dbsnp-databaselisted

# dbSNP Database ## Overview NCBI dbSNP is the primary public repository for short human genetic variants, cataloguing over 1 billion SNPs, indels, and MNVs with allele frequencies, functional annotations, and cross-references to ClinVar, gnomAD, and 1000 Genomes. Variants are identified by stable rsIDs (reference SNP cluster IDs). Access is free via two APIs: the legacy NCBI E-utilities and the newer NCBI Variation Services REST API, which returns structured JSON. ## When to Use - Looking up allele frequencies and variant class for a known rsID - Searching all dbSNP variants in a gene or chromosomal region by name or coordinates - Resolving rsIDs to genomic coordinates (GRCh38/GRCh37) and HGVS notation - Checking whether a variant of interest has clinical significance links to ClinVar entries - Batch-fetching hundreds of rsIDs efficiently using epost+efetch history server - Cross-referencing a list of variant positions to dbSNP rsIDs for downstream annotation - For clinical pathogenicity classifications use `clinvar-database`; dbSNP provides IDs and frequency but not curated clinical significance - For population frequency stratified by ancestry use `gnomad-database`; dbSNP MAF is a single aggregate frequency ## Prerequisites - **Python packages**: `requests`, `pandas`, `matplotlib`, `xml.etree.ElementTree` (stdlib) - **Data requirements**: rsIDs (`rs80357906`), gene symbols, or chromosomal coordinates - **Environment**: internet connection; NCBI Entrez email required