Saudi cohort v1 · GRCh38 · 1,378 participants
Enigma Clinical Platform
Genomic evidence for variant interpretation and discovery.
Any spelling of a variant opens the same page. Press ⌘K (Ctrl K) to search from anywhere.
Enigma Genomics
- 1,378
- exomes and genomes
- 10M+
- high-confidence variants
- 58.9K+
- Saudi-enriched variants
- GRCh38
- reference build
Search examples
54 examples, one for each format the search box accepts. Select one to run it; coordinates are GRCh38 unless prefixed with hg19.
Genes and transcripts
Variant identifiers
HGVS
Regions
Structural variants and CNVs
Cytogenetics
Fusions and repeat expansions
Pharmacogenomics, phenotypes and diseases
What you can explore
Navigate across genes, fusions, variants, copy number alterations, repeat expansions, and clinical star evidence tiers.
Explore each variant class below. Clinical significance is labelled separately.
Genes & transcripts
Every cohort variant in a gene drawn on its canonical transcripts, with constraint metrics, missense tolerance, and linked reference annotations.
Open BRCA1Variants (SNVs & InDels)
Allele counts, frequencies and homozygotes in the cohort, with predicted consequences, in-silico scores (CADD, REVEL) and ClinVar records.
Open HBB c.20A>T (HbS)CNVs & Structural Variants
Large copy-number alterations, microdeletions, duplications, chromosomal anomalies, and mobile element insertions with breakpoint resolution.
Explore MYC duplicationRepeat Expansions (RE)
Clinical short-tandem-repeat loci (HTT, FMR1, C9ORF72) mapped with verified reference, intermediate, and pathogenic expansion thresholds.
Open HTT-CAG-42Star Alleles & PGx ⭐
Pharmacogenomic star alleles across actionable drug-metabolizing genes (CYP2C19, CYP2D6, DPYD, HLA-B) mapped to CPIC guidelines.
Search CYP2C19*2Gene fusions
Ordered gene partners, fusion evidence, protein domains, literature and clinical trial records in one view.
Open BCR::ABL1Cohort vs gnomAD
Compare cohort frequencies with gnomAD v4 genetic ancestry groups to identify variants enriched in the Saudi population or absent elsewhere.
Compare frequenciesPhenotypes & Diseases
Human Phenotype Ontology (HPO) terms and MONDO or Orphanet disease identifiers to connect clinical signs with genomic variation.
Search seizuresGenomic Architecture & Evidence Standards
Enigma Clinical connects population variation with clinical evidence and pharmacogenomics for research.
Variant classes and genomic context
Enigma Clinical integrates multiple genomic classes into a single reference catalogue, standardized on GRCh38:
- SNV & InDel
Single Nucleotide Variants & Small Indels
Over 713,000 quality-filtered sites annotated with functional consequences (VEP), CADD, REVEL, and SpliceAI scores.
- CNV & SV
Copy Number & Structural Variants
Deletions, duplications, chromosomal rearrangements, cytobands, and mobile-element insertions with exact breakpoint coordinates.
- RE / STR
Short Tandem Repeat Expansions
Pathogenic repeat loci for neurodegenerative and muscular disorders, including Huntington (HTT), Fragile X (FMR1), and ALS (C9ORF72).
- Fusion
Gene Fusions & Translocations
Oncogenic breakpoint fusions (e.g., BCR::ABL1, EML4::ALK) indexed by 5′ and 3′ partner genes and chromosome junctions.
Clinical Evidence Stars & Pharmacogenomics ⭐
Standardized interpretation frameworks ensure variant findings are ready for clinical contextualization:
- ★★★★
ClinVar 0–4 Star Review System
Variants categorized by curation rigor: Practice Guidelines (★★★★), Expert Panels (★★★), Multiple Submitters (★★), and Single Submitters (★).
- CPIC / PGx
Pharmacogenomics Star Alleles
Standardized star-allele nomenclature (e.g. CYP2C19*2, CYP2D6*4, SLCO1B1*5, HLA-B*57:01) to support precision medicine and dosage optimization.
- Saudi Baseline
Population-Specific Novelty
Over 58,900 variants observed in Saudi individuals are unrepresented in global reference datasets, providing an essential local baseline.
The data
Saudi cohort
- Release
- Saudi cohort v1
- Samples
- 1,378
- Sequencing
- Whole-exome sequencing
- Participants
- Healthy individuals and patients with childhood-onset genetic disorders
- Reference build
- GRCh38
- Quality control
- Genotypes with GQ < 20 removed; low-quality sites flagged
Reference data sources
- gnomAD v4(opens in a new tab)
Gene models, constraint metrics and global allele frequencies for comparison
- ClinVar(opens in a new tab)
Germline classifications and review status
- GENCODE / Ensembl(opens in a new tab)
Gene and transcript annotation (via gnomAD)
- MANE(opens in a new tab)
Matched Ensembl/RefSeq reference transcripts
- Ensembl VEP(opens in a new tab)
Variant consequence annotation
- GTEx(opens in a new tab)
Tissue expression (pext) shown on gene pages
- Human Phenotype Ontology(opens in a new tab)
Standardised phenotype terms
Work with the data
Request data access
Access is limited to approved institutions and researchers in accordance with ethical guidelines and data-sharing policies. Write to the data access team to apply.
sgp-data@enigmagenomics.comContribute data
Laboratories and research centres interested in contributing genomic data can submit a request after signing in.
Start a submission requestPartnerships
For institutional collaborations and formal partnerships with the Enigma Clinical team.
sgp-partnerships@enigmagenomics.comEnigma Clinical Platform is built and operated by Enigma Genomics, connecting population data and public genomic evidence for research and variant interpretation.