Gallstones are hardened deposits of digestive fluid that form in the gallbladder. They can range in size and may cause no symptoms, or they can block bile ducts, causing intense abdominal pain, nausea, and inflammation. Risk factors include obesity, rapid weight loss, female sex, and genetic predisposition.
Score Details
This score comes from the PGS Catalog, an open repository of published polygenic scoring models used in genomic research.
- PGS ID
- PGS001256
- Score Name
- GBE_HC188
- Reported Trait
- Gallstones
- Additional Info
- https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC188
- Development Method
- snpnet
- Number of Variants
- 876
- Original Genome Build
- GRCh37
- Weight Type
- NR
- Release Date
- October 21, 2021
Source Publication
Significant sparse polygenic risk scores across 813 traits in UK Biobank.
Development Samples
Polygenic risk scores are developed against large reference datasets. This score was built using the UK Biobank, a biomedical cohort with genetic and health data from roughly 500,000 participants — large enough to identify reliable genetic associations.
| Ancestry | Sample Size | Country | Cohort |
|---|---|---|---|
| European(white British ancestry) | 269,704 | UK | UKB |
Ancestry Distribution
Development (269,704 individuals)
Evaluation (5 sample sets)
Performance Evaluations
Polygenic risk scores are usually developed and validated in populations of European ancestry. Predictive accuracy can vary across ancestries because of differences in genetic architecture, linkage disequilibrium patterns, and allele frequencies. For binary traits like disease risk, AUROC measures how well the score separates cases from controls (0.5 = random, 1.0 = perfect). Values substantially below the best-performing ancestry are highlighted to flag reduced transferability.
| AncestryThe broad ancestral population of the evaluation sample. | NNumber of individuals in the evaluation sample. | R²Proportion of variance explained by the full model (PGS + covariates). Higher is better. | PGS R²Proportion of variance explained by the PGS alone, without covariates. Isolates the predictive power of the genetic score. | AUROCArea Under the Receiver Operating Characteristic curve. Measures how well the score discriminates cases from controls. 0.5 = random, 1.0 = perfect. |
|---|---|---|---|---|
| African | 6,497 | 0.0497 | 0.0078 | 0.6869[0.6433, 0.7306] |
| East Asian | 1,704 | 0.0619 | 0.0006 | 0.6779[0.6058, 0.7500] |
| European | 24,905 | 0.0517 | 0.0275 | 0.6681[0.6516, 0.6845] |
| South Asian | 7,831 | 0.0581 | 0.0077 | 0.6874[0.6564, 0.7184] |
| European | 67,425 | 0.0548 | 0.0249 | 0.6723[0.6632, 0.6814] |
Covariates: age, sex, UKB array type, Genotype PCs
Downloads & Links
Frequently asked questions
Can I check my gallstones polygenic risk score with 23andMe data?
Yes. Upload a raw data file from 23andMe, AncestryDNA, MyHeritage, or tellmeGen, or a single-sample whole-genome VCF, and the Genomisaur Health Report computes PGS001256 along with the other scores in your report. Array files are imputed to roughly 30 million variants first. Results are ready in about 20 minutes, and no new DNA test is needed.
What does a high polygenic risk score for gallstones mean?
It means your genetic variants, added up, place you higher than most people in the reference population for gallstones. It is a statement about relative genetic predisposition, not a diagnosis: lifestyle, environment, and family history matter too, and many people with high scores never develop the condition.
Where does the PGS001256 score come from?
PGS001256 is listed in the PGS Catalog and was published by Tanigawa Y et al. in PLoS Genet (2022). It combines 876 genetic variants. Performance metrics and the ancestry of the study participants are shown on this page.
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.