VariantEffect / mavedb-ui / 31422915522

3%

Build Type

push

github

Committed by bencap

Commit Message

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

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.

Coverage Stats

202 of 296 branches covered (68.24%)

Branch coverage included in aggregate %.

36 of 48 new or added lines in 4 files covered. (75.0%)

143 existing lines in 12 files now uncovered.

487 of 10608 relevant lines covered (4.59%)

0.51 hits per line