thrombophilia 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/thrombophilia/README.md

@@ -0,0 +1,115 @@
+# Thrombophilia — inherited blood-clotting risk (v2.0.0)
+
+This module reads the places in your DNA that change the chance of a blood clot forming in a vein
+(venous thromboembolism, VTE: deep vein thrombosis or a clot in the lungs). It covers the classic
+inherited thrombophilias (factor V Leiden, the prothrombin change), rare disease-causing changes in the
+three natural "brake" genes of clotting (antithrombin *SERPINC1*, protein C *PROC*, protein S *PROS1*),
+and the common risk spots found by the largest genetic studies of VTE up to 2025.
+
+Most of the common spots change risk by only a few percent each. A result here is not a diagnosis:
+age, body weight, surgery, long immobility, cancer, pregnancy and hormone medicines matter far more,
+and a clotting blood test, not a DNA file, is how a deficiency is confirmed.
+
+## What is in it
+
+| Tier | What | rsIDs | Rows | Source |
+|---|---|---|---|---|
+| A | every genome-wide-significant lead of Ghouse et al. 2023 (93 loci; 1 dropped, 2 already legacy rows) | 90 new (+2 legacy) | 270 | PMID 36658437, Supplementary Table 2 |
+| A | loci genome-wide significant in Thibord et al. 2022 lying >500 kb from every Ghouse lead | 48 | 144 | PMID 36154123, GWAS Catalog v2 |
+| A | GBMI 2025 novel loci with an expressible allele and consistent direction | 2 | 6 | PMID 40554366, Table 1 |
+| B | functional variants: *F5* rs4524, *ABO* non-O rs8176719, *PROCR* rs867186 | 3 | 9 | PMIDs 31420334, 38561338 |
+| B | *SERPINC1*/*PROC*/*PROS1* changes ClinVar classifies Pathogenic or Pathogenic/Likely pathogenic with ≥2 review stars | 72 | 144 | ClinVar (snapshot 2026-06-27 via eutils/registry); ORs PMIDs 29452444, 7742536, 40029645 |
+| C | Olga Borysova's original expert-curated rows, kept verbatim | 8 | 24 | legacy studies.csv |
+| | **total** | **223** | **597** | 244 study rows, 31 papers, 146 genes |
+
+## Selection rule
+
+1. **Anchor**: Ghouse J et al., *Nat Genet* 2023 (PMID 36658437), 81,190 VTE cases and 1,419,671 controls
+   from six cohorts, 93 independent loci at p<5×10⁻⁸. All 93 lead variants were taken with the paper's
+   effect allele, EAF and per-allele log-OR (beta). Positions in that table are GRCh37, so rows are
+   authored by rsID only and placed on GRCh38 by enrichment.
+2. **Merged loci**: Thibord F et al., *Circulation* 2022 (PMID 36154123). Associations at p<5×10⁻⁸ from the
+   combined discovery+replication analyses (cross-ancestry GCST90797305, European GCST90244158, African
+   GCST90244159, Hispanic GCST90244160; discovery-only GCST90797304 excluded) whose GRCh38 position is
+   more than 500 kb from every retained Ghouse lead were clustered at 500 kb, and the smallest-p variant
+   with a usable effect allele and beta was kept per cluster (59 clusters → 48 kept).
+3. **GBMI**: the 4 potentially novel loci of the GBMI multipopulation GWAS (PMID 40554366, Table 1);
+   2 kept. The 34 known GBMI loci sit in a supplement no reachable host serves; they are known loci and
+   were not re-added.
+4. **Tier B** as in the table; the 72 ClinVar variants are every SERPINC1/PROC/PROS1 record that is
+   Pathogenic or Pathogenic/Likely pathogenic, ≥2 stars, has an rsID and a single matching allele
+   (SERPINC1 28, PROC 29, PROS1 15). rs2227624 (*SERPINC1*, 3★) is already a Ghouse lead and is scored once.
+5. **Drops**: strand-ambiguous A/T or C/G SNPs whose effect-allele frequency does not settle the strand;
+   effect alleles not among the variant's alleles; a direction not replicated; structural alleles;
+   LD proxies of a kept functional variant. The full list is in `REBUILD_REPORT.md`.
+
+## Weights — two scales in one module
+
+- **Rows with `curator = ai-agent:module-rebuild-2026`** (all Tier A and B rows): `weight = −ln(OR)` for VTE,
+  additive per allele and oriented on the risk-increasing allele (where a study reported the
+  lower-risk allele, its OR was inverted) — one copy of the risk allele = −ln(OR per allele), two
+  copies = −2·ln(OR), two copies of the lower-risk allele = 0 (`state = neutral`), 3 decimals. All these
+  weights are therefore ≤ 0; negative = higher risk than the lower-risk homozygote.
+  `effect_size`/`effect_allele` on each row give the per-allele OR and the allele it refers to.
+  Tier-B deficiency variants use the published gene-level carrier OR (antithrombin 14.0; protein C 6.5;
+  protein S loss-of-function 14.01, other protein S 1.977), capped to [−3, 3]. Only carrier genotypes
+  are authored for these rare variants; non-carriers get no row.
+- **Rows with the module default curator (`just-dna-seq`, `expert-curated`)** are Olga Borysova's 2019-era
+  rows on her own curator-set scale (−2 … 0). They were not rescaled.
+- The two scales are not interchangeable, and the module's summed "net weight" also double-counts a few
+  signals that appear twice (ABO, F11, PROCR, fibrinogen; see `weighting.note`). Read rows, not the sum.
+
+## Limits
+
+- Effect sizes come mostly from people of European ancestry; Thibord adds African, Hispanic and some
+  Asian ancestry, and one locus (*COL6A2*) is African-ancestry-specific.
+- Five Thibord loci are on the X chromosome. Men carry one X, so a DNA file may show a man as
+  homozygous; those rows are written for two copies.
+- Rare deficiency rows use gene-level risks; individual variants (for example antithrombin type II
+  heparin-binding-site variants) can carry lower risk. Rare positions are where DNA files most often err.
+- Positions of indels follow the resolver's left-aligned representation (e.g. rs8176719 is G/GC at
+  9:133257520).
+
+## Origin and review
+
+Version 1.x was curated by Olga Borysova (dna-seq/just_thrombophilia). Version 2.0.0 (2026-11-03) is an
+AI-assisted Data + Evidence pass that added Tier A/B rows on the rules above; no human has reviewed the
+new rows yet, and no legacy value was edited. Enrichment ran on the polygon registry (`remote_derive`,
+target test); literature was checked with `enrich_literature_pass` (31/31 PMIDs resolve).
+
+## 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 | 75 (3) |
+| A | Well established, small effect (research grade): genome-wide significant in the anchor GWAS and in ≥ 1 further publication, same direction | 20 (1) |
+| B | Single-study signal, small effect (research grade): genome-wide significant in the anchor GWAS only | 124 (0) |
+| C | Early evidence (research only): not genome-wide significant for this trait | 1 (1) |
+| D | Not supported: contradicted, or null in large GWAS / meta-analysis | 3 (3) |
+
+S holds factor V Leiden, prothrombin G20210A, the ABO non-O tag and the ClinVar antithrombin, protein C and protein S deficiency 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 7 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 |
+|---|---|---|---|
+| rs1799963 | A/A | conclusion | the homozygote (A/A) row named 'GA carriers' |
+| rs1800790 | A/A | conclusion | the homozygote (A/A) row named the 'GA variant' |
+| rs2519093 | C/T | conclusion | the heterozygote (C/T) row repeated the T/T sentence ('TT genotype is associated...') |
+| rs6025 | T/T | conclusion | the Leiden homozygote row opened with the C/C sentence ('CC genotype is NOT associated with increased risk') |
+| rs6025 | C/T | conclusion | the genotype was written 'CA', mixing the genomic reference base with the coding-strand Leiden base |
+| rs1799889 | G/G | weight | the row's own text says that for G/G (5G/5G) the risk of blood clotting is not increased, while the row carried a risk weight (-0.3) in this venous-thrombosis module |
+
+### Reference rows for the deficiency variants
+
+Each of the 72 ClinVar antithrombin, protein C and protein S deficiency variants has a neutral row for the reference genotype, so a person who does not carry the variant sees that result rather than no row.

data/thrombophilia/annotations.parquet

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data/thrombophilia/frequencies.parquet

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data/thrombophilia/literature.parquet

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data/thrombophilia/logs/authoring.log

@@ -0,0 +1,7 @@
+2026-11-04T07:36:44Z authored rs1799963 conclusion='A/A: AA carriers have 6.74x risk of thrombosis [PMID 23900608].' (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
+2026-11-04T07:36:46Z authored rs1800790 conclusion='A/A: AA variant is associated with increased cardiovascular diseases risk.' (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
+2026-11-04T07:36:48Z authored rs2519093 conclusion='C/T: CT genotype carries one copy of the risk allele T and is associated with an increased venous thromboembolism risk.' (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
+2026-11-04T07:36:51Z authored rs6025 conclusion='T/T: TT carriers (factor V Leiden homozygotes; coding-strand AA) have 11.4x higher risk of thrombosis. Oral contraceptives usage increase risk...; C/T: CT carriers (factor V Leiden heterozygotes; coding-strand GA) have 3.5-4.4x risk of thrombosis. Oral contraceptives usage increase thromb...' (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
+2026-11-04T07:36:53Z authored rs1799889 weight='G/G: 0.0' (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
+2026-11-04T07:36:56Z authored rs1799889 state='G/G: neutral' (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
+2026-11-04T07:48:01Z table variants.csv rows='added 72 reference-homozygote rows (weight 0.0, state neutral), one per Tier-B ClinVar SERPINC1/PROC/PROS1 site; 0 rows removed; 597 -> 669 genotype rows' (source resolution.csv (GRCh38 REF allele per site); the compiler reported that 72 sites stated two genotypes but not the reference homozygote, so a person carrying neither alternate matched nothing; each added row uses the REF allele that resolution.csv records for its site and copies the site metadata of its carrier rows) by=AI agent (just-module-creator), 2026 rebuild human_reviewed=false

data/thrombophilia/manifest.json

@@ -2,15 +2,15 @@
   "manifest_version": "1.0",
   "schema_version": "1.0",
   "identity": {
-    "namespace": "just-dna-seq",
+    "namespace": null,
     "name": "thrombophilia",
-    "version": "1.1.0",
+    "version": "2.0.0",
     "version_coerced_from": null,
-    "canonical_id": "just-dna-seq/thrombophilia@1.1.0"
+    "canonical_id": null
   },
   "display": {
     "title": "Thrombophilia",
-    "description": "Inherited blood-clotting risk variants (Factor V Leiden, prothrombin, and related loci)",
+    "description": "Inherited blood-clotting risk, from Factor V Leiden to deficiency genes",
     "report_title": "Thrombophilia Risk",
     "icon": "droplets",
     "icon_set": "fomantic",
@@ -21,96 +21,301 @@
   "method": "expert-curated",
   "license": null,
   "authority_precedence": [],
-  "weighting": null,
-  "owner": "just-dna-seq",
+  "weighting": {
+    "scale": "Mixed, by row origin. Rows with curator=just-dna-seq / method=expert-curated (Tier C, 24 rows, 8 rsIDs) keep Olga Borysova's original curator-set scale (roughly -2..0, not derived from a formula). All rows with curator=ai-agent:module-rebuild-2026 use weight = -ln(OR_genotype) for venous thromboembolism, additive per allele, oriented on the risk-increasing allele (the study's per-allele OR is inverted where its effect allele lowered risk, so every OR used is >1): one copy of the risk allele = -ln(OR_allele), two copies = -2*ln(OR_allele), homozygous for the lower-risk allele = 0.0 (state neutral); rounded to 3 dp. Negative = higher VTE risk, positive = lower risk (protective). Tier-B rare deficiency variants use a published gene-level carrier OR and are capped to [-3, 3].",
+    "method": "Tier A (method=gwas-lead-2026): every independent genome-wide-significant (p<5e-8) lead variant from Ghouse et al. 2023 Nat Genet (PMID 36658437; 81,190 cases / 1,419,671 controls; 93 loci; per-allele log-OR from Supplementary Table 2), plus every locus genome-wide significant in Thibord et al. 2022 Circulation (PMID 36154123; GWAS Catalog GCST90797305 cross-ancestry combined, GCST90244158 European, GCST90244159 African, GCST90244160 Hispanic) whose lead lies more than 500 kb from every retained Ghouse lead (one smallest-p variant per 500-kb cluster), plus the GBMI 2025 Blood Adv novel loci (PMID 40554366, Table 1) with an expressible SNV and a consistent direction. Tier B (method=functional-variant-2026 / clinvar-plp-2026): F5 rs4524 (PMID 31420334), ABO non-O rs8176719 and PROCR rs867186 (PMID 38561338), and SERPINC1/PROC/PROS1 variants that ClinVar classifies Pathogenic or Pathogenic/Likely pathogenic with >=2 review stars and a single resolvable allele (SERPINC1 OR 14.0, PMID 29452444; PROC OR 6.5, PMID 7742536; PROS1 loss-of-function OR 14.01 and other PROS1 OR 1.977, PMID 40029645). Tier C: legacy rows kept verbatim.",
+    "note": "Not comparable with other modules' weights. Weights are not a calibrated polygenic score: several loci are represented by more than one row (ABO: rs2519093 legacy, rs635634 Tier A, rs8176719 Tier B; F11: rs2036914 legacy, rs2289252 Tier A; PROCR: rs6060308 Tier A, rs867186 Tier B; fibrinogen: rs1800790 legacy FGB, rs2066864 Tier A FGG), so a summed net weight double-counts those signals. Legacy rows are on a different, larger scale than the formula rows. Tier-B rare-variant ORs are gene-level carrier estimates, not variant-specific."
+  },
+  "owner": null,
   "authors": [],
-  "authorship": [],
+  "authorship": [
+    {
+      "who": "Olga Borysova",
+      "role": "created",
+      "kind": [
+        "human",
+        "human_expert"
+      ],
+      "at": null
+    },
+    {
+      "who": "ai-agent:module-rebuild-2026",
+      "role": "edited",
+      "kind": [
+        "ai",
+        "agent"
+      ],
+      "at": "2026-11-03"
+    }
+  ],
   "created_at": null,
-  "published_at": "2026-09-26T23:44:13Z",
+  "published_at": null,
   "stats": {
-    "variant_count": 8,
-    "weights_rows": 24,
-    "study_count": 27,
-    "gene_count": 8,
+    "variant_count": 223,
+    "weights_rows": 669,
+    "study_count": 244,
+    "gene_count": 146,
     "genes": [
+      "A2ML1",
+      "A4GALT",
+      "ABCA6",
       "ABO",
+      "AEBP2",
+      "AFAP1",
+      "AK5",
+      "AKIRIN2",
+      "AKT3",
+      "ALOX12",
+      "ANGPT1",
+      "APOC1P1",
+      "APOH",
+      "ARHGAP24",
+      "ARHGAP4",
+      "ARHGAP6",
+      "ARHGEF28",
+      "ARID4A",
+      "ATXN2",
+      "BANK1",
+      "C3orf22",
+      "C4BPB",
+      "CALCRL",
+      "CARMIL1",
+      "CD93",
+      "CDK6",
+      "CELSR2",
+      "CFDP1",
+      "CHD3",
+      "CIART",
+      "CLMB",
+      "COL6A2",
+      "COPZ1",
+      "CPS1",
+      "CRIM1",
+      "CSRNP1",
+      "DHODH",
+      "DHRS3",
+      "EFEMP1",
+      "ENTPD4-DT",
+      "ETV6",
+      "F10",
       "F11",
       "F2",
+      "F2RL3",
       "F5",
+      "F9",
+      "FADS2",
+      "FAM168A",
+      "FAM47B",
+      "FCGR3B",
+      "FER",
       "FGB",
+      "FGG",
+      "FTO",
+      "FUNDC2",
+      "GJA1",
+      "GP6",
+      "GRK5",
+      "H6PD",
+      "HCG9",
+      "HLA-DQA1",
+      "HMGB3P26",
+      "HSPA4",
+      "HSPE1P19",
+      "INTS4",
       "ITGB3",
+      "JAZF1",
+      "KNG1",
+      "LEKR1",
+      "LIFR",
+      "LIN54",
+      "LINC01800",
+      "LINC02103",
+      "LINC02680",
+      "LNPEP",
+      "MAMSTR",
+      "MAPT-AS1",
+      "MCTP2",
+      "MIR1587",
+      "MIR4708",
+      "MLLT10",
+      "MS4A4A",
       "MTHFR",
-      "SERPINE1"
+      "MTOR",
+      "NAV1",
+      "NDE1",
+      "NEK4",
+      "NPC1",
+      "NPR3",
+      "OR4C13",
+      "OSGIN1",
+      "P2RX3",
+      "PDIA3",
+      "PEPD",
+      "PLCE1",
+      "PLCG2",
+      "PLEK",
+      "PNPLA3",
+      "PPP1R3B",
+      "PROC",
+      "PROCR",
+      "PROS1",
+      "PTPRR",
+      "QSER1",
+      "RBPMS",
+      "RCOR1",
+      "REST",
+      "RFTN2",
+      "RFX2",
+      "RORA",
+      "RSPH6A",
+      "SBNO1",
+      "SCARA5",
+      "SERPINA1",
+      "SERPINC1",
+      "SERPINE1",
+      "SERPINE2",
+      "SETD1A",
+      "SLC20A2",
+      "SLC35D2",
+      "SLC44A2",
+      "SMG6",
+      "SOX6",
+      "ST3GAL4",
+      "STAB2",
+      "STXBP5",
+      "SYK",
+      "SYN3",
+      "TAB1",
+      "TAOK1",
+      "TC2N",
+      "TENT5C",
+      "TGFB2",
+      "TRIM58",
+      "TSPAN15",
+      "VWF",
+      "XKR5",
+      "XXYLT1",
+      "YLPM1",
+      "ZBTB16",
+      "ZBTB7B",
+      "ZFPM1",
+      "ZFPM2",
+      "ZMIZ1",
+      "ZNF444"
+    ],
+    "categories": [
+      "Tier A: GWAS lead (Ghouse 2023)",
+      "Tier A: distinct locus (Thibord 2022)",
+      "Tier A: novel locus (GBMI 2025)",
+      "Tier B: ClinVar P/LP",
+      "Tier B: functional 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": "2026-09-26T23:44:13Z",
+    "compiled_by": null,
+    "compiler_version": "just-dna-compiler 0.7.2",
+    "ensembl_reference": null,
+    "compiled_at": "2026-11-04T09:01:09Z",
     "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 341/357 allele(s) in resolution.csv (96%) — 16 carry no ga4gh:VA. id. Anything keying on the VA sees only the covered fraction.",
+      "  16 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 341/357 allele(s) in resolution.csv (96%) — 16 carry no ga4gh:VA. id. Anything keying on the VA sees only the covered fraction.",
+      "  16 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": 24,
+    "resolution_subjects": 669,
     "expanded_keys": 0,
     "expanded_rows": 0,
-    "resolution_signature": "sha256:25223241b8f875afcd3822e0ff384cf60b9201e16b2c1257117e3bef3a6b4e40",
+    "resolution_signature": "sha256:5c8167c58cec025674cabc90fa1c7a09152307896d533db019d582f293d39f3f",
     "resolution_sources": [
-      "cache"
+      "cache",
+      "clinvar"
     ],
-    "vrs_alleles": 12,
-    "vrs_alleles_identified": 12,
+    "vrs_alleles": 357,
+    "vrs_alleles_identified": 341,
     "positional_rows": 0,
     "positional_rows_placed": 0
   },
-  "frequency": null,
+  "frequency": {
+    "signature": "sha256:eb1c8b984b04030f961779b5af32ffd0831a227ac6236130511377cffc4ed043",
+    "sources": [
+      "gnomad"
+    ],
+    "datasets": [
+      "gnomad_v4.1_joint"
+    ],
+    "populations": [
+      "global",
+      "afr",
+      "ami",
+      "amr",
+      "asj",
+      "eas",
+      "fin",
+      "mid",
+      "nfe",
+      "remaining",
+      "sas"
+    ],
+    "row_count": 2837,
+    "variant_count": 357
+  },
   "gene_metrics": null,
   "gene_validity": null,
   "clinical_assertions": null,
   "gwas_effects": null,
   "expression_effects": null,
   "literature": {
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+    "signature": "sha256:c830586e82a7731120f6141ceb582413ababe826d7cf338e2ad5d01382e039e4",
     "sources": [
       "pubmed"
     ],
-    "row_count": 24,
-    "resolved_count": 24,
+    "row_count": 31,
+    "resolved_count": 31,
     "missing_count": 0,
-    "open_access_count": 3,
+    "open_access_count": 5,
     "abstract_only_count": 0,
     "quotes_authored": 0,
     "quotes_found": 0,
-    "quotes_unchecked": 24
+    "quotes_unchecked": 31
   },
   "clin_sig_concordance": null,
   "sources": {
-    "signature": "sha256:b1c5043ccc97b5c15683fcdc1c63de32c6da8e270295619f2c4954817ed8332f",
+    "signature": "sha256:7f9c619658f9637f8c76b0a5cb66cbf1ad5570f86974ce5d7b27e5df85f85f68",
     "sources": [
-      "ensembl"
+      "clinvar",
+      "ensembl",
+      "gnomad"
     ],
     "layers": [
+      "frequency",
       "resolution"
     ],
     "licenses": [
-      "Apache-2.0"
+      "Apache-2.0",
+      "CC0-1.0",
+      "public-domain"
     ],
     "attributions": [
-      "Ensembl (https://www.ensembl.org)"
+      "ClinVar, NCBI (https://www.ncbi.nlm.nih.gov/clinvar/)",
+      "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).",
+      "US-government work, no copyright asserted. NCBI asks that ClinVar be cited and states the records are submitter assertions, not a clinical diagnosis."
     ],
-    "notices": [],
     "share_alike_layers": [],
     "noncommercial_layers": [],
     "unknown_terms_sources": [],
@@ -120,37 +325,19 @@
     ],
     "commercial_use": true,
     "redistribution": true,
-    "row_count": 1
+    "row_count": 3
   },
   "verification": {
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-    "module_hash": "sha256:5fce340f69e54da9c3b8ce633dda98e2774af88876f91b4f4f8866a638a33b81",
-    "producer": "just-dna-enricher 0.7.0",
-    "produced_at": "2026-09-26T23:44:11Z",
-    "closure": null,
+    "signature": "sha256:5ea902a260ab64a4c4f7af896d4a1bf8b5c930ae3af30981312dc6e579d34917",
+    "module_hash": "sha256:171300f015fd1ceb842465ddf2e30ffcef7c907816317ddccabc8eb8192cbb92",
+    "producer": "just-dna-enricher 0.7.3",
+    "produced_at": "2026-11-04T09:00:58Z",
+    "closure": {
+      "closed_at": "2026-11-04T09:01:05Z",
+      "closed_by": "A. Kulaga (maintainer); AI agent (just-module-creator), 2026 rebuild",
+      "signature": null
+    },
     "checks": [
-      {
-        "check": "citation_existence",
-        "subjects": 24,
-        "findings": 0,
-        "skipped": null,
-        "detail": null,
-        "source": "pubmed",
-        "release": null,
-        "checked_at": "2026-09-26T17:33:06Z",
-        "producer": "just-dna-enricher 0.7.2"
-      },
-      {
-        "check": "citation_identifier",
-        "subjects": 0,
-        "findings": 0,
-        "skipped": "nothing_to_check",
-        "detail": "none of 24 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": "2026-09-26T17:33:06Z",
-        "producer": "just-dna-enricher 0.7.2"
-      },
       {
         "check": "clinical_significance",
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@@ -159,8 +346,8 @@
         "detail": null,
         "source": "clinvar",
         "release": "clinvar_2026-06-27",
-        "checked_at": "2026-09-26T23:44:11Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "dataset_currency",
@@ -170,8 +357,8 @@
         "detail": "the module records no release, so it makes no claim about where its rows came from",
         "source": null,
         "release": null,
-        "checked_at": "2026-09-26T23:44:11Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "evidence_status_currency",
@@ -181,8 +368,8 @@
         "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": "2026-09-26T23:44:11Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "genome_build_agreement",
@@ -192,19 +379,8 @@
         "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": "2026-09-26T23:44:11Z",
-        "producer": "just-dna-enricher 0.7.0"
-      },
-      {
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-        "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": "2026-09-26T17:33:06Z",
-        "producer": "just-dna-enricher 0.7.2"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "published_refutation",
@@ -214,19 +390,19 @@
         "detail": "no authored direction sits beside a published refutation (basis accepted)",
         "source": "civic",
         "release": "civic_01-Sep-2026",
-        "checked_at": "2026-09-26T23:44:11Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "reference_allele",
-        "subjects": 8,
+        "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": "2026-09-26T17:32:59Z",
-        "producer": "just-dna-enricher 0.7.2"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "rsid_coordinate_agreement",
@@ -236,62 +412,67 @@
         "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": "2026-09-26T23:44:11Z",
-        "producer": "just-dna-enricher 0.7.0"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       },
       {
         "check": "rsid_currency",
-        "subjects": 8,
+        "subjects": 0,
         "findings": 0,
-        "skipped": null,
+        "skipped": "not_requested",
         "detail": null,
         "source": "dbsnp",
         "release": null,
-        "checked_at": "2026-09-26T17:32:59Z",
-        "producer": "just-dna-enricher 0.7.2"
+        "checked_at": "2026-11-04T09:00:58Z",
+        "producer": "just-dna-enricher 0.7.3"
       }
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   "inputs": [
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+      "sha256": "sha256:f94d51fd09ae994d40c6a1a0ab04381534dba91565cca56d422ab1e1822119bc",
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-      "sha256": "sha256:f5b1136a4737ae9ef7c48579c054dc20836c6a467018c48f3d100a8b286efad4",
-      "size": 10773
+      "sha256": "sha256:9956f888f63b77acd2103dea3d39a45aabefa4067e3cc05295525a94636af3e8",
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+  "content_signature": "sha256:e463659d3ca231e156cd950800c9a416a761014a0b1b5b0a6e00ce97c51e230e",
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+    "digest": "sha256:d9edac1a82a5fdba5bab78a0c499dfea4b03fe025eb2dc8a86ea61f252217ba8",
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+        "sha256": "sha256:cf8e0535ce7aaf2ef50b37b0c125017b80d52afa4e577020b3861e864d492dae",
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@@ -305,33 +486,38 @@
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-        "sha256": "sha256:fd6913c2b6d909e0fa354fcde37d95aea6ae4d236b06b22e7047dbe4fdf024f1",
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   "logs": [
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-      "sha256": "sha256:2176f12edfdc1f530ef323cfae4ef49d9b5a1f1f947b63cb199c59747bb65ab2",
-      "size": 983
+      "name": "logs/authoring.log",
+      "sha256": "sha256:75ed7f1554ba73091f0edf46739e285905fbf5d21117b5092f6d85ba469875db",
+      "size": 2508
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-      "sha256": "sha256:f0748b1b7bd5096ad2d0f53f6046b6e64087619bc66f44b222f52a0f744441b2",
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+      "sha256": "sha256:f024993e1c19ad258545c100966848361cbcf6bbf21f8952a619779bc7267691",
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-      "sha256": "sha256:cedd36956d2f5556a348b3e66f364b0dee9419cf5f2ac569f25260b17216d57d",
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+      "sha256": "sha256:9afda45659e16fc25e5f349d7ed956c5eab632d0c384385b5ec23d3a8ef6b02c",
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+    },
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+      "sha256": "sha256:5ac54eac3f0e1e89120292a83f601f61552654df0bdc49d21c53d58502503da9",
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     {
       "name": "clin_sig_concordance.csv",
@@ -345,17 +531,28 @@
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-      "sha256": "sha256:288b7c81407b72e49f2581af04efca839f54f6a70d7919cd1940c582b498a1bd",
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   ],
-  "provenance": null,
+  "provenance": {
+    "generator": "just-module-creator",
+    "model": null,
+    "agent_version": null,
+    "item_count": 7,
+    "file": "provenance.json",
+    "sha256": "sha256:722f0985f67da021e6a7280d09b6d6bd906924f5b433373bc4cc183053a06602"
+  },
   "panel": null,
   "logo": {
     "name": "logo.png",
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     "size": 109928
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-  "readme": null,
+  "readme": {
+    "name": "README.md",
+    "sha256": "sha256:b1b25a71abeb5bd93bfad86947047562d7c29a4dd09bdb563df94a9d40238588",
+    "size": 8912
+  },
   "signature": null
 }

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