VA-Spec Documentation Updates#691
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bencap merged 3 commits intoJun 23, 2026
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Both statement layers serialize with type "Statement"; document distinguishing them via proposition.type and correct the pathogenicity example to use the GA4GH schema values. Add a warning that the pathogenicity classification reflects MaveDB functional evidence only, not a complete clinical determination.
Add a heuristic table mapping a variant's state (mapped, scored, calibrated) to the highest VA-Spec layer it qualifies for, consolidating the per-variant availability rules previously only described in prose. Also document that a score falling outside every calibration range is annotated at the layer above as Indeterminate/Uncertain Significance with a Neutral direction, rather than demoted to a lower layer.
Align classification, direction, strength, and evidenceOutcome code values in the examples, prose, and tables with the lowercase form MaveDB actually emits (e.g. `pathogenic`, `abnormal`, `supports`), and note the convention so consumers do not match on the wrong casing. ACMG criterion codes such as `PS3` and `BS3_supporting` keep their conventional casing.
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coverage: 2.596%. remained the same — docs/bencap/va-spec-type-identification into release-2026.2.4 |
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Documentation updates to support and clarify changes in VariantEffect/mavedb-api#728