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Search examples

Every query format the Enigma Clinical search understands

The search box at the top of every page accepts identifiers, HGVS descriptions, genomic coordinates, structural variants, chromosomal events, phenotypes, diseases, drugs and articles. Upper and lower case are treated alike, and coordinates are read as GRCh38 unless a GRCh37 prefix says otherwise. Whatever form a variant is typed in, search converts it to one canonical identifier, so every spelling of the same variant opens the same page.

Select an example to run it, or copy it into the search box. The label beside each example is what the search recognises it as. Opening results needs a free Enigma Clinical account.

101 examples
All formats
Variant identifiers
HGVS: DNA level
HGVS: protein level
Chromosome, position, REF and ALT
Reference length instead of bases
VCF line
Positions, regions and cytobands
GRCh37 coordinates
Genes and transcripts
Structural variants and CNVs
Gene fusions
Repeat expansions
Uniparental disomy, aneuploidy and karyotypes
Phenotypes and diseases
Drugs and pharmacogenomics
Literature

Variant identifiers

Database identifiers are converted to the GRCh38 variant they describe. dbSNP and ClinVar records are read live from NCBI; ClinGen Allele Registry IDs from the registry itself.

  • rs334

    dbSNP rsID · HBB sickle-cell variant

    dbSNP rsID
  • rs113993960

    dbSNP rsID of an indel · CFTR p.Phe508del

    dbSNP rsID
  • VCV000015333

    ClinVar variation record

    ClinVar accession
  • RCV000016352

    ClinVar record for one variant–condition pair

    ClinVar accession
  • clinvar:15333

    ClinVar variation ID without the VCV prefix

    ClinVar accession
  • CA123643

    ClinGen Allele Registry ID · BRAF V600E

    ClinGen Allele Registry ID
  • NC_000011.10:5227001:T:A

    SPDI (0-based position, as NCBI writes it)

    SPDI
  • NC_000015.10:73027477:1:C

    SPDI with the deleted length instead of bases

    SPDI
  • COSV56056643

    COSMIC genomic mutation ID

    Recognised, but COSMIC data needs a COSMIC licence; search explains how to look the variant up by HGVS instead.

    COSMIC ID

HGVS: DNA level

Coding (c.), non-coding (n.), genomic (g.) and mitochondrial (m.) HGVS on a gene symbol, a RefSeq or Ensembl accession, or both. Without a version, the current MANE transcript is used.

HGVS: protein level

One-letter or three-letter amino-acid codes, with or without "p.". Substitutions, stop changes and in-frame deletions are matched to the DNA variants that cause them, through ClinVar, dbNSFP coordinates and Ensembl.

Chromosome, position, REF and ALT

Chromosome, 1-based position, reference and alternate bases separated by dashes, colons, spaces, underscores or ">". "chr" is optional; upper and lower case both work. An empty REF or ALT means an insertion or a deletion; the platform reads the reference and adds the anchor base.

Reference length instead of bases

The REF field can be a number of reference bases (0 for a pure insertion). the platform looks the bases up in GRCh38 and writes the variant in its canonical form.

VCF line

Paste a data line from a VCF file (CHROM POS ID REF ALT and any further columns, tab- or space-separated). Each ALT allele becomes one result; symbolic ALT alleles such as <DEL> are not read.

Positions, regions and cytobands

A single position or a range opens the region view with every variant class in it. Thousands separators are ignored.

GRCh37 coordinates

Prefix a position, region, variant or ISCN string with hg19:, GRCh37: or b37: and the platform lifts it over to GRCh38. hg38: and GRCh38: are accepted and change nothing.

Genes and transcripts

HGNC symbols (any case), gene identifiers from HGNC, NCBI Gene, UniProt and Ensembl, and RefSeq or Ensembl transcripts.

Structural variants and CNVs

Intervals with a type (DEL, DUP, INV, CNV, CPX), insertions with a length, translocation breakpoints and mobile-element insertions. The canonical ID, the VarSome-style colon form, the reporting-system form and ISCN microarray notation all lead to the same page.

Gene fusions

Fusions in HGVS "::" notation, 5′ partner first.

Repeat expansions

Repeat loci from the gnomAD short-tandem-repeat catalogue, by locus, locus and motif, an allele size, or HGVS repeat notation. Motifs are written on the gene’s strand, as in the literature.

Uniparental disomy, aneuploidy and karyotypes

Sample-level chromosomal events in ISCN or plain words. Their pages describe the event and its syndromes; cohort counts never identify individuals.

Phenotypes and diseases

Human Phenotype Ontology terms and disease identifiers from MONDO, Orphanet and OMIM, or their names. Names are matched against HPO and MONDO through the EBI Ontology Lookup Service.

Drugs and pharmacogenomics

Drug names (generic or brand, through NLM RxNorm) and pharmacogene star alleles.

  • clopidogrel

    Generic drug name

    Gene symbol
  • Plavix

    Brand name, mapped to its ingredient

    Gene symbol
  • CYP2C19*2

    Star allele (opens the pharmacogene)

    Pharmacogene star allele
  • HLA-B*57:01

    HLA allele (opens the gene)

    Pharmacogene star allele

Literature

PubMed IDs, with or without a colon.

  • PMID:11870241

    PubMed article · imatinib in chronic myeloid leukaemia

    PubMed article
  • PMID 25741868

    Space instead of a colon · ACMG/AMP 2015 variant guidelines

    PubMed article