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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 20-45898107-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=45898107&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 45898107,
"ref": "A",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000646241.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu",
"transcript": "NM_000308.4",
"protein_id": "NP_000299.3",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 480,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1402,
"cdna_end": null,
"cdna_length": 1858,
"mane_select": "ENST00000646241.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu",
"transcript": "ENST00000646241.3",
"protein_id": "ENSP00000493613.2",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 480,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1402,
"cdna_end": null,
"cdna_length": 1858,
"mane_select": "NM_000308.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1411A>G",
"hgvs_p": "p.Lys471Glu",
"transcript": "ENST00000372484.8",
"protein_id": "ENSP00000361562.3",
"transcript_support_level": 1,
"aa_start": 471,
"aa_end": null,
"aa_length": 498,
"cds_start": 1411,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 2483,
"cdna_end": null,
"cdna_length": 2939,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu",
"transcript": "ENST00000191018.9",
"protein_id": "ENSP00000191018.5",
"transcript_support_level": 1,
"aa_start": 453,
"aa_end": null,
"aa_length": 480,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1442,
"cdna_end": null,
"cdna_length": 1898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu",
"transcript": "ENST00000372459.7",
"protein_id": "ENSP00000361537.2",
"transcript_support_level": 1,
"aa_start": 453,
"aa_end": null,
"aa_length": 480,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1540,
"cdna_end": null,
"cdna_length": 1996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.4112A>G",
"hgvs_p": null,
"transcript": "ENST00000484855.4",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1411A>G",
"hgvs_p": "p.Lys471Glu",
"transcript": "ENST00000677394.1",
"protein_id": "ENSP00000504790.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 498,
"cds_start": 1411,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 2337,
"cdna_end": null,
"cdna_length": 2774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu",
"transcript": "NM_001127695.3",
"protein_id": "NP_001121167.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 480,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1448,
"cdna_end": null,
"cdna_length": 1904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu",
"transcript": "ENST00000607482.6",
"protein_id": "ENSP00000475524.2",
"transcript_support_level": 3,
"aa_start": 453,
"aa_end": null,
"aa_length": 480,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1443,
"cdna_start": 1431,
"cdna_end": null,
"cdna_length": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1306A>G",
"hgvs_p": "p.Lys436Glu",
"transcript": "NM_001167594.3",
"protein_id": "NP_001161066.2",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 463,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 1351,
"cdna_end": null,
"cdna_length": 1807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1306A>G",
"hgvs_p": "p.Lys436Glu",
"transcript": "ENST00000354880.9",
"protein_id": "ENSP00000346952.5",
"transcript_support_level": 2,
"aa_start": 436,
"aa_end": null,
"aa_length": 463,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 1364,
"cdna_end": null,
"cdna_length": 1820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "c.1267A>G",
"hgvs_p": "p.Lys423Glu",
"transcript": "ENST00000678443.1",
"protein_id": "ENSP00000504006.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 450,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 1267,
"cdna_end": null,
"cdna_length": 1697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.5494A>G",
"hgvs_p": null,
"transcript": "ENST00000480961.3",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.1724A>G",
"hgvs_p": null,
"transcript": "ENST00000493522.8",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.381A>G",
"hgvs_p": null,
"transcript": "ENST00000606000.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.1848A>G",
"hgvs_p": null,
"transcript": "ENST00000606066.3",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.1478A>G",
"hgvs_p": null,
"transcript": "ENST00000606782.3",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.*722A>G",
"hgvs_p": null,
"transcript": "ENST00000606788.5",
"protein_id": "ENSP00000476235.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.4281A>G",
"hgvs_p": null,
"transcript": "ENST00000607187.3",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.1568A>G",
"hgvs_p": null,
"transcript": "ENST00000607212.3",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.3108A>G",
"hgvs_p": null,
"transcript": "ENST00000607814.7",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.*104A>G",
"hgvs_p": null,
"transcript": "ENST00000676597.1",
"protein_id": "ENSP00000503904.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
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"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"hgvs_c": "n.*696A>G",
"hgvs_p": null,
"transcript": "ENST00000678939.1",
"protein_id": "ENSP00000503404.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CTSA",
"gene_hgnc_id": 9251,
"dbsnp": "rs137854549",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9768359661102295,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.7940000295639038,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.934,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9508,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.93,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.847482098702227,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000646241.3",
"gene_symbol": "CTSA",
"hgnc_id": 9251,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1357A>G",
"hgvs_p": "p.Lys453Glu"
}
],
"clinvar_disease": " late infantile,Galactosialidosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Galactosialidosis, late infantile",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}