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Variant representation formats

GeneBe supports a wide range of variant representation formats. This allows users to search for genetic variants in the style most familiar to them — from simple SNVs to clinical notations and large CNVs.

Below is an overview of the supported variant formats, grouped by type, with example queries and their corresponding links.

Acceptable forms​

Single nucleotide variants (SNVs) and multiple nucleotide variants (MNVs)​

These are simple base substitutions or multi-base changes. They may use different delimiters or notations (chr, hyphen, colon, etc.).

FormatExampleLink
chr-prefixed, colon-separatedchr6:160585140-T>GView
Hyphenated format7-69599651-A-GView
Space-separated format22 28695868 AG AView
Numeric with colon and arrow1:11796321-G>AView
RefSeq chromosome notationNC_000021.9-37505319-A-GView
SPDI notation (0-based)chrX:153803771:1:AView
VCF line (chr/pos/id/ref/alt)chr2 141254732 . T CView

Variants by external database ID​

Genebe.net supports searching for variants via stable IDs from various bioinformatics resources.

FormatExampleLink
dbSNP rsIDrs1228544607View
ClinGen Allele Registry (CA ID)CA123062477View

HGVS descriptions​

These include both nucleotide- and protein-level HGVS notations.

FormatExampleLink
ENST (Ensembl transcript)ENST00000679957.1:c.803C>TView
RefSeq transcriptNM_018136.4:c.567_569delView
RefSeq with protein-level changeNM_000277.2(PAH):c.169G>A (p.Glu57Lys)View
Genomic HGVS (g.)NC_000005.10:g.91204234G>AView
Non-coding transcript HGVS (n.)XR_001742795.1:n.38-1534C>TView

For HGVS with p. notation, see the "Protein-level notations" section.

HGVS nomenclature is complex, and some valid expressions may not parse correctly. If your HGVS input isn’t recognized:

  • Ensure correct letter casing.
  • Remove extra spaces.
  • Verify the transcript and reference sequence.
  • Check consistency between the reference base or amino acid and the selected genome build.

If problems persist, feel free to contact us.

❌ Example that will not work: NC_000021.9:g.(?_34787801)_(35048958_?)del

Protein-level notations​

Protein substitutions are supported using either full amino acid names or single-letter codes.

FormatExampleLink
Full amino acid namesAGT Met259ThrView
Short formAGT M259TView
HGVS-like formatAGT:p.M259TView

⚠️ Only single amino acid to single amino acid substitutions are supported.

Small insertions and deletions (Indels)​

Indels are supported in several formats, including deletion, insertion, and substitution styles.

FormatExampleLink
Deletion22-28695869-G-View
Equivalent deletion22-28695868-AG-AView
Insertion22-28695869--GView
Equivalent insertion22-28695868-A-AGView

Indels can also be represented using HGVS or SPDI formats.

Copy Number Variants (CNVs) — Experimental​

These represent large-scale deletions or duplications and are currently supported in experimental mode.

FormatExampleLink
Deletion CNVDEL chr7:72846244-74187855View
You can use , in notationDEL chr7:72,846,244-74,187,855View
Duplication CNVDUP chr7:72846244-74187855View

Mitochondrial variants​

Genebe.net accepts mitochondrial variants using common notations and the m. prefix.

FormatExampleLink
Mitochondrialm.13513G>AView

Gene-level searches​

You can also search by gene names — either official symbols or aliases.

FormatExampleLink
GeneAUTS2View
AliasmthfrView

Notes on URL construction​

  • All variant URLs follow the structure: https://genebe.net/variant/hg38/<variant-string> where <variant-string> is the encoded variant.
  • For gene searches, use: https://genebe.net/gene/hg38/<gene-name>
  • Genome version is part of the path (hg38 in these examples). hg19 is also partially supported.

API​

If you have variants in any of the forms above and you wish to translate them into the "canonical" chr-pos-ref-alt form, check our convert API endpoint.