GA4GH Beacon v2 Explorer

Federated genomic variant discovery API and interactive explorer for Enigma Clinical Platform (ECP) with Saudi PDPL small-cell privacy suppression.

GA4GH v2.0.0
Beacon Specification: GRCh38 / hg38
Genome Assembly: Saudi PDPL (k=5)
Privacy Standard: 3 Active Routes
Federated Endpoints

Sovereign Privacy Compliance & Small-Cell K-Anonymity (Saudi PDPL)

Enigma Clinical Platform (ECP) implements the international GA4GH Beacon v2.0.0 protocol under the regulatory framework of the Saudi Personal Data Protection Law (PDPL). To eliminate any re-identification risks for individuals harboring ultra-rare variants, queries returning fewer than 5 alleles (1 ≤ AC < 5) return exists: true for federated discovery but suppress exact counts and frequencies.

Interactive Presets

Select a curated benchmark variant to test boolean discovery, exact cohort counts, or small-cell privacy suppression.

Genomic Variant Query Builder

Search for sequence-resolved alleles and short variations in the Enigma Clinical Platform (ECP) GRCh38 exome cohort.

Assembly ID

GRCh38 / hg38 canonical

Reference Name (Chr)

1–22, X, Y, M

Start Position (1-based / 0-based)

Genomic coordinate

Reference Bases (REF)

A, C, G, T or indel

Alternate Bases (ALT)

Alternative allele

Requested Granularity

Production Beacon v2 Endpoints

Standard GA4GH Beacon v2 REST API contracts hosted at clinical.enigmagenomics.com.

GET/api/beacon/v2/info

Returns institutional metadata, welcome URLs, supported GA4GH Beacon v2 specifications, open-access datasets, and sovereign governance terms.

GETPOST/api/beacon/v2/g_variants

Genomic variant discovery query. Supports assemblyId, referenceName, start, referenceBases, alternateBases, and requestedGranularity (boolean, count, record). Enforces Saudi PDPL privacy.

Active in query builder above. Fully federated with CORS support.

GET/api/beacon/v2/filtering_terms

Returns supported alphanumeric and ontology filtering terms across Human Phenotype Ontology (HPO), MONDO, ClinVar, ACMG/AMP criteria, and Sequence Ontology.

Ontology & Alphanumeric Filtering Terms

Beacon v2 filtering terms supported by Enigma Clinical Platform (ECP) for phenotypic and clinical variant stratification.

All

HPO

MONDO

ClinVar

ACMG

Consequence

Zygosity

Term Identifier	Label / Description	Category	Type	Applicable Scopes
`HP:0001250`	Seizures	HPO	ontology	individuals biosamples
`HP:0001249`	Intellectual disability	HPO	ontology	individuals biosamples
`HP:0000252`	Microcephaly	HPO	ontology	individuals biosamples
`HP:0001257`	Spasticity	HPO	ontology	individuals biosamples
`HP:0001627`	Abnormal heart morphology	HPO	ontology	individuals biosamples

Term Identifier	Label / Description	Category	Type	Applicable Scopes
`HP:0001250`	Seizures	HPO	ontology	individuals biosamples
`HP:0001249`	Intellectual disability	HPO	ontology	individuals biosamples
`HP:0000252`	Microcephaly	HPO	ontology	individuals biosamples
`HP:0001257`	Spasticity	HPO	ontology	individuals biosamples
`HP:0001627`	Abnormal heart morphology	HPO	ontology	individuals biosamples
`HP:0000007`	Autosomal recessive inheritance	HPO	ontology	individuals biosamples
`HP:0001518`	Small stature / growth restriction	HPO	ontology	individuals biosamples
`HP:0000505`	Visual impairment	HPO	ontology	individuals biosamples
`HP:0000365`	Hearing impairment	HPO	ontology	individuals biosamples
`HP:0002011`	Morphological abnormality of central nervous system	HPO	ontology	individuals biosamples
`MONDO:0000508`	Mendelian disease	MONDO	ontology	individuals biosamples
`MONDO:0005044`	Sickle cell anemia	MONDO	ontology	individuals biosamples
`MONDO:0009688`	Meckel syndrome	MONDO	ontology	individuals biosamples
`MONDO:0011571`	Sanjad-Sakati syndrome	MONDO	ontology	individuals biosamples
`MONDO:0009061`	Cystic fibrosis	MONDO	ontology	individuals biosamples
`MONDO:0019052`	Inborn errors of metabolism	MONDO	ontology	individuals biosamples
`MONDO:0007254`	Hereditary breast ovarian cancer syndrome	MONDO	ontology	individuals biosamples
`MONDO:0005041`	Familial hypercholesterolemia	MONDO	ontology	individuals biosamples
`ClinVar:Pathogenic`	Pathogenic	ClinVar	alphanumeric	g_variants
`ClinVar:Likely_pathogenic`	Likely Pathogenic	ClinVar	alphanumeric	g_variants
`ClinVar:VUS`	Variant of Uncertain Significance	ClinVar	alphanumeric	g_variants
`ClinVar:Likely_benign`	Likely Benign	ClinVar	alphanumeric	g_variants
`ClinVar:Benign`	Benign	ClinVar	alphanumeric	g_variants
`ACMG:PVS1`	Null variant in gene where loss of function is known disease mechanism	ACMG	alphanumeric	g_variants
`ACMG:PS1`	Same amino acid change as established pathogenic variant	ACMG	alphanumeric	g_variants
`ACMG:PM2`	Absent or extremely rare in population databases	ACMG	alphanumeric	g_variants
`ACMG:PP3`	Multiple lines of in silico computational evidence predict damaging effect	ACMG	alphanumeric	g_variants
`ACMG:BA1`	Allele frequency above 5% in population databases (Stand-Alone Benign)	ACMG	alphanumeric	g_variants
`ACMG:BS1`	Allele frequency greater than expected for disorder	ACMG	alphanumeric	g_variants
`SO:0001587`	stop_gained (nonsense)	Consequence	ontology	g_variants
`SO:0001589`	frameshift_variant	Consequence	ontology	g_variants
`SO:0001575`	splice_donor_variant	Consequence	ontology	g_variants
`SO:0001574`	splice_acceptor_variant	Consequence	ontology	g_variants
`SO:0001583`	missense_variant	Consequence	ontology	g_variants
`SO:0001819`	synonymous_variant	Consequence	ontology	g_variants
`ECP:homozygous`	Homozygous state observed in cohort	Zygosity	custom	g_variants individuals
`ECP:heterozygous`	Heterozygous carrier state observed in cohort	Zygosity	custom	g_variants individuals
`ECP:founder_variant`	Verified founder mutation in cohort	Zygosity	custom	g_variants

GA4GH Beacon v2 Explorer

Sovereign Privacy Compliance & Small-Cell K-Anonymity (Saudi PDPL)

Interactive Presets

HBB c.20A>T (HbS)

BRAF V600E

FANCA Founder Variant

BRCA2 Frameshift

Absent Genomic Locus

Genomic Variant Query Builder

Production Beacon v2 Endpoints

Ontology & Alphanumeric Filtering Terms