Population & Clinical Databases

intermediate

Key Genomic Databases at a Glance

🌍gnomAD v4.1807K exomes + 76K genomes | 8 ancestries | Gold standard for AF filtering | AF>1% usually benign

🏥ClinVar2.6M variants | 1800+ submitters | Free access | P/LP/VUS/LB/B classifications | Expert panel 4-star

📚OMIMGene-disease relationships | 25K+ entries | Phenotypic series | Inheritance patterns | Free via API

💼HGMD Pro400K+ disease mutations | Subscription | More complete than ClinVar | Used in clinical labs

gnomAD v4.1 (2024) - 807,162 exomes + 76,215 genomes; 8 ancestry groups; strongest AF resource
gnomAD AF threshold: variants with AF>0.01 (1%) in any population unlikely to cause rare Mendelian disease
1000 Genomes Phase 3 - 2,504 individuals from 26 populations; used for population stratification in GWAS
UK Biobank - 500,000 participants; phenotype + genotype; WES data for 469,000
TOPMed - 180,000 WGS; diverse populations; deep coverage allele frequencies
ALFA (dbSNP) - Allele Frequency Aggregator; integrates multiple studies
ABraOM - Brazilian population frequencies; important for South American patients

ClinVar - NCBI; 2.6M variants with interpretations from 1,800+ submitters; free access
OMIM - Online Mendelian Inheritance in Man; gene-disease relationships; phenotypic series
HGMD Professional - >400,000 disease mutations; subscription required; more comprehensive than ClinVar
LOVD - Leiden Open Variation Database; gene-specific locus databases for BRCA1, MLH1, etc.
ClinGen - expert-curated gene-disease validity and variant interpretations
DECIPHER - chromosomal imbalances and SNVs in rare disease patients; phenotype matching
MedGen - aggregates clinical relationships from ClinVar, OMIM, GTR

UniProt - protein function, domains, and disease associations
dbNSFP v4.7 - 30+ pathogenicity scores for all possible missense variants
COSMIC v97 - 30M somatic mutations; cancer type associations; tier 1 cancer genes
CIViC - Clinical Interpretation of Variants in Cancer; actionable variant database
PharmGKB - pharmacogenomics; drug-gene interactions
SpliceAI (Illumina) - deep learning splice prediction; delta >0.5 = strong evidence
AlphaMissense (Google DeepMind) - pathogenicity prediction for 71M missense variants