| Framework | Points | ||||||
|---|---|---|---|---|---|---|---|
| Evidence category | Scoring step | Category (GWAS / non-GWAS) | Points | Max | Count | Total | Counted |
| Study design | Sets thresholds used in 3A and 4 | GWAS | – | – | 0 | No points | |
| Non-GWAS | – | 3 | |||||
| Allele / haplotype | Step 1A: Allele or Haplotype | Allele | 0 | 2 | 3 | 0 | 0 |
| Haplotype | 2 | 0 | |||||
| Step 1B: Allele Resolution | 1-field | 0 | 3 | 0 | 0 | ||
| 2-field, P-group | 1 | 0 | |||||
| 3-field, G-group | 2 | 0 | |||||
| 4-field | 3 | 0 | |||||
| Step 1C: Zygosity | Monoallelic (heterozygous) | 0 | 0.5 | 3 | 0 | ||
| Biallelic (homozygous) | 0.5 | 0 | |||||
| Step 1D: Phase | Phase confirmed | 0.5 | 0.5 | 0 | 0 | ||
| Typing method | Step 2: Typing Method | Tagging / Tag SNPs / Microarrays | 0 | 5 | 0 | 0 | 0 |
| Serological | 1 | 0 | |||||
| Imputation | 2 | 0 | |||||
| Molecular genotyping (low and high resolution) / Whole exome sequencing / RNA sequencing | 3 | 0 | |||||
| Sanger-sequencing-based typing / Whole gene sequencing | 4 | 0 | |||||
| Whole genome sequencing / Panel-based next generation sequencing (> 50x coverage) / Long-read sequencing | 5 | 0 | |||||
| Statistical evidence | Step 3A: Statistics (p-value) | ≥0.0001 / ≥0.05 | 0 | 2 | 0 | 0 | 0 |
| <0.0001 / <0.05 | 0.5 | 0 | |||||
| <5E-8 / <0.01 | 1 | 0 | |||||
| <1E-11 / <0.0005 | 1.5 | 0 | |||||
| <1E-14 / <0.0001 | 2 | 0 | |||||
| Step 3B: Multiple Testing Correction | Overall correction for multiple testing | 1 | 2 | 0 | 0 | ||
| 2-step p-value correction | 2 | 0 | |||||
| Step 3C: Statistics (Effect Size)* | OR/RR ≥2 or ≤0.5; Beta ≥0.5 or ≤-0.5 | 1 | 2 | 0 | 0 | ||
| CI does not cross 1 (OR/RR) or 0 (beta) | 1 | 0 | |||||
| Cohort | Step 4: Cohort Size | <1000 / <50 | 0 | 4 | 0 | 0 | 0 |
| 1000–2499 / 50–99 | 1 | 0 | |||||
| 2500–4999 / 100–249 | 2 | 0 | |||||
| 5000–9999 / 250–499 | 3 | 0 | |||||
| ≥10000 / ≥500 | 4 | 0 | |||||
| Phenotype | Step 5: Additional Phenotypes | Has specific disease-related phenotype | 2 | 2 | 0 | 0 | 0 |
| Only disease tested | 0 | 0 | |||||
| Multipliers | Step 6A: Weighing Association (multiplier) | Significant association with disease | ×1 | – | 0 | Applied per publication; ×0 in PMID: 37638053, 30946743, 30729696 | |
| No significant association | ×0 | 3 | |||||
| Step 6B: Low Field Resolution (multiplier) | 1-field resolution | ×0.5 | – | 0 | |||
| > 1-field resolution | ×1 | 3 | |||||
| Total score | 0 | ||||||
*OR (Odds Ratio), RR (Relative Risk), CI (Confidence Interval).
*Step 3C can award points for both categories (OR/RR/Beta and CI), granting a total of up to 2.