Resources

Enigma Clinical API

The 63 JSON endpoints behind the Enigma Clinical web application, with parameters, authentication and example requests.

Overview

Every endpoint answers JSON over HTTPS. Variant IDs are GRCh38 chrom-pos-ref-alt (for example 7-140753336-A-T). Most endpoints return public reference data, need no credentials and are cached at the CDN. The machine-readable description is at /api/openapi.json; import it into Postman, Insomnia or an OpenAPI client generator.

Cohort data needs a Firebase ID token in an Authorization: Bearer … header: any signed-in account for aggregate statistics, and an account approved by an administrator for row-level variant data. Get the token from the Firebase SDK (await auth.currentUser.getIdToken()) after signing in to Enigma Clinical; it expires after an hour. Cohort endpoints return aggregates only and never sample identifiers.

This API serves the web application. There are no API keys yet, no rate-limit guarantees, and response shapes may change between releases. Please respect the licence of each upstream source (see Data sources) and cite the platform when you use it.

PublicNo credentials needed.

Signed-in accountSend Authorization: Bearer <Firebase ID token> for any signed-in account.

Approved accountSend Authorization: Bearer <Firebase ID token> for a verified account approved by an administrator.

Search

Turn free text into genes, variants and other targets.

GET/api/search/Public

Gene and rsID suggestions

Fast suggestions for the search box (genes and rsIDs, via gnomAD). Other formats return no results and the parsed kind, so callers know to ask /api/resolve.

Caching: Server data cache and CDN.

Parameter	In	Description	Example
`q`required	query	Search text (truncated to a safe length).	`BRCA`

curl -s \
  "https://clinical.enigmagenomics.com/api/search/?q=BRCA"

GET/api/resolve/Public

Resolve any supported query

Turns any supported search format (gene, variant ID, rsID, HGVS c./p./g., ClinGen allele, region, cytoband, ISCN, SV, HPO/MONDO/OMIM/Orphanet ID …) into canonical targets: { query, kind, recognisedAs, results[], message? }.

Caching: Server data cache and CDN; explained misses are cached too.

Parameter	In	Description	Example
`q`required	query	Query in any supported format.	`NM_000546.6:c.743G>A`

curl -s \
  "https://clinical.enigmagenomics.com/api/resolve/?q=NM_000546.6%3Ac.743G%3EA"

Cohort

Saudi cohort data. Aggregates only; sample identifiers are never returned.

POST/api/hasura/Approved account

Read-only GraphQL proxy

Forwards a read-only GraphQL query to the Saudi cohort database. Mutations, subscriptions and introspection are rejected. Frequencies are stored as percentages.

Caching: Not cached.

curl -s \
  -X POST \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"target":"sgp","query":"query { exomes_samples24dec(where: {symbol: {_eq: \"HBB\"}}, limit: 5) { variant_id allele_count allele_number allele_frequency } }","variables":{}}' \
  "https://clinical.enigmagenomics.com/api/hasura/"

GET/api/igv/sgp/Approved account

Cohort variants in a window

Variant ID, cohort allele frequency (fraction) and first VEP consequence for every cohort variant in a window; used by the genome browser track.

Caching: Private browser cache only.

Parameter	In	Description	Example
`chrom`required	query	Chromosome without "chr".	`11`
`start`required	query	Window start (1-based).	`5226900`
`end`required	query	Window end.	`5227100`

curl -s \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  "https://clinical.enigmagenomics.com/api/igv/sgp/?chrom=11&start=5226900&end=5227100"

GET/api/insights/Signed-in account

Cohort statistics

Variants by consequence and ClinVar group, novelty against gnomAD, frequency spectrum, top genes and phenotype counts. Counts of fewer than five individuals are withheld.

curl -s \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  "https://clinical.enigmagenomics.com/api/insights/"

GET/api/knockouts/Approved account

Homozygous loss-of-function registry

Every cohort site with at least one homozygous individual and a predicted loss-of-function VEP consequence (transcript ablation, splice acceptor/donor, stop gained, frameshift, start lost): { terms[], rows[], truncated, generatedAt }. Site-level rows only (variant, gene, allele counts, homozygotes, gnomAD max AF, consequence, ClinVar); sample identifiers are never returned. LOFTEE confidence is not applied, so some sites are low-confidence LoF. `truncated` is true when the list hit its 30,000-row ceiling.

Caching: Private browser cache for an hour; the server keeps the assembled list for a day.

curl -s \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  "https://clinical.enigmagenomics.com/api/knockouts/"

GET/api/clinvar-discordance/Approved account

ClinVar discordance alerts

Cohort sites whose ClinVar germline classification the cohort argues against (P/LP above BA1 or BS1, P/LP homozygotes in dominant-only genes, B/LB loss-of-function in haploinsufficient genes), each with reason codes and a severity.

Caching: One day on the server; one hour in the browser (private). Sources: ClinVar, GenCC, ClinGen Dosage Sensitivity.

curl -s \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  "https://clinical.enigmagenomics.com/api/clinvar-discordance/"

GET/api/stats/Public

Headline counts

Live aggregate counts from the cohort table for the home page.

Caching: One day, server and CDN.

curl -s \
  "https://clinical.enigmagenomics.com/api/stats/"

GET/api/founder-variants/Approved account

Founder variant registry

ClinVar pathogenic or likely pathogenic cohort sites enriched at least 10× over the gnomAD v4 maximum genetic-ancestry-group AF, or absent from gnomAD with AC ≥ 2: { criteria, rows[], truncated, generatedAt }. Site-level rows only; frequencies are percentages.

Caching: One day on the server; private one hour in the browser.

curl -s \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  "https://clinical.enigmagenomics.com/api/founder-variants/"

Variant

Annotation and evidence for one GRCh38 small variant (chrom-pos-ref-alt).

GET/api/gnomad/variant/{id}/Public

gnomAD v4 variant

gnomAD v4 frequencies by genetic-ancestry group, consequences and ClinVar for one variant.

Caching: One day. Sources: gnomAD (ODbL).

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/gnomad/variant/7-140753336-A-T/"

GET/api/clinvar/variant/{id}/Public

Live ClinVar record

Germline classification, somatic clinical impact and oncogenicity, matched on the exact allele.

Sources: NCBI E-utilities (public domain).

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/clinvar/variant/7-140753336-A-T/"

GET/api/classification/variant/{id}/Public

Automated ACMG/AMP classification

Points-based germline classification from licence-free public evidence, with ClinGen CSpec rules where implemented and expert-panel classifications. Research use only; each source fails soft and unreachable sources are listed.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/classification/variant/7-140753336-A-T/"

GET/api/myvariant/variant/{id}/Public

In-silico predictors (dbNSFP)

Licence-free dbNSFP predictor scores via MyVariant.info. "No record" is `available: false`, not a 404.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/myvariant/variant/7-140753336-A-T/"

GET/api/protein/transcripts/{id}/Public

Transcript consequences

Every Ensembl and RefSeq transcript the variant falls in or near (Ensembl VEP): HGVS c./p., consequence, exon/intron, MANE flags.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/protein/transcripts/7-140753336-A-T/"

GET/api/gtex/variant/{id}/Public

GTEx eQTLs and sQTLs

Significant single-tissue eQTLs and sQTLs (GTEx V11) for the exact allele. Empty lists mean no significant QTL.

Caching: One week.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/gtex/variant/7-140753336-A-T/"

GET/api/variant-sv/{id}/Public

Structural context of a position

gnomAD-SV and exome CNV records overlapping the position, ClinGen dosage regions and genes containing it, and gnomAD coverage.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/variant-sv/7-140753336-A-T/"

GET/api/variant-sv/{id}/clinvar/Public

ClinVar SVs over a position

Live ClinVar structural records (≥ 50 bp) that overlap the variant’s span.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/variant-sv/7-140753336-A-T/clinvar/"

GET/api/rare-disease/variant/{id}/Public

Conditions for a variant

Conditions ClinVar records for the variant with MONDO, Orphanet and OMIM IDs, the aggregate classification per condition and the gene–disease validity of `gene`.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`
`gene`	query	Gene symbol hint from the page (optional).	`BRAF`

curl -s \
  "https://clinical.enigmagenomics.com/api/rare-disease/variant/7-140753336-A-T/?gene=BRAF"

Gene

Gene-level annotation, expression, somatic and structural context.

GET/api/gnomad/gene/{id}/Public

gnomAD gene annotation

Gene model, constraint and transcripts from gnomAD.

Caching: One day, server and CDN.

Parameter	In	Description	Example
`id`required	path	Gene symbol or Ensembl gene ID.	`ENSG00000157764`

curl -s \
  "https://clinical.enigmagenomics.com/api/gnomad/gene/ENSG00000157764/"

GET/api/gnomad/gene/{id}/clinvar/Public

ClinVar variants in a gene

ClinVar variants in the gene, via gnomAD.

Caching: One day.

Parameter	In	Description	Example
`id`required	path	Ensembl gene ID.	`ENSG00000157764`

curl -s \
  "https://clinical.enigmagenomics.com/api/gnomad/gene/ENSG00000157764/clinvar/"

GET/api/gnomad/gene/{id}/coverage/Public

gnomAD read depth over a gene

gnomAD v4 exome and genome read depth over the coding exons of the gene's MANE Select (else canonical) transcript: per-exon summaries and a binned profile.

Caching: One day. Sources: gnomAD (ODbL).

Parameter	In	Description	Example
`id`required	path	Ensembl gene ID or gene symbol.	`ENSG00000157764`

curl -s \
  "https://clinical.enigmagenomics.com/api/gnomad/gene/ENSG00000157764/coverage/"

GET/api/gnomad/gene/{id}/rmc/Public

Regional missense constraint

gnomAD v2.1.1 regional missense constraint (published on GRCh37; amino-acid ranges are build-independent). `status` says whether regions were found, the gene was searched without evidence, or it was not searched. 404 when gnomAD v2 has no such gene.

Caching: One day. Sources: gnomAD (ODbL).

Parameter	In	Description	Example
`id`required	path	Ensembl gene ID or gene symbol.	`ENSG00000157764`

curl -s \
  "https://clinical.enigmagenomics.com/api/gnomad/gene/ENSG00000157764/rmc/"

GET/api/gnomad/transcript/{id}/Public

Transcript

One transcript from gnomAD with its MANE Select / Plus Clinical status. RefSeq IDs are mapped through MANE.

Caching: One day.

Parameter	In	Description	Example
`id`required	path	Ensembl (ENST) or RefSeq (NM_) transcript ID.	`ENST00000646891`

curl -s \
  "https://clinical.enigmagenomics.com/api/gnomad/transcript/ENST00000646891/"

GET/api/gtex/gene/{id}/Public

GTEx tissue expression

Per-tissue TPM summaries with violin densities and median isoform expression (GTEx V11). 404 `{ notFound: true }` when GTEx has no such gene.

Caching: One week.

Parameter	In	Description	Example
`id`required	path	Ensembl gene ID or symbol.	`BRAF`
`chrom`	query	Picks between same-symbol genes (PAR).	`7`

curl -s \
  "https://clinical.enigmagenomics.com/api/gtex/gene/BRAF/?chrom=7"

GET/api/gene/{gene}/somatic/Public

Cancer-driver role and CIViC

IntOGen driver role and CIViC summary with evidence counts per molecular profile.

Sources: IntOGen, CIViC (CC0).

Parameter	In	Description	Example
`gene`required	path	HGNC gene symbol.	`BRAF`

curl -s \
  "https://clinical.enigmagenomics.com/api/gene/BRAF/somatic/"

GET/api/gene/{gene}/mutations/Public

Somatic mutations (TCGA)

Mutation frequency by cancer type and samples per residue / protein change across TCGA PanCancer Atlas, with protein length and Pfam domains. Counts only.

Parameter	In	Description	Example
`gene`required	path	HGNC gene symbol.	`BRAF`

curl -s \
  "https://clinical.enigmagenomics.com/api/gene/BRAF/mutations/"

GET/api/gene/{gene}/protein/Public

Protein length and Pfam domains

Reviewed human UniProt entry for the gene (accession, name, length) and its Pfam domains from InterPro. Feeds the gene-page protein lollipop.

Caching: One week. Sources: UniProt (CC BY 4.0), InterPro/Pfam (CC0).

Parameter	In	Description	Example
`gene`required	path	HGNC gene symbol.	`BRAF`

curl -s \
  "https://clinical.enigmagenomics.com/api/gene/BRAF/protein/"

GET/api/gene/{gene}/sv/Public

SVs and CNVs in a gene

gnomAD-SV v4 and exome CNV v4 records in the gene, with ClinGen dosage sensitivity for the gene and the curated regions it lies in.

Parameter	In	Description	Example
`gene`required	path	Gene symbol or Ensembl gene ID.	`PMP22`

curl -s \
  "https://clinical.enigmagenomics.com/api/gene/PMP22/sv/"

GET/api/protein/clinvar/{gene}/Public

ClinVar P/LP on protein codons

Pathogenic and likely pathogenic ClinVar variants of a gene placed on the codons of one transcript, with its coding intervals.

Parameter	In	Description	Example
`gene`required	path	HGNC gene symbol.	`BRAF`
`transcript`required	query	Ensembl transcript ID.	`ENST00000646891`

curl -s \
  "https://clinical.enigmagenomics.com/api/protein/clinvar/BRAF/?transcript=ENST00000646891"

GET/api/protein/uniprot/{accession}/Public

Protein features and structure

UniProt features, Pfam domains (InterPro), AlphaFold DB model with per-residue pLDDT and per-residue AlphaMissense means.

Parameter	In	Description	Example
`accession`required	path	UniProtKB accession.	`P15056`

curl -s \
  "https://clinical.enigmagenomics.com/api/protein/uniprot/P15056/"

GET/api/protein/cancer-counts/Public

Tumour mutations at a codon

Tumour mutations at one codon and in the whole protein across cBioPortal public studies.

Parameter	In	Description	Example
`entrez`required	query	NCBI Gene ID.	`673`
`codon`required	query	Codon number.	`600`
`length`required	query	Protein length in residues.	`766`

curl -s \
  "https://clinical.enigmagenomics.com/api/protein/cancer-counts/?entrez=673&codon=600&length=766"

GET/api/repeat/{locus}/Public

STR allele-size distributions

gnomAD v4 short-tandem-repeat allele sizes for one catalogued locus, by repeat unit and genetic-ancestry group.

Sources: gnomAD (ODbL).

Parameter	In	Description	Example
`locus`required	path	Catalogued repeat locus ID.	`HTT`

curl -s \
  "https://clinical.enigmagenomics.com/api/repeat/HTT/"

Structural variants

SVs, CNVs, insertions, MEIs and translocations.

GET/api/dosage/Public

ClinGen dosage sensitivity

ClinGen haploinsufficiency and triplosensitivity scores for one gene (`gene`), or the curated genes and recurrent CNV regions overlapping a GRCh38 interval (`region`, at most 50 Mb): { genesListDate, regionsListDate, gene?, genes[], regions[] }. Pass exactly one of the two parameters; `gene` is null when ClinGen has not curated the gene.

Caching: CDN (bundled curation lists). Sources: ClinGen Dosage Sensitivity (CC0).

Parameter	In	Description	Example
`gene`	query	HGNC gene symbol (or use region).	`PMP22`
`region`	query	GRCh38 interval chrom-start-end or chrom:start-end (or use gene).	`17-14000000-16000000`

curl -s \
  "https://clinical.enigmagenomics.com/api/dosage/?gene=PMP22&region=17-14000000-16000000"

GET/api/sv/{id}/Public

SV / CNV summary

Names, genes and exons, ClinGen dosage, gnomAD-SV and exome CNV overlaps and automated ACMG CNV points.

Parameter	In	Description	Example
`id`required	path	chrom-start-end-TYPE (DEL, DUP, INV, CNV, CPX), chrom-pos-L<length>-INS, chromA-posA-chromB-posB-BND, or chrom-pos-ALU\|L1\|SVA\|HERVK.	`22-18912231-21465672-DEL`

curl -s \
  "https://clinical.enigmagenomics.com/api/sv/22-18912231-21465672-DEL/"

GET/api/sv/{id}/transcripts/Public

Transcripts hit by an SV

GENCODE transcripts overlapped by the interval, with MANE flags, exons hit and the share of span, exons and coding bases inside the event.

Parameter	In	Description	Example
`id`required	path	chrom-start-end-TYPE (DEL, DUP, INV, CNV, CPX), chrom-pos-L<length>-INS, chromA-posA-chromB-posB-BND, or chrom-pos-ALU\|L1\|SVA\|HERVK.	`22-18912231-21465672-DEL`

curl -s \
  "https://clinical.enigmagenomics.com/api/sv/22-18912231-21465672-DEL/transcripts/"

GET/api/sv/{id}/clinvar/Public

Overlapping ClinVar SVs

Live ClinVar structural records (≥ 50 bp) overlapping the event, or near an insertion / breakend.

Parameter	In	Description	Example
`id`required	path	chrom-start-end-TYPE (DEL, DUP, INV, CNV, CPX), chrom-pos-L<length>-INS, chromA-posA-chromB-posB-BND, or chrom-pos-ALU\|L1\|SVA\|HERVK.	`22-18912231-21465672-DEL`

curl -s \
  "https://clinical.enigmagenomics.com/api/sv/22-18912231-21465672-DEL/clinvar/"

GET/api/sv/{id}/literature/Public

Publications for an SV region

Europe PMC publications for the cytoband, ClinGen region diseases and dosage-sensitive genes the event overlaps.

Parameter	In	Description	Example
`id`required	path	chrom-start-end-TYPE (DEL, DUP, INV, CNV, CPX), chrom-pos-L<length>-INS, chromA-posA-chromB-posB-BND, or chrom-pos-ALU\|L1\|SVA\|HERVK.	`22-18912231-21465672-DEL`

curl -s \
  "https://clinical.enigmagenomics.com/api/sv/22-18912231-21465672-DEL/literature/"

GET/api/sv/{id}/phenotype/Public

Phenotype match for an SV

For each HPO term, the genes in the event that HPO annotates to the term or a more specific one.

Parameter	In	Description	Example
`id`required	path	chrom-start-end-TYPE (DEL, DUP, INV, CNV, CPX), chrom-pos-L<length>-INS, chromA-posA-chromB-posB-BND, or chrom-pos-ALU\|L1\|SVA\|HERVK.	`22-18912231-21465672-DEL`
`hpo`required	query	Comma-separated HPO term IDs.	`HP:0001250,HP:0000252`

curl -s \
  "https://clinical.enigmagenomics.com/api/sv/22-18912231-21465672-DEL/phenotype/?hpo=HP%3A0001250%2CHP%3A0000252"

Pharmacogenomics

CPIC gene–drug pairs, star alleles and drug facts.

GET/api/pgx/drugs/Public

Drugs with CPIC pairs

Every drug with a CPIC gene–drug pair, best CPIC level first.

curl -s \
  "https://clinical.enigmagenomics.com/api/pgx/drugs/"

GET/api/pgx/drug/{name}/Public

One drug

CPIC gene–drug pairs, guidelines, dosing recommendations, Drug Repurposing Hub mechanisms and indications, and star-allele functions. Unknown drugs are 404 with `suggestions`.

Parameter	In	Description	Example
`name`required	path	Drug name.	`clopidogrel`

curl -s \
  "https://clinical.enigmagenomics.com/api/pgx/drug/clopidogrel/"

GET/api/pgx/gene/{symbol}/Public

CPIC facts for a gene

CPIC facts and gene–drug pairs for one gene (`{ gene: null, pairs: [] }` when CPIC has none).

Parameter	In	Description	Example
`symbol`required	path	HGNC gene symbol.	`CYP2C19`

curl -s \
  "https://clinical.enigmagenomics.com/api/pgx/gene/CYP2C19/"

GET/api/gene/{gene}/alleles/Public

CPIC star alleles

Star alleles of a pharmacogene with clinical function, activity value, evidence strength and Near Eastern frequency.

Sources: CPIC (CC0).

Parameter	In	Description	Example
`gene`required	path	HGNC gene symbol.	`CYP2C19`

curl -s \
  "https://clinical.enigmagenomics.com/api/gene/CYP2C19/alleles/"

GET/api/pgx/variant/{id}/Public

PGx at a variant

CPIC star alleles defined at the position, the gene–drug pairs of its gene and the ClinPGx accession.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`10-94781859-G-A`
`rsid`	query	rsID hint (optional).	`rs4244285`
`gene`	query	Gene symbol hint from the page (optional).	`CYP2C19`

curl -s \
  "https://clinical.enigmagenomics.com/api/pgx/variant/10-94781859-G-A/?rsid=rs4244285&gene=CYP2C19"

Disease & phenotype

Rare-disease catalogue, MONDO diseases and HPO phenotypes.

GET/api/rare-disease/catalogue/Public

Rare-disease catalogue

Every active Orphanet entry in compact rows, with MONDO mappings, GenCC and ClinGen validity.

Sources: Orphanet (CC BY 4.0), GenCC and ClinGen (CC0).

curl -s \
  "https://clinical.enigmagenomics.com/api/rare-disease/catalogue/"

GET/api/rare-disease/disease/{id}/Public

Rare-disease facts

Orphanet inheritance, onset, prevalence, category and genes, and ClinGen / GenCC gene–disease validity.

Parameter	In	Description	Example
`id`required	path	MONDO, ORPHA or OMIM disease ID.	`MONDO:0011382`

curl -s \
  "https://clinical.enigmagenomics.com/api/rare-disease/disease/MONDO%3A0011382/"

GET/api/rare-disease/gene/{symbol}/Public

Rare diseases for a gene

ClinGen and GenCC gene–disease validity (every submitter) and Orphanet disorders.

Parameter	In	Description	Example
`symbol`required	path	HGNC gene symbol.	`HBB`

curl -s \
  "https://clinical.enigmagenomics.com/api/rare-disease/gene/HBB/"

GET/api/ontology/disease/{id}/Public

MONDO disease

Definition, inheritance, genes (Monarch) and ancestor/child graph (OLS4). OMIM and Orphanet IDs are mapped to MONDO.

Parameter	In	Description	Example
`id`required	path	MONDO, OMIM or Orphanet ID.	`MONDO:0011382`

curl -s \
  "https://clinical.enigmagenomics.com/api/ontology/disease/MONDO%3A0011382/"

GET/api/ontology/disease/{id}/phenotypes/Public

Phenotypes of a disease

HPO phenotypes annotated to a disease, with frequency and onset where given.

Parameter	In	Description	Example
`id`required	path	MONDO disease ID.	`MONDO:0011382`

curl -s \
  "https://clinical.enigmagenomics.com/api/ontology/disease/MONDO%3A0011382/phenotypes/"

GET/api/ontology/phenotype/{id}/Public

HPO term

Definition, synonyms, references and ancestor/child graph.

Parameter	In	Description	Example
`id`required	path	HPO term ID.	`HP:0001250`

curl -s \
  "https://clinical.enigmagenomics.com/api/ontology/phenotype/HP%3A0001250/"

GET/api/ontology/phenotype/{id}/associations/Public

Genes and diseases for an HPO term

Genes and diseases annotated directly to the term (Monarch Initiative).

Parameter	In	Description	Example
`id`required	path	HPO term ID.	`HP:0001250`

curl -s \
  "https://clinical.enigmagenomics.com/api/ontology/phenotype/HP%3A0001250/associations/"

Literature

Articles, citations and variants mentioned in them.

GET/api/literature/variant/{id}/Public

Publications for a variant

Publications from LitVar2, Europe PMC, PubTator3 and PubMed. gene, hgvsp, hgvsc and rsid are optional hints.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`
`mode`	query	Germline or somatic ranking.One of: germline, somatic	`somatic`
`gene`	query	Gene symbol hint from the page (optional).	`BRAF`
`hgvsp`	query	Protein change hint.	`p.Val600Glu`
`hgvsc`	query	Coding change hint.	—

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`
`mode`	query	Germline or somatic ranking.One of: germline, somatic	`somatic`
`gene`	query	Gene symbol hint from the page (optional).	`BRAF`
`hgvsp`	query	Protein change hint.	`p.Val600Glu`
`hgvsc`	query	Coding change hint.	—
`rsid`	query	rsID hint.	`rs113488022`

curl -s \
  "https://clinical.enigmagenomics.com/api/literature/variant/7-140753336-A-T/?mode=somatic&gene=BRAF&hgvsp=p.Val600Glu&rsid=rs113488022"

GET/api/article/{pmid}/Public

One article

PubMed record and abstract, Europe PMC citation count and full-text links, PubTator3 concepts.

Parameter	In	Description	Example
`pmid`required	path	PubMed ID.	`12068308`

curl -s \
  "https://clinical.enigmagenomics.com/api/article/12068308/"

GET/api/article/{pmid}/citations/Public

Articles citing an article

The 100 most-cited or most recent citing articles from Europe PMC, with the total count.

Parameter	In	Description	Example
`pmid`required	path	PubMed ID.	`12068308`
`sort`	query	Order.One of: cited, recent	`cited`

curl -s \
  "https://clinical.enigmagenomics.com/api/article/12068308/citations/?sort=cited"

GET/api/article/{pmid}/variants/Public

Variants mentioned in an article

Variants PubTator3 finds in the title and abstract, resolved to canonical variant IDs.

Parameter	In	Description	Example
`pmid`required	path	PubMed ID.	`12068308`

curl -s \
  "https://clinical.enigmagenomics.com/api/article/12068308/variants/"

Oncology

Somatic evidence, oncogenicity facts, tumour types, fusions and trials.

GET/api/somatic/variant/{id}/Public

Somatic evidence

CIViC, cBioPortal, GDC, Cancer Genome Interpreter and FDA companion diagnostics for a variant. Counts and public identifiers only.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/somatic/variant/7-140753336-A-T/"

GET/api/somatic/oncogenicity/{id}/Public

Oncogenicity and tier evidence

Licence-free facts for the SVIG-UK oncogenicity and AMP/ASCO/CAP tier engines, which run in the browser.

Parameter	In	Description	Example
`id`required	path	GRCh38 small variant as chrom-pos-ref-alt.	`7-140753336-A-T`

curl -s \
  "https://clinical.enigmagenomics.com/api/somatic/oncogenicity/7-140753336-A-T/"

GET/api/somatic/oncotree/Public

OncoTree tumour types

Bundled OncoTree tumour types for the tumour-type picker.

Caching: One week. Sources: OncoTree (CC BY 4.0).

curl -s \
  "https://clinical.enigmagenomics.com/api/somatic/oncotree/"

GET/api/fusion/{id}/Public

Gene fusion

Evidence for an ordered gene pair.

Parameter	In	Description	Example
`id`required	path	Ordered gene pair (5′::3′).	`BCR::ABL1`

curl -s \
  "https://clinical.enigmagenomics.com/api/fusion/BCR%3A%3AABL1/"

GET/api/trials/Public

Clinical trials

ClinicalTrials.gov search (one page of 100 studies), the merged list for a variant or gene page (`scope`), or the country facet (`facet=countries`). A search needs at least one of cond, term, intr, locn or country; filters use ClinicalTrials.gov's own codes, so results match the same search on clinicaltrials.gov. Each study carries its eligible sex, minimum and maximum age and standard age groups (`ageGroups`: CHILD, ADULT, OLDER_ADULT).

Caching: Six hours. Sources: ClinicalTrials.gov (public domain).

Parameter	In	Description	Example
`cond`	query	Condition.	`Breast Cancer`
`term`	query	Other terms (gene, protein change, keyword).	—
`intr`	query	Intervention.	—
`locn`	query	Location text (city, region).	—
`country`	query	Country name or "gulf".	`Saudi Arabia`

Parameter	In	Description	Example
`cond`	query	Condition.	`Breast Cancer`
`term`	query	Other terms (gene, protein change, keyword).	—
`intr`	query	Intervention.	—
`locn`	query	Location text (city, region).	—
`country`	query	Country name or "gulf".	`Saudi Arabia`
`status`	query	Comma-separated status codes (rec, not, enr, act, ava, com, sus, ter, wit, unk …), or "active". In scope lists: active or all.	`rec,not`
`phase`	query	Comma-separated phases (0, 1, 2, 3, 4, NA).	`2,3`
`type`	query	Comma-separated study types (int, obs, exp).	—
`age`	query	Comma-separated age groups the study accepts (ClinicalTrials.gov standard ages): child (birth–17), adult (18–64), older (65+).	`child`
`sex`	query	Studies that accept this sex (studies open to all included). Leave out for all.One of: f, m	—
`funder`	query	Comma-separated funder types (industry, nih, fed, other).	—
`sort`	query	Sort order (default relevance).One of: relevance, updated, start, enrolment	—
`scope`	query	Merged list for a page.One of: variant, gene	—
`variant`	query	Variant ID when scope=variant.	—
`gene`	query	Gene symbol when scope is set.	—
`hgvsp`	query	HGVS protein change when scope=variant, e.g. p.Val600Glu.	—
`mode`	query	Context list mode when scope is set.One of: germline, somatic	—
`facet`	query	Facet list instead of studies.One of: countries	—
`page`	query	Next-page token.	—

curl -s \
  "https://clinical.enigmagenomics.com/api/trials/?cond=Breast+Cancer&country=Saudi+Arabia&status=rec%2Cnot&phase=2%2C3&age=child"

Tools

Coordinate conversion between genome builds.

GET/api/liftover/Public

Lift one position, variant, region or SV

Converts one line between GRCh38 (hg38), GRCh37 (b37) and hg19: a small variant (11-5227002-T-A, chr11:5227002:T:A), a position (7-140753336), a region (chr7:140753336-140753500) or an SV/MEI ID (8-127734450-127764981-DUP). Returns { from, to, results[1], sources }. A line that cannot be read or lifted comes back as a `failed` result, not a 400; reference bases are checked against the target build.

Caching: Server data cache and CDN; unreadable lines are kept for an hour. Sources: Ensembl REST assembly map and sequence.

Parameter	In	Description	Example
`q`required	query	One line (at most 300 characters).	`11-5227002-T-A`
`from`	query	Source build (default hg38). GRCh38 and GRCh37 are accepted.One of: hg38, b37, hg19	`hg38`
`to`	query	Target build (default b37 from hg38, else hg38).One of: hg38, b37, hg19	`b37`

curl -s \
  "https://clinical.enigmagenomics.com/api/liftover/?q=11-5227002-T-A&from=hg38&to=b37"

POST/api/liftover/Public

Lift a batch of lines

The batch form of GET /api/liftover/: send `queries` (an array of strings) or `text` (one query per line), with optional `from` and `to`. At most 500 lines of 300 characters each. Returns { from, to, results[], sources, error? }, one result per line in order; `error` reports lines that failed because Ensembl did not respond.

Caching: Not cached. Sources: Ensembl REST assembly map and sequence.

curl -s \
  -X POST \
  -H "Content-Type: application/json" \
  -d '{"queries":["11-5227002-T-A","chr7:140753336-140753500"],"from":"hg38","to":"b37"}' \
  "https://clinical.enigmagenomics.com/api/liftover/"

Account

Records kept for the signed-in account.

POST/api/audit/Signed-in account

Append an audit event

Appends one event to the tamper-evident (hash-chained) audit log. The account comes from the verified ID token, never from the body; the server sets the time and the chain hash. Any signed-in account may log its own activity, at most 60 events a minute. Returns 201 { stored: true, seq, hash }, or 202 { stored: false, reason } when the log store is not configured (local development).

Caching: Never cached (no-store).

curl -s \
  -X POST \
  -H "Authorization: Bearer $FIREBASE_ID_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"action":"view_variant","target":"7-140753336-A-T"}' \
  "https://clinical.enigmagenomics.com/api/audit/"

Overview

Search

Gene and rsID suggestions

Resolve any supported query

Cohort

Read-only GraphQL proxy

Cohort variants in a window

Cohort statistics

Homozygous loss-of-function registry

ClinVar discordance alerts

Headline counts

Founder variant registry

Variant

gnomAD v4 variant

Live ClinVar record

Automated ACMG/AMP classification

In-silico predictors (dbNSFP)

Transcript consequences

GTEx eQTLs and sQTLs

Structural context of a position

ClinVar SVs over a position

Conditions for a variant

Gene

gnomAD gene annotation

ClinVar variants in a gene

gnomAD read depth over a gene

Regional missense constraint

Transcript

GTEx tissue expression

Cancer-driver role and CIViC

Somatic mutations (TCGA)

Protein length and Pfam domains

SVs and CNVs in a gene

ClinVar P/LP on protein codons

Protein features and structure

Tumour mutations at a codon

STR allele-size distributions

Structural variants

ClinGen dosage sensitivity

SV / CNV summary

Transcripts hit by an SV

Overlapping ClinVar SVs

Publications for an SV region

Phenotype match for an SV

Pharmacogenomics

Drugs with CPIC pairs

One drug

CPIC facts for a gene

CPIC star alleles

PGx at a variant

Disease & phenotype

Rare-disease catalogue

Rare-disease facts

Rare diseases for a gene

MONDO disease

Phenotypes of a disease

HPO term

Genes and diseases for an HPO term

Literature

Publications for a variant

One article

Articles citing an article

Variants mentioned in an article

Oncology

Somatic evidence

Oncogenicity and tier evidence

OncoTree tumour types

Gene fusion

Clinical trials

Tools

Lift one position, variant, region or SV

Lift a batch of lines

Account

Append an audit event

Meta

This OpenAPI document