lipidmetabolism 2.0.0: 2026 evidence rebuild of the Generation I expert module (O. Borysova). Adds every independent genome-wide-significant lead of the largest 2021-2026 GWAS for the trait plus functional variants, with evidence tiers (S-D); errors in the original rows corrected with recorded reasons (provenance in logs/authoring.log); gnomAD v4.1 frequencies; closed. Built with just-dna-compiler main a05cd54.

data/lipidmetabolism/README.md

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+# Lipid Metabolism (v2.0.0)
+
+Which versions of your DNA shift blood cholesterol, triglycerides and lipoprotein(a), the blood fats
+that drive narrowing of the arteries. Each result is one small piece of a picture that a routine blood
+lipid test (and, once in life, an Lp(a) test) shows directly. Nothing here is a diagnosis.
+
+Original expert curation: **Olga Borysova** (v1.x, 15 variants). v2.0.0 is an AI-assisted evidence
+rebuild (2026-11-03) that keeps every one of her rows unchanged and adds the 2021–2026 GWAS and
+functional-variant evidence described below. No human has reviewed the v2.0.0 additions yet.
+
+## What is in the module
+
+| Group (`method` column) | Variants | Genotype rows | Source |
+|---|---|---|---|
+| Legacy, expert-curated (`expert-curated`, curator `just-dna-seq`) | 15 | 45 | O. Borysova, v1.1.0 |
+| Tier A — LDL-C / triglyceride GWAS index variants (`gwas-index-beta`) | 1,016 | 3,048 | Graham et al. 2021, *Nature* (GLGC, 1.65 M people, five ancestry groups), PMID 34887591 |
+| Tier A — Lp(a) conditionally independent variants in *LPA* (`gwas-conditional-beta`) | 21 | 63 | Sinnott-Armstrong et al. 2021, *Nat Genet* (UK Biobank), PMID 33462484 |
+| Tier B — functional / high-impact variants (`published-OR`) | 10 | 30 | PMIDs 29020353, 16554528, 24941081, 20032323, 28506971 |
+| **Total** | **1,062** | **3,186** | 45 papers, 1,102 `studies.csv` rows, 854 gene labels |
+
+Of the 1,016 Tier A variants, 802 are multi-ancestry index variants for LDL-C or triglycerides, and
+214 are HDL-C index variants kept because the same variant also reaches p < 5×10⁻⁸ for LDL-C or
+triglycerides. Across all 1,016, 430 are scored on LDL-C and 586 on triglycerides.
+
+### Selection rule (Tier A)
+
+1. **LDL-C and triglycerides — all of them.** Every multi-ancestry index variant with genome-wide
+   significance (MR-MEGA p < 5×10⁻⁸) flagged `independent = yes` in GLGC 2021 Supplementary Table 5,
+   for LDL-C (416) or log-triglycerides (461): 843 unique variants. No subsampling.
+2. **HDL-C only where it also moves a causal lipid.** HDL-C index variants (461 not already in step 1)
+   are kept only if the same variant has p < 5×10⁻⁸ for LDL-C or triglycerides in the GLGC
+   multi-ancestry summary statistics (GWAS Catalog harmonised files GCST90239655 / GCST90239661), or
+   for ApoB in any GWAS Catalog association: 225 qualified (via LDL-C/TG; none via ApoB alone),
+   **236 excluded**, because raising HDL-C has not been shown to lower heart risk.
+3. **Non-HDL-C and total-cholesterol-only index variants (445) are not included** (outside the rule;
+   decision for a human).
+4. **One set of rows per variant.** When a variant is significant for both LDL-C and triglycerides, the
+   weight uses the trait with the larger |β|; the other trait is mentioned in the conclusion and
+   recorded in `studies.csv`. 46 variants move LDL-C and triglycerides in opposite directions and carry
+   `flags = pleiotropic`.
+5. **Lp(a):** the 22 conditionally independent genome-wide significant variants mapped to *LPA* in
+   GWAS Catalog GCST90019513; rs3798220 is authored once, in Tier B. These are joint-model
+   (conditional) effects and carry `flags = conditional`.
+6. **Legacy overlap:** where a GWAS index variant equals one of Olga Borysova's rsIDs (rs12740374,
+   rs676210, rs429358, rs7412, rs1800961), her rows are kept and the GWAS evidence is added to
+   `studies.csv` only.
+
+### Tier B
+
+| Gene | Variant | Effect allele | Published effect (CHD) | PMID |
+|---|---|---|---|---|
+| PCSK9 | R46L (rs11591147) | T | OR 0.77 per allele | 29020353 (also 16554528) |
+| PCSK9 | Y142X (rs67608943), C679X (rs28362286) | G, A | HR 0.11 (carriers of either) | 16554528 |
+| APOC3 | R19X (rs76353203), IVS2+1G>A (rs138326449), IVS3+1G>T (rs140621530), A43T (rs147210663) | T, A, T, A | OR 0.60 (carriers of any) | 24941081 (also 34548093) |
+| LPA | rs10455872, rs3798220 | G, C | OR 1.70, 1.92 per allele | 20032323 |
+| CETP | IVS14+1G>A (rs5742907) | A | OR 0.70 (PTV carriers; 0.69 in Japanese) | 28506971 |
+| APOE | ε2/ε4 (rs7412 / rs429358) | — | Olga Borysova's legacy rows, unchanged | — |
+
+Aggregate (carrier-of-any) estimates are applied to each variant in the group. ANGPTL3 and LPL
+loss-of-function alleles were **not** authored as Tier B rows: the primary studies (PMID 28538136 for
+ANGPTL3, OR 0.59; PMID 28267856 for LPL) report pooled carrier estimates for many ultra-rare alleles
+without per-variant effect alleles. The ANGPTL3 and LPL loci are represented by their Tier A index
+variants and by the legacy LPL rows (rs328, rs268).
+
+## Weights — the module mixes three scales
+
+Positive = favourable, negative = risk; a homozygote for the non-effect allele scores 0.0 (`neutral`).
+
+* **Legacy rows** — Olga Borysova's curator-set values in [−3, 3].
+* **Tier A rows** — `weight = −β × copies`, β in standard-deviation units of the trait per effect
+  allele (GLGC: inverse-normal-transformed LDL-C or log-TG, METAL fixed-effect β; UK Biobank: SD of
+  Lp(a)). Most rows are between 0.005 and 0.2 per copy.
+* **Tier B rows** — `weight = −ln(OR) × copies` for coronary heart disease, capped to [−3, 3]
+  (the PCSK9 nonsense homozygote rows hit the cap).
+
+A summed "net weight" across this module is dominated by about a thousand tiny Tier A rows. It is **not**
+a validated polygenic score and is not comparable with any other module. The `weighting:` block in
+`module_spec.yaml` says the same.
+
+## What this module does not duplicate
+
+The ClinVar **cardio** module (just_dna_seq/cardio 2.0.0) already reports ClinVar pathogenic and
+likely-pathogenic variants for monogenic familial hypercholesterolaemia (*LDLR*, *LDLRAP1*). None of
+those rsIDs is authored here (all 1,062 candidates were checked against its 37,901 rsIDs; no overlap was
+found), and *APOB*/*PCSK9* gain-of-function FH variants are not added. Read the two modules together.
+
+## Limits
+
+* GWAS effects are averages from mostly European samples (1.32 M of 1.65 M in GLGC; 273 k of 284 k
+  in the Lp(a) study). Frequencies quoted in conclusions are estimated from the study's allele
+  frequency under Hardy–Weinberg proportions.
+* 124 strand-ambiguous (A/T, C/G) Tier A SNPs were kept because their effect-allele frequency is
+  outside 0.40–0.60 and the GWAS Catalog harmonised GRCh38 file reports them on the forward strand
+  (harmonisation codes 1, 2, 5 or 6); no gnomAD frequency table was produced in this enrichment run, so
+  this orientation is not independently confirmed (provisional). 21 others were dropped.
+* 24 indels were dropped because the study's allele spelling did not match the Ensembl GRCh38 record.
+* Lp(a) per-variant effects are conditional on each other and on nearby variants and should not be
+  added up as if independent.
+* Conclusions were written from templates for the Tier A rows; the module-voice lay-reader and
+  scientific reviews have not been run yet.
+
+## Sources
+
+Graham SE et al. *The power of genetic diversity in genome-wide association studies of lipids.*
+Nature 2021 (PMID 34887591; Supplementary Table 5 = `41586_2021_4064_MOESM4_ESM.xlsx`, sheet
+"ST.5 Multiancestry Results"; GWAS Catalog GCST90239649/55/61). Sinnott-Armstrong N et al. *Genetics of
+35 blood and urine biomarkers in the UK Biobank.* Nat Genet 2021 (PMID 33462484; GCST90019513). Tier B
+papers as in the table above. Searches for 2023–2026 lipid, ApoB and Lp(a) GWAS (PubMed, Europe PMC,
+web) found no larger multi-ancestry LDL-C/TG meta-analysis with a published index-variant table; the
+2025 GLGC review (PMID 39602359) summarises the consortium's results as over 923 loci from more than
+1.65 million individuals, i.e. the 2021 study used here.
+
+## Changelog
+
+* **2.0.0** (2026-11-03, AI-assisted) — tiered evidence rebuild (Tier A GWAS, Tier B functional,
+  legacy kept), `weighting:` declared, authorship recorded.
+* 1.1.0 — Olga Borysova's expert-curated module (15 variants).
+
+## Evidence tiers
+
+Every variant carries an evidence tier in `flags` (`tier:S` … `tier:D`) and in `priority`
+(S = high, A = medium, B/C/D = low). The tier never changes `weight`. Most variants in this module are
+weak signals, so the top tier is **S**, kept for the few variants that matter on their own. New (2026) rows
+also start their conclusion with the tier's label.
+
+| Tier | Meaning | Variants (of which legacy) |
+|---|---|---|
+| S | Strong evidence: an effect large enough to matter on its own (OR/HR ≥ 1.5 or ≤ 0.67, or ≥ 0.5 SD), robustly supported | 10 (1) |
+| A | Well established, small effect (research grade): genome-wide significant in the anchor GWAS and in ≥ 1 further publication, same direction | 341 (11) |
+| B | Single-study signal, small effect (research grade): genome-wide significant in the anchor GWAS only | 711 (3) |
+| C | Early evidence (research only): not genome-wide significant for this trait | 0 (0) |
+| D | Not supported: contradicted, or null in large GWAS / meta-analysis | 0 (0) |
+
+S holds the variants that move a lipid by half a standard deviation or more, or change coronary risk by 1.5-fold or more: APOE ε2, the PCSK9 and APOC3 loss-of-function alleles and the main LPA variants. Replication was read from the GWAS Catalog (REST v2, retrieved 2026-11-03; cohorts of different
+publications may overlap). `also_in:<module>` marks the 29 variants that also appear in another just-dna
+module. Summing weights across modules counts those twice. The rules are adapted from the Longevity Map v2
+requirements (`docs/longevitymap_v2/`).
+
+## Corrections to the original expert-curated rows
+
+The 2026 audit of the Generation I content (Supplementary Table S14 of the Just-DNA-Lite paper) found errors that were still present in v1.1.0. Version 2.0.0 corrects them, changing only the cell that was wrong. Each change is recorded with its reason in `provenance.json` and `logs/authoring.log`.
+
+| Variant | Genotype | Field | What was wrong |
+|---|---|---|---|
+| rs429358 | C/T | conclusion | the conclusion ended mid-sentence ('Some studies') |
+
+### Gene column for GWAS rows
+
+The GWAS index variants' gene cell names the HGNC gene the variant lies in (33 variants), or the nearest HGNC protein-coding gene when it is within 100 kb (13 variants, flag `gene:nearest`). Otherwise the cell is blank (28 variants), with the nearest gene and its distance in `flags` (`nearest_gene:`, `nearest_kb:`). Neither is a claim that the gene causes the effect. The anchor study's own label is kept as `gwas_label:`.

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data/lipidmetabolism/logs/authoring.log

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+2026-11-04T07:36:42Z authored rs429358 conclusion='C/T: You are a carrier of unfavourable C-allele in rs429358, which ia a part of e4 APOE genotype estimation. If your genotype also harbors the...' (judged; no value from the row's own conclusion and the module's other genotype rows to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:30Z authored rs1883783 gene='SSBP3' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:32Z authored rs186538116 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:35Z authored rs115292790 gene='STXBP3' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:37Z authored rs1689797 gene='LINC01344' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:40Z authored rs1689801 gene='LINC01344' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:45Z authored rs1434282 gene='LINC01221' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:47Z authored rs59770119 gene='LYPLAL1-AS1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:49Z authored rs508293 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:54Z authored rs553427 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:56Z authored rs557933 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:45:58Z authored rs11679703 gene='LINC00299' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:46:01Z authored rs759257847 gene='LINC01808' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:46:04Z authored rs114040256 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:46:19Z authored rs1883783 gene='SSBP3' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:21Z authored rs186538116 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:23Z authored rs115292790 gene='STXBP3' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:26Z authored rs1689797 gene='LINC01344' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:28Z authored rs1689801 gene='LINC01344' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:30Z authored rs1434282 gene='LINC01221' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:32Z authored rs59770119 gene='LYPLAL1-AS1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:35Z authored rs508293 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:37Z authored rs553427 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:39Z authored rs557933 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:42Z authored rs11679703 gene='LINC00299' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:44Z authored rs759257847 gene='LINC01808' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:46Z authored rs114040256 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false [replaced an earlier record]
+2026-11-04T08:46:49Z authored rs191450029 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:46:51Z authored rs116500366 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:46:53Z authored rs4665495 gene='LINC01830' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:46:57Z authored rs11889451 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:00Z authored rs17050272 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:02Z authored rs954244 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:05Z authored rs11688682 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:07Z authored rs563563230 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:10Z authored rs6430090 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:12Z authored rs7571848 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:15Z authored rs2203452 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:17Z authored rs2972145 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:20Z authored rs9831084 gene='EPM2AIP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:23Z authored rs79287178 gene='LINC02068' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:26Z authored rs71610255 gene='USP53' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:28Z authored rs26008 gene='FNIP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:30Z authored rs11167778 gene='SPRY4-AS1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:33Z authored rs6924805 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:35Z authored rs12189754 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:38Z authored rs635769 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:41Z authored rs17585887 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:43Z authored rs36126113 gene='LINC02941' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:45Z authored rs2283038 gene='HBP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:47Z authored rs2921064 gene='LINC02950' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:50Z authored rs4739514 gene='LINC01605' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:52Z authored rs9298506 gene='RP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:55Z authored rs6471886 gene='LINC01301' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:47:57Z authored rs400824 gene='ZBTB10' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:00Z authored rs6473280 gene='FABP4' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:02Z authored rs1561929 gene='LINC00824' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:04Z authored rs2773513 gene='GLDC' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:06Z authored rs10961056 gene='LINC01235' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:09Z authored rs1590404 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:11Z authored rs543458 gene='NFIB' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:13Z authored rs7864568 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:16Z authored rs11789974 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:19Z authored rs72619338 gene='RXRA' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:21Z authored rs10827239 gene='NRP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:23Z authored rs4934932 gene='NRP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:26Z authored rs776902938 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:29Z authored rs117288140 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:32Z authored rs11045171 gene='PDE3A' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:34Z authored rs11045172 gene='PDE3A' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:37Z authored rs7132434 gene='SSPN-AS1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:40Z authored rs275179 gene='LINC02694' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:42Z authored rs6493583 gene='LINC02490' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:45Z authored rs11636087 gene='USP3' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:48Z authored rs2469128 gene='LINC01169' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:50Z authored rs145437104 gene='RABEP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:53Z authored rs2008998 gene='MIR4733HG' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:55Z authored rs525767 gene='LASP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:48:58Z authored rs11650182 gene='SKAP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:01Z authored rs28394864 gene='ZNF652-AS1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:03Z authored rs41292412 gene='MIR122' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:06Z authored rs6567160 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:08Z authored rs1135908 gene='PTBP1' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:11Z authored rs572546175 gene='LINC03078' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:14Z authored rs4810280 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:17Z authored rs4811348 gene='LINC01524' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:19Z authored rs12106385 gene='(blank)' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false
+2026-11-04T08:49:22Z authored rs4822458 gene='DDT' (judged; no value from Ensembl REST overlap/region, GRCh38, queried 2026-11-04 to disagree with) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false

data/lipidmetabolism/manifest.json

@@ -2,11 +2,11 @@
   "manifest_version": "1.0",
   "schema_version": "1.0",
   "identity": {
-    "namespace": "just-dna-seq",
+    "namespace": null,
     "name": "lipidmetabolism",
-    "version": "1.1.0",
+    "version": "2.0.0",
     "version_coerced_from": null,
-    "canonical_id": "just-dna-seq/lipidmetabolism@1.1.0"
+    "canonical_id": null
   },
   "display": {
     "title": "Lipid Metabolism",
@@ -21,100 +21,980 @@
   "method": "expert-curated",
   "license": null,
   "authority_precedence": [],
-  "weighting": null,
-  "owner": "just-dna-seq",
+  "weighting": {
+    "scale": "Mixed, by row group (see the method column). (1) Legacy rows (method expert-curated, curator just-dna-seq; Olga Borysova): curator-set values in [-3, 3], unchanged from v1.1.0. (2) Tier A GWAS rows (method 'gwas-index-beta' / 'gwas-conditional-beta'): weight = -beta x copies of the effect allele, beta in standard-deviation units of the trait per allele (LDL-C or triglycerides from Graham et al. 2021, PMID 34887591; Lp(a) from Sinnott-Armstrong et al. 2021, PMID 33462484); homozygous for the other allele = 0.0 (neutral). Typical magnitude 0.005-0.5 per row. (3) Tier B functional rows (method 'published-OR'): weight = -ln(OR) per copy of the effect allele for coronary heart disease from the cited study (het = -ln OR, hom = -2 ln OR, other = 0.0), capped to [-3, 3]. Positive = favourable (lower LDL-C / triglycerides / Lp(a) or lower CHD risk); negative = risk.",
+    "method": "Tier A: every conditionally independent multi-ancestry index variant (p < 5e-8, MR-MEGA) for LDL-C or triglycerides in GLGC 2021 Supplementary Table 5 (independent = yes), plus HDL-C index variants only where the same variant reaches p < 5e-8 for LDL-C or triglycerides in the GLGC multi-ancestry summary statistics (GWAS Catalog GCST90239655 / GCST90239661) or for ApoB in any GWAS Catalog association; the weight uses the LDL-C or triglyceride beta with the larger absolute value (both reported in studies.csv). Lp(a): the 21 conditionally independent genome-wide significant variants mapped to LPA in GWAS Catalog GCST90019513 (rs3798220 moved to Tier B). Tier B: PCSK9 (R46L, Y142X, C679X), APOC3 (R19X, IVS2+1G>A, IVS3+1G>T, A43T), LPA (rs10455872, rs3798220) and CETP (IVS14+1G>A) with published coronary odds/hazard ratios. Where a GWAS lead equals a legacy rsID, Olga Borysova's rows are kept and the GWAS evidence is added to studies.csv only.",
+    "note": "Not comparable with any other module's weights, and the three row groups are on different scales inside this module: a Tier A row is a per-allele shift of a blood lipid in SD units, a Tier B row is a log odds ratio for heart disease, and legacy rows are curator-set. A summed net weight is dominated by the ~1,000 small Tier A rows and is not a validated polygenic score; use a published PGS (e.g. the GLGC LDL-C scores in the PGS Catalog) for that purpose."
+  },
+  "owner": null,
   "authors": [],
-  "authorship": [],
+  "authorship": [
+    {
+      "who": "Olga Borysova",
+      "role": "created",
+      "kind": [
+        "human_expert"
+      ],
+      "at": null
+    },
+    {
+      "who": "just-dna-seq rebuild agent (AI-assisted, 2026)",
+      "role": "edited",
+      "kind": [
+        "ai",
+        "agent"
+      ],
+      "at": "2026-11-03"
+    }
+  ],
   "created_at": null,
-  "published_at": "2026-09-26T23:44:28Z",
+  "published_at": null,
   "stats": {
-    "variant_count": 15,
-    "weights_rows": 45,
-    "study_count": 44,
-    "gene_count": 12,
+    "variant_count": 1062,
+    "weights_rows": 3186,
+    "study_count": 1102,
+    "gene_count": 832,
     "genes": [
+      "A1CF",
+      "ABCA1",
+      "ABCA6",
+      "ABCA8",
+      "ABCB11",
+      "ABCB4",
       "ABCG8",
+      "ABHD15",
+      "ABO",
+      "ABRACL",
+      "ACAA2",
+      "ACACB",
+      "ACO1",
+      "ACTB",
+      "ACTRT2",
+      "ACVR1",
+      "ACVR1C",
+      "ADAM15",
+      "ADAMTS3",
+      "ADCY5",
+      "ADD1",
+      "ADGRV1",
+      "ADH4",
+      "ADPGK-AS1",
+      "ADRB1",
+      "ADTRP",
+      "AFF1",
+      "AGBL4",
+      "AGPAT4",
+      "AGPAT5",
+      "AHR",
+      "AKNA",
+      "AKR1C4",
+      "ALDH1A2",
+      "ALKBH5",
+      "ANGPTL4",
+      "ANGPTL8",
+      "ANKRD17",
+      "ANKRD28",
+      "ANO3",
+      "ANXA9",
+      "AOC1",
       "APOB",
+      "APOC1",
       "APOC3",
       "APOE",
+      "APOH",
+      "APOL3",
+      "APOL6",
+      "APPL2",
+      "ARCN1",
+      "AREG",
+      "ARFGEF2",
+      "ARHGAP10",
+      "ARHGEF15",
+      "ARHGEF19",
+      "ARHGEF19-AS1",
+      "ARID1A",
+      "ARID2",
+      "ARID5B",
+      "ARL15",
+      "ARMC2",
+      "ARNILA",
+      "ARNT",
+      "ARSG",
+      "ASAP3",
+      "ASGR1",
+      "ATF1",
+      "ATG4C",
+      "ATP2B4",
+      "ATP8B1",
+      "ATXN2",
+      "AURKB",
+      "AVPR1A",
+      "AXL",
+      "B4GALNT3",
+      "B4GALNT4",
+      "BACE2",
+      "BAHD1",
+      "BAIAP2L1",
+      "BANF2",
+      "BANP",
+      "BCAS1",
+      "BCKDK",
+      "BCL2",
+      "BCL2L11",
+      "BDNF",
+      "BDNF-AS",
+      "BEND3",
+      "BICD2",
+      "BICRAL",
+      "BISPR",
+      "BLMH",
+      "BMAL1",
+      "BMF",
+      "BMP7",
+      "BMPR2",
+      "BNC2",
+      "BPTF",
+      "BRD1",
+      "BTD",
+      "C10orf88",
+      "C2",
+      "C2orf42",
+      "C4orf17",
+      "C5orf67",
+      "CACNA1A",
+      "CACNA2D1",
+      "CACUL1",
+      "CADM1",
+      "CADPS",
+      "CAMKMT",
+      "CAND2",
+      "CARINH",
+      "CARMIL1",
+      "CASC15",
+      "CASC17",
+      "CATSPER2P1",
+      "CAVIN1",
+      "CCDC106",
+      "CCDC170",
+      "CCDC200",
+      "CCDC63",
+      "CCDC77",
+      "CCDC92",
+      "CCND1",
+      "CCND2",
+      "CD300LG",
+      "CDCA2",
+      "CDKAL1",
+      "CDKN1A",
+      "CDKN2B-AS1",
+      "CEBPG",
       "CELSR2",
+      "CEP164",
+      "CEP68",
+      "CERT1",
+      "CES1",
       "CETP",
+      "CFAP251",
+      "CFL1",
+      "CFL2",
+      "CFTR",
+      "CHEK2",
+      "CHLSN",
+      "CIBAR2",
+      "CLDN23",
+      "CLEC14A",
+      "CLLU1-AS1",
+      "CMIP",
+      "CMTM6",
+      "CNIH4",
+      "CNKSR1",
+      "COBLL1",
+      "COG2",
+      "COG5",
+      "COL18A1",
+      "COL25A1",
+      "COL27A1",
+      "COL4A2",
+      "COL6A1",
+      "COLEC11",
+      "COLEC12",
+      "COMT",
+      "CORO1C",
+      "COX16",
+      "COX4I2",
+      "CPEB2",
+      "CPEB4",
+      "CPT1A",
+      "CREB3L2",
+      "CREB3L3",
+      "CRPPA",
+      "CRYZL2P-SEC16B",
+      "CSF1",
+      "CSMD1",
+      "CSNK1G3",
+      "CSNK2A1",
+      "CTCFL",
+      "CUX2",
+      "CXCL1",
+      "CYB5B",
+      "CYP26A1",
+      "CYP26B1",
+      "CYP2A6",
+      "CYP4F12",
+      "CYP7A1",
+      "CYRIA",
+      "CYSTM1",
+      "CYTL1",
+      "DAB1",
+      "DCAF12",
+      "DCP2",
+      "DCT",
+      "DDT",
+      "DDX19A-DT",
+      "DDX46",
+      "DDX56",
+      "DENND4C",
+      "DENND6B",
+      "DGKQ",
+      "DHODH",
+      "DHPS",
+      "DIP2B",
+      "DIXDC1",
+      "DLC1",
+      "DLEU1",
+      "DLG4",
+      "DMGDH",
+      "DMRT2",
+      "DMTN",
+      "DNAH1",
+      "DNAH11",
+      "DNAH12",
+      "DNAJC13",
+      "DNAJC16",
+      "DNAJC17",
+      "DNM3",
+      "DNMT1",
+      "DOCK6",
+      "DOCK7",
+      "DPYD",
+      "DR1",
+      "DRAIC",
+      "DSTYK",
+      "E2F3",
+      "EBF1",
+      "EEPD1",
+      "EFNA1",
+      "EGF",
+      "EHBP1",
+      "EIF4E",
+      "ELAVL1",
+      "ELF1",
+      "EMILIN2",
+      "EML3",
+      "ENTPD6",
+      "EPM2AIP1",
+      "ERGIC2",
+      "ERGIC3",
+      "ERICH2",
+      "ERLIN1",
+      "ETNK1-DT",
+      "EVI5",
+      "EVI5L",
+      "EYA1",
+      "EYA2",
+      "EYA3",
+      "FABP4",
+      "FADS1",
+      "FAF1",
+      "FAM117B",
+      "FAM13A",
+      "FAM228A",
+      "FARP2",
+      "FASN",
+      "FBLN1",
+      "FBRSL1",
+      "FBXL17",
+      "FBXW10",
+      "FCGR2C",
+      "FCGRT",
+      "FENDRR",
+      "FER1L4",
+      "FFAR4",
+      "FGB",
+      "FGF21",
+      "FGFR1",
+      "FGFR4",
+      "FIZ1",
+      "FLACC1",
+      "FLT1",
+      "FN1",
+      "FNBP1L",
+      "FNIP1",
+      "FOXA3",
+      "FOXN3",
+      "FRK",
+      "FRY",
+      "FST",
+      "FTO",
+      "FUT2",
+      "FUT3",
+      "FZD2",
+      "GAB2",
+      "GABBR1",
+      "GADD45G",
+      "GALK1",
+      "GALNT2",
+      "GALNT4",
+      "GALNT6",
+      "GAREM1",
+      "GAS6",
+      "GATA4",
+      "GATA6",
+      "GBF1",
+      "GC",
+      "GCC2",
+      "GCK",
+      "GCKR",
+      "GEN1",
+      "GIGYF1",
+      "GIMAP7",
+      "GLDC",
+      "GLP2R",
+      "GLTPD2",
+      "GPAM",
+      "GPCPD1",
+      "GPIHBP1",
+      "GPR180",
+      "GRIK2",
+      "GRIK4",
+      "GRM4",
+      "GSTA12P",
+      "GSTA2",
+      "GSTM5",
+      "HAVCR1",
+      "HAX1",
+      "HBP1",
+      "HBS1L",
+      "HCAR1",
+      "HCG20",
+      "HDGFL2",
+      "HDHD5",
+      "HEATR5A",
+      "HELZ",
+      "HERC1",
+      "HFM1",
+      "HGFAC",
+      "HIC1",
+      "HK1",
+      "HLA-A",
+      "HLA-B",
+      "HLA-DQA1",
+      "HLA-DQB1",
+      "HLA-DRB5",
+      "HLMR1",
+      "HMGN1",
+      "HMGXB4",
+      "HNF1A",
       "HNF1A-AS1",
       "HNF4A",
+      "HORMAD2",
+      "HOXB3",
+      "HPN",
+      "HPR",
+      "HSPA4",
+      "HTT",
+      "IDE",
+      "IFT80",
+      "IGF1",
+      "IGF2R",
+      "IKZF3",
+      "IL10RA",
+      "IL1RN",
+      "IL38",
+      "ILRUN",
+      "INHBA",
+      "INKILN",
+      "INPP4B",
+      "INPP5A",
+      "INSIG1-DT",
+      "INSIG2",
+      "INSR",
+      "IRAG1",
+      "IRS1",
+      "ITCH",
+      "ITGA1",
+      "ITGB6",
+      "ITIH3",
+      "JAZF1",
+      "JMJD1C",
+      "JMY",
+      "KAT5",
+      "KBTBD8",
+      "KCNJ2",
+      "KCNK17",
+      "KCNK3",
+      "KCNU1",
+      "KDM4B",
+      "KDSR",
+      "KIF13B",
+      "KLF12",
+      "KLF13",
+      "KLF14",
+      "KLF15",
+      "KLF2-DT",
+      "KLHDC7A",
+      "KLHL31",
+      "KMT2E",
+      "KMT5A",
+      "KPNB1",
+      "KRAS",
+      "KRT78",
+      "L3MBTL3",
+      "LAMB1",
+      "LAMC1",
+      "LASP1",
+      "LCORL",
+      "LCTL",
+      "LDLR",
+      "LEPR",
+      "LGR6",
+      "LHCGR",
+      "LILRA5",
+      "LINC00243",
+      "LINC00299",
+      "LINC00466",
+      "LINC00511",
+      "LINC00824",
+      "LINC00880",
+      "LINC01091",
+      "LINC01122",
+      "LINC01153",
+      "LINC01169",
+      "LINC01221",
+      "LINC01235",
+      "LINC01301",
+      "LINC01344",
+      "LINC01524",
+      "LINC01605",
+      "LINC01808",
+      "LINC01830",
+      "LINC02068",
+      "LINC02490",
+      "LINC02603",
+      "LINC02694",
+      "LINC02941",
+      "LINC02950",
+      "LINC03078",
+      "LINGO2",
+      "LIPA",
+      "LIPG",
+      "LITAF",
+      "LMAN1L",
+      "LMF1",
+      "LNROP",
+      "LNX1",
+      "LPA",
+      "LPAR1",
+      "LPAR5",
       "LPL",
+      "LRBA",
+      "LRMDA",
+      "LRRK2-DT",
+      "LYPLAL1-AS1",
+      "LYZ",
+      "LZTS1",
+      "MACO1",
+      "MAF",
+      "MAFB",
+      "MAFF",
+      "MAFTRR",
+      "MAGOH3P",
+      "MAP1A",
+      "MAP3K4",
+      "MAP3K6",
+      "MAPK10",
+      "MAPK8IP1",
+      "MARCHF8",
+      "MARCO",
+      "MARK2",
+      "MBD3L1",
+      "MBL2",
+      "MBTD1",
+      "MC4R",
+      "MCC",
+      "MCM6",
+      "MEGF9",
+      "MEIS1",
+      "MET",
+      "MGA",
+      "MGAT5",
+      "MGRN1",
+      "MICAL3",
+      "MIDEAS",
+      "MIMS1",
+      "MIMT1",
+      "MIR122",
+      "MIR4733HG",
+      "MISO1",
+      "MITF",
+      "MLXIPL",
+      "MLYCD",
+      "MMAB",
+      "MON2",
+      "MPPED2",
+      "MSI2",
+      "MSRA-DT",
+      "MTARC1",
+      "MTSS1",
+      "MTTP",
+      "MTUS1",
+      "MUC2",
+      "MYBL2",
+      "MYCT1",
+      "MYLIP",
+      "NAT2",
+      "NCDN",
+      "NDC1",
+      "NDRG2",
+      "NECTIN1-DT",
+      "NEDD4L",
+      "NEGR1",
+      "NEO1",
+      "NFAT5",
+      "NFE2L3",
+      "NFIA",
+      "NFIB",
+      "NIBAN1",
+      "NINL",
+      "NIPSNAP1",
+      "NKX3-1",
+      "NOSTRIN",
+      "NPC1",
+      "NR1H3",
+      "NR1H4",
+      "NR1I2",
+      "NR5A2",
+      "NRDC",
+      "NRL",
+      "NRP1",
+      "NRXN3",
+      "NSD1",
+      "NTSR1",
+      "NUCKS1",
+      "NUDT3",
+      "NXPH1",
+      "NYNRIN",
+      "OIT3",
+      "OPRL1",
+      "OR51A5P",
+      "OR8J1",
+      "OTUD7B",
+      "P2RX3",
+      "PABPC4",
+      "PACRG",
+      "PALM3",
+      "PARP6",
+      "PATL2",
+      "PCBP1-AS1",
+      "PCCB",
       "PCIF1",
+      "PCM1",
+      "PCNPP2",
+      "PCSK5",
+      "PCSK6",
+      "PCSK9",
+      "PDE3A",
+      "PDE3B",
+      "PDE4C",
+      "PDGFC",
+      "PDGFD",
+      "PDXDC1",
+      "PEMT",
+      "PEPD",
+      "PEX6",
+      "PGS1",
+      "PHC1",
+      "PHF11",
+      "PID1",
+      "PIK3R1",
+      "PINX1",
+      "PKD2L1",
+      "PKN3",
+      "PLA2G12A",
+      "PLA2G12B",
+      "PLA2G3",
+      "PLA2G6",
+      "PLCE1",
+      "PLD1",
+      "PLEC",
+      "PLEKHG1",
+      "PLIN1",
+      "PLXND1",
+      "PNKD",
+      "PNLIPRP2",
+      "PNPLA3",
+      "POC5",
+      "POLR1HASP",
+      "POR",
+      "PPARG",
+      "PPIF",
+      "PPM1A",
+      "PPP1R13B",
+      "PPP1R3B-DT",
+      "PPP2R2A",
+      "PPP4R1",
+      "PPP5C",
+      "PPP6R2",
+      "PRDM1",
+      "PRKAG1",
+      "PRKAG3",
+      "PRKAR2B",
+      "PRKCE",
+      "PRKN",
+      "PRMT6",
+      "PROX2",
+      "PRSS38",
+      "PSG3",
+      "PSKH1",
+      "PSMD12",
+      "PSMG1",
+      "PTBP1",
+      "PTEN",
+      "PTGER3",
+      "PTPN3",
+      "PTPRJ",
+      "PXK",
+      "QARS1",
+      "QKI",
+      "QRICH2",
+      "R3HDM2",
+      "RAB10",
       "RAB11B",
-      "TTC39B"
+      "RAB1A",
+      "RAB21",
+      "RABEP1",
+      "RAPGEF3",
+      "RBBP5",
+      "RBFADN",
+      "RBMS2",
+      "RCN3",
+      "RER1",
+      "RETREG3",
+      "RFLNA",
+      "RFX4",
+      "RGS17",
+      "RIC8B",
+      "RIGI",
+      "RILPL2",
+      "RMI1",
+      "RN7SL140P",
+      "RNA5SP69",
+      "RNF111",
+      "RNF150",
+      "RNF157",
+      "RNF168",
+      "RNF212B",
+      "RNU6-200P",
+      "ROR1",
+      "RORA",
+      "RP1",
+      "RPH3A",
+      "RPL31",
+      "RPL31P12",
+      "RPSAP52",
+      "RRAGC",
+      "RRBP1",
+      "RREB1",
+      "RSPO3",
+      "RTRAF",
+      "RXRA",
+      "SACS",
+      "SARM1",
+      "SBNO1",
+      "SCAF4",
+      "SCARB1",
+      "SCCPDH",
+      "SEC16A",
+      "SECISBP2L",
+      "SERPINA1",
+      "SERTAD2",
+      "SESN1",
+      "SETBP1",
+      "SETD5",
+      "SF3B4",
+      "SH2D4A",
+      "SH3YL1",
+      "SHROOM3",
+      "SIM1",
+      "SIPA1",
+      "SIPA1L3",
+      "SKAP1",
+      "SKI",
+      "SLC12A2",
+      "SLC12A2-DT",
+      "SLC12A4",
+      "SLC16A9",
+      "SLC17A2",
+      "SLC25A19",
+      "SLC25A29",
+      "SLC25A30",
+      "SLC25A31",
+      "SLC26A2",
+      "SLC2A2",
+      "SLC33A1",
+      "SLC39A8",
+      "SLC67A1",
+      "SLC9B1",
+      "SLCO1B1",
+      "SMAD3",
+      "SMAD7",
+      "SMIM14-DT",
+      "SMIM20",
+      "SNX10",
+      "SNX11",
+      "SNX13",
+      "SNX14",
+      "SNX27",
+      "SNX8",
+      "SORCS2",
+      "SORL1",
+      "SOS2",
+      "SP1",
+      "SPATA20",
+      "SPDYE7P",
+      "SPON1",
+      "SPRY4",
+      "SPRY4-AS1",
+      "SPTA1",
+      "SPTLC3",
+      "SPTY2D1",
+      "SSBP3",
+      "SSH1",
+      "SSPN",
+      "SSPN-AS1",
+      "ST13",
+      "ST3GAL4",
+      "STAB1",
+      "STAT5B",
+      "STMN1",
+      "STX1B",
+      "STXBP3",
+      "SULT2A1",
+      "SUN2",
+      "SYNE2",
+      "SYTL1",
+      "TAOK2",
+      "TBC1D13",
+      "TBC1D3JP",
+      "TCEA3",
+      "TCF12",
+      "TESK2",
+      "TET2",
+      "TF",
+      "TFG",
+      "THADA",
+      "THNSL2",
+      "THOC1-DT",
+      "THOP1",
+      "THRB",
+      "TM4SF5",
+      "TM6SF2",
+      "TMEM106B",
+      "TMEM147",
+      "TMEM175",
+      "TMEM59L",
+      "TMEM70",
+      "TMPRSS11E",
+      "TMPRSS5",
+      "TMPRSS6",
+      "TNFAIP8",
+      "TNKS",
+      "TNKS2",
+      "TNPO1",
+      "TP53",
+      "TPM1",
+      "TPRA1",
+      "TRAM2-AS1",
+      "TRANK1",
+      "TRIB1AL",
+      "TRIM2",
+      "TRIM31",
+      "TRIM5",
+      "TRMU",
+      "TRPS1",
+      "TSC22D2",
+      "TSHZ2",
+      "TTC38",
+      "TTC39B",
+      "TUBD1",
+      "TULP1",
+      "TXNDC11",
+      "UBASH3B",
+      "UBE2E2",
+      "UBE2L3",
+      "UBE3B",
+      "UGT1A1",
+      "UGT1A11P",
+      "UGT2B10",
+      "UGT2B15",
+      "UGT2B25P",
+      "UNC5CL",
+      "USP3",
+      "USP39",
+      "USP53",
+      "VCAN",
+      "VEGFA",
+      "VEGFB",
+      "VGLL3",
+      "VIM",
+      "VLDLR",
+      "VN1R1",
+      "VN1R11P",
+      "VPS53",
+      "WDR20",
+      "WDR72",
+      "WDR81",
+      "XPO1",
+      "XRN1",
+      "YLPM1",
+      "ZBTB10",
+      "ZBTB41",
+      "ZC3H11B",
+      "ZC3H4",
+      "ZCCHC8",
+      "ZDHHC18",
+      "ZDHHC24",
+      "ZFHX3",
+      "ZFP28-DT",
+      "ZFPM1",
+      "ZFPM2",
+      "ZHX3",
+      "ZNF148",
+      "ZNF160",
+      "ZNF283",
+      "ZNF285",
+      "ZNF329",
+      "ZNF341",
+      "ZNF385B",
+      "ZNF404",
+      "ZNF423",
+      "ZNF487",
+      "ZNF652-AS1",
+      "ZNF746",
+      "ZNF76",
+      "ZNF800",
+      "ZNF846",
+      "ZPR1",
+      "ZRANB3",
+      "ZSCAN23"
+    ],
+    "categories": [
+      "Functional / high-impact variant (Tier B)",
+      "LDL cholesterol (GWAS index variant)",
+      "Lipoprotein(a) (GWAS independent variant)",
+      "Triglycerides (GWAS index variant)"
     ],
-    "categories": [],
     "clinvar_count": 0,
     "pathogenic_count": 0,
     "benign_count": 0
   },
   "compilation": {
     "compile_success": true,
-    "compiled_by": "marketplace-server",
-    "compiler_version": "just-dna-compiler 0.7.0",
-    "ensembl_reference": "just-dna-seq/ensembl_variations",
-    "compiled_at": "2026-09-26T23:44:28Z",
+    "compiled_by": null,
+    "compiler_version": "just-dna-compiler 0.7.2",
+    "ensembl_reference": null,
+    "compiled_at": "2026-11-04T09:01:31Z",
     "warnings": [
-      "This module records no closure: nothing in it states that authoring is finished, so a consumer cannot tell a spec still being edited from one its author considers done. Run `just-dna-compiler close <spec-dir>` when the module is complete — closing is a deliberate act, it is never stamped by a passing check, and editing any authored file afterwards drops the closure again. Compiling without one is a warning today; requiring it is filed for 1.0 (RM73)."
+      "VRS allele identity covers 1745/1750 allele(s) in resolution.csv (100%) — 5 carry no ga4gh:VA. id. Anything keying on the VA sees only the covered fraction.",
+      "  5 allele(s): an indel or MNV: justification needs the reference sequence, so only the enricher can mint it (re-run it online)"
+    ],
+    "carried": [
+      "VRS allele identity covers 1745/1750 allele(s) in resolution.csv (100%) — 5 carry no ga4gh:VA. id. Anything keying on the VA sees only the covered fraction.",
+      "  5 allele(s): an indel or MNV: justification needs the reference sequence, so only the enricher can mint it (re-run it online)"
     ],
-    "carried": [],
     "warnings_summary": {
-      "module_not_closed": 1
+      "vrs_coverage_incomplete": 2
     },
     "dropped_rows": {},
     "resolution_mode": "strict",
     "fully_resolved": true,
-    "resolution_subjects": 45,
+    "resolution_subjects": 3186,
     "expanded_keys": 0,
     "expanded_rows": 0,
-    "resolution_signature": "sha256:f686b6fbe101a8bd720e3cde10acde2accc7c436cdc343082ed87e5569bdb985",
+    "resolution_signature": "sha256:0b11116334606c147116e6b644013dd9e317df5fa24534e987b1b368e58de8d2",
     "resolution_sources": [
       "cache"
     ],
-    "vrs_alleles": 24,
-    "vrs_alleles_identified": 24,
+    "vrs_alleles": 1750,
+    "vrs_alleles_identified": 1745,
     "positional_rows": 0,
     "positional_rows_placed": 0
   },
-  "frequency": null,
+  "frequency": {
+    "signature": "sha256:b5eced295ef864a9f41ffcb5a033bdb0995ca6ed704128c7fab74d0e74330105",
+    "sources": [
+      "gnomad"
+    ],
+    "datasets": [
+      "gnomad_v4.1_joint"
+    ],
+    "populations": [
+      "global",
+      "afr",
+      "ami",
+      "amr",
+      "asj",
+      "eas",
+      "fin",
+      "mid",
+      "nfe",
+      "remaining",
+      "sas"
+    ],
+    "row_count": 15000,
+    "variant_count": 1750
+  },
   "gene_metrics": null,
   "gene_validity": null,
   "clinical_assertions": null,
   "gwas_effects": null,
   "expression_effects": null,
   "literature": {
-    "signature": "sha256:58e76f27c8d2b992796b85848329bfcccea0a1a2f094b42ee2081312138a2d8e",
+    "signature": "sha256:4b87a6a95b0224dd8b6b7768c06f7249e98edffc7ae14bab9e784d61710f66cb",
     "sources": [
       "pubmed"
     ],
-    "row_count": 37,
-    "resolved_count": 37,
+    "row_count": 45,
+    "resolved_count": 45,
     "missing_count": 0,
-    "open_access_count": 19,
+    "open_access_count": 22,
     "abstract_only_count": 0,
     "quotes_authored": 0,
     "quotes_found": 0,
-    "quotes_unchecked": 37
+    "quotes_unchecked": 45
   },
   "clin_sig_concordance": null,
   "sources": {
-    "signature": "sha256:b1c5043ccc97b5c15683fcdc1c63de32c6da8e270295619f2c4954817ed8332f",
+    "signature": "sha256:9a8b8fd5943172acf8898b6828e361cc677fca41edd1371fa301624d18f76b7b",
     "sources": [
-      "ensembl"
+      "ensembl",
+      "gnomad"
     ],
     "layers": [
+      "frequency",
       "resolution"
     ],
     "licenses": [
-      "Apache-2.0"
+      "Apache-2.0",
+      "CC0-1.0"
     ],
     "attributions": [
-      "Ensembl (https://www.ensembl.org)"
+      "Ensembl (https://www.ensembl.org)",
+      "gnomAD, Broad Institute (https://gnomad.broadinstitute.org)"
+    ],
+    "notices": [
+      "CC0 public-domain dedication for the primary exome/genome data; attribution requested but not required. Users agree not to attempt to reidentify participants. Some layered annotations carry their own terms (SpliceAI is CC BY-NC 4.0, academic/non-commercial)."
     ],
-    "notices": [],
     "share_alike_layers": [],
     "noncommercial_layers": [],
     "unknown_terms_sources": [],
@@ -124,37 +1004,19 @@
     ],
     "commercial_use": true,
     "redistribution": true,
-    "row_count": 1
+    "row_count": 2
   },
   "verification": {
-    "signature": "sha256:37a0d67fbf16969a77af04294072b8cc74e0397fc5300250cf03d8d020be5bf4",
-    "module_hash": "sha256:ebee2be955f078d131c91c4b93e6f3257fcd91ecb541ac1d753f2a306a4c1cb1",
-    "producer": "just-dna-enricher 0.7.0",
-    "produced_at": "2026-09-26T23:44:25Z",
-    "closure": null,
+    "signature": "sha256:5ea902a260ab64a4c4f7af896d4a1bf8b5c930ae3af30981312dc6e579d34917",
+    "module_hash": "sha256:6e30a1268026adc354342eacb9f1d4a95b0ffbc37a22be5fa18a2c0a4d2eaf0f",
+    "producer": "just-dna-enricher 0.7.3",
+    "produced_at": "2026-11-04T09:01:17Z",
+    "closure": {
+      "closed_at": "2026-11-04T09:01:26Z",
+      "closed_by": "A. Kulaga (maintainer); AI agent (just-module-creator), 2026 rebuild",
+      "signature": null
+    },
     "checks": [
-      {
-        "check": "citation_existence",
-        "subjects": 37,
-        "findings": 0,
-        "skipped": null,
-        "detail": null,
-        "source": "pubmed",
-        "release": null,
-        "checked_at": "2026-09-26T17:35:11Z",
-        "producer": "just-dna-enricher 0.7.2"
-      },
-      {
-        "check": "citation_identifier",
-        "subjects": 0,
-        "findings": 0,
-        "skipped": "nothing_to_check",
-        "detail": "none of 37 citation(s) carries an authored DOI or PMC id, so there was nothing to compare against PubMed's own",
-        "source": "pubmed",
-        "release": null,
-        "checked_at": "2026-09-26T17:35:11Z",
-        "producer": "just-dna-enricher 0.7.2"
-      },
       {
         "check": "clinical_significance",
         "subjects": 0,
@@ -163,8 +1025,8 @@
         "detail": null,
         "source": "clinvar",
         "release": "clinvar_2026-06-27",
-        "checked_at": "2026-09-26T23:44:25Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "dataset_currency",
@@ -174,8 +1036,8 @@
         "detail": "the module records no release, so it makes no claim about where its rows came from",
         "source": null,
         "release": null,
-        "checked_at": "2026-09-26T23:44:25Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "evidence_status_currency",
@@ -185,8 +1047,8 @@
         "detail": "this module records no citation drafted from CIViC's API, so there is no recorded curation status to re-ask about",
         "source": "civic",
         "release": null,
-        "checked_at": "2026-09-26T23:44:25Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "genome_build_agreement",
@@ -196,19 +1058,8 @@
         "detail": "the GRCh37 service is the only thing that can tell an old-assembly coordinate from a wrong ref, and there is no local GRCh37 data",
         "source": "ensembl-grch37",
         "release": null,
-        "checked_at": "2026-09-26T23:44:25Z",
-        "producer": "just-dna-enricher 0.7.0"
-      },
-      {
-        "check": "provenance_quote",
-        "subjects": 0,
-        "findings": 0,
-        "skipped": "nothing_to_check",
-        "detail": "no provenance quote or regex on any citation, so none of them asked this question",
-        "source": "europepmc",
-        "release": null,
-        "checked_at": "2026-09-26T17:35:11Z",
-        "producer": "just-dna-enricher 0.7.2"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "published_refutation",
@@ -218,19 +1069,19 @@
         "detail": "no authored direction sits beside a published refutation (basis accepted)",
         "source": "civic",
         "release": "civic_01-Sep-2026",
-        "checked_at": "2026-09-26T23:44:25Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "reference_allele",
-        "subjects": 15,
+        "subjects": 0,
         "findings": 0,
-        "skipped": null,
-        "detail": null,
+        "skipped": "offline",
+        "detail": "no sequence access this run, so no authored ref was compared",
         "source": "seqrepo",
         "release": null,
-        "checked_at": "2026-09-26T17:35:00Z",
-        "producer": "just-dna-enricher 0.7.2"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "rsid_coordinate_agreement",
@@ -240,62 +1091,67 @@
         "detail": "no row authors both an rsID and a coordinate, so the module makes no pair claim to compare — this is not a comparison that found nothing",
         "source": "ensembl",
         "release": null,
-        "checked_at": "2026-09-26T23:44:25Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:01:17Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "rsid_currency",
-        "subjects": 15,
+        "subjects": 0,
         "findings": 0,
-        "skipped": null,
+        "skipped": "not_requested",
         "detail": null,
         "source": "dbsnp",
         "release": null,
-        "checked_at": "2026-09-26T17:35:00Z",
-        "producer": "just-dna-enricher 0.7.2"
+        "checked_at": "2026-11-04T09:01:17Z",
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