Each SCV contributes its submitted classification, review status, last assessment date, submitter, source order, assertion identity, and SCV version. Disease-scoped arbitration also uses the condition links attached to the SCV. Named policy profiles and per-call submitter exclusions can remove evidence without deleting it from the imported source tables.
Matching is case-insensitive for XML-derived policy views. Submitted labels are collapsed as follows.
| Policy bin | Submitted ClinVar labels |
|---|---|
| Pathogenic/Likely Pathogenic | Pathogenic; Likely pathogenic; Pathogenic, low penetrance; Likely pathogenic, low penetrance; Pathogenic/Likely pathogenic |
| Benign | Benign; Likely benign; Benign/Likely benign; protective |
| VUS | Uncertain significance; Uncertain risk allele |
| Unknown | every other or missing label |
Unknown rows are ineligible and do not enter the
denominator used below. This follows the actual upstream collection
path, which discards unknown classifications before arbitration.
The intended upstream qualified exclusion removes a benign submission
whose normalized submitter is exactly
illumina laboratory services; illumina. RClinVarbitration
applies that rule. At the pinned upstream commit, an inner-loop
continue does not actually remove that row; this package
follows the documented intent rather than that Python control-flow
accident.
The package then applies exclusions stored in
clinvar_policy_submitter_exclusions for the selected
profile. A row may apply to every classification from a submitter or to
one classification bin only. The Parquet export can add
submitter_exclusions for a blinded run. Names are trimmed
and matched case-insensitively; the imported evidence is unchanged.
XML can expose versioned assertion structure that is absent from the upstream flat-file row model. The XML policy views retain one row per assertion identity within each decision group, preferring the highest SCV version, then a stable assertion/source order. Disease-scoped deduplication includes the disease key. The flat-file differential reproducer intentionally does not add this XML-only step.
An eligible submission is called modern when either:
date_last_evaluated is on or after 2016-01-01; orpractice guideline or
reviewed by expert panel.If a decision group contains at least one modern submission, only modern submissions are retained. Otherwise, all eligible submissions are retained. A missing date is treated as 1970-01-01. Strong reviews are therefore never removed solely because their date is old or missing.
The views expose both eligible and retained counts and whether this filter was applied.
If any retained submission has review status
practice guideline or
reviewed by expert panel, the first such submission in
source order supplies the decision. This is an order rule, not a vote
and not a rule that always puts a practice guideline ahead of an earlier
expert-panel row. The source ordinal is retained explicitly so this
behavior is reproducible.
When no strong review is decisive, let:
The first matching rule wins:
Conflicting.VUS. This threshold is strictly greater than 60%.Pathogenic/Likely Pathogenic.Benign.VUS.VUS submissions are part of the denominator. This matters: six pathogenic, two benign, and two VUS submissions pass the rule (60% and 20%), whereas six pathogenic and three benign submissions fail the minority threshold.
Stars are calculated from the same retained evidence, but only pathogenic and benign bins can contribute:
no assertion criteria provided: 1 star;This is a maximum evidence level. A strong VUS submission can determine the classification through the strong-review rule, but it does not itself add stars, matching the pinned upstream implementation.
Disease-scoped decisions prefer a source condition identifier. The
normalized key is lower(database):identifier. Where no such
pair is available, the fallback order is ClinVar trait-set ID,
normalized disease name, then the package’s condition entity ID.
Canonical cross-references are selected in this order: MedGen, MONDO,
OMIM, Orphanet, MeSH, UMLS, then OMIM phenotypic series. These are
pragmatic grouping rules and are audited as deviations from NCBI’s own
aggregate semantics in the deviation
and differential audit.
The decision views retain policy/release/profile identity, source VCV and allele IDs, classification, stars, eligible and retained counts, distinct SCV and submitter counts, per-bin counts, modern-filter status, and the latest retained assessment date. Disease decisions additionally retain disease identity and name.
The March 2026 archived flat files were executed through both the pinned upstream 2.2.11 TSV code and this package’s flat reproducer. All 4,125,389 keys, classifications, and star values matched exactly. The manifest records input, code, configuration, and output digests.
The monthly XML and flat products are not row-equivalent: 16 shared
keys differ and 361 keys occur on only one path. Every key is classified
in the audit with source-row receipts. Of 377 total, 369 arise because
the flat classification is - while XML has a current
germline classification, one is a divergent three-row flat
representation of one XML SCV assertion, five use different source
vocabularies, and two are child locations of compound CYP2C19 alleles
excluded by the top-level allele compatibility export. These are
source-model and documented scope differences, not unexplained decision
arithmetic.
Use source tables to inspect a result rather than treating the projected label as sufficient evidence:
SELECT d.*, s.scv_accession, s.submitter_name, s.classification,
s.review_status, s.date_last_evaluated
FROM clinvar_policy_decisions d
JOIN clinvar_disease_submissions s
ON s.release_id = d.release_id
AND s.vcv_accession = d.vcv_accession
AND s.allele_id = d.allele_id
AND s.disease_key = d.disease_key
WHERE d.release_id = 'my-release'
AND d.vcv_accession = 'VCV000091629';