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.

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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.).

Format	Example	Link
chr-prefixed, colon-separated	chr6:160585140-T>G	View
Hyphenated format	7-69599651-A-G	View
Space-separated format	22 28695868 AG A	View
Numeric with colon and arrow	1:11796321-G>A	View
RefSeq chromosome notation	NC_000021.9-37505319-A-G	View
SPDI notation (0-based)	chrX:153803771:1:A	View
VCF line (chr/pos/id/ref/alt)	chr2 141254732 . T C	View

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Variants by external database ID

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

Format	Example	Link
dbSNP rsID	rs1228544607	View
ClinGen Allele Registry (CA ID)	CA123062477	View

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HGVS descriptions

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

Format	Example	Link
ENST (Ensembl transcript)	ENST00000679957.1:c.803C>T	View
RefSeq transcript	NM_018136.4:c.567_569del	View
RefSeq with protein-level change	NM_000277.2(PAH):c.169G>A (p.Glu57Lys)	View
Genomic HGVS (g.)	NC_000005.10:g.91204234G>A	View
Non-coding transcript HGVS (n.)	XR_001742795.1:n.38-1534C>T	View

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

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Protein-level notations

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

Format	Example	Link
Full amino acid names	AGT Met259Thr	View
Short form	AGT M259T	View
HGVS-like format	AGT:p.M259T	View

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

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Small insertions and deletions (Indels)

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

Format	Example	Link
Deletion	22-28695869-G-	View
Equivalent deletion	22-28695868-AG-A	View
Insertion	22-28695869--G	View
Equivalent insertion	22-28695868-A-AG	View

Indels can also be represented using HGVS or SPDI formats.

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Copy Number Variants (CNVs) — Experimental

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

Format	Example	Link
Deletion CNV	DEL chr7:72846244-74187855	View
You can use , in notation	DEL chr7:72,846,244-74,187,855	View
Duplication CNV	DUP chr7:72846244-74187855	View

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Mitochondrial variants

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

Format	Example	Link
Mitochondrial	m.13513G>A	View

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Gene-level searches

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

Format	Example	Link
Gene	AUTS2	View
Alias	mthfr	View

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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.

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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.