bottom-aligned so provenance lines up across the card's columns.
- Read the record from the score set's variant data CSV via
  gnomadFromVariantRow, which normalises the namespace's NA sentinels. A
  variant absent from gnomAD reports as having no record, not zero frequency.
- Derive GnomadFrequency from the generated OpenAPI schema, so renaming or
  retyping a field on the API model breaks compilation here.
- Split HISTOGRAM_VARIANT_DATA_NAMESPACES into SCORE_SET_CHART_NAMESPACES and
  VARIANT_PAGE_NAMESPACES. One list fed two screens under a name describing
  neither, and only the variant page reads gnomAD, so the score set charts no
  longer fetch seven unused columns on every row.

Requires the widened gnomad CSV namespace in the API.
@bencap
bencap force-pushed the feature/bencap/447/gnomad-allele-frequency branch from 7ffaa12 to 36c43e5 Compare August 12, 2026 18:39
@bencap
bencap merged commit 6d80c90 into release-2026.2.4.1 Aug 12, 2026
1 check passed
@bencap bencap mentioned this pull request Aug 12, 2026
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

gnomAD minor allele frequency display

2 participants