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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: 2-63921216-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=63921216&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 63921216,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_016516.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "NM_016516.3",
"protein_id": "NP_057600.2",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 977,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000272322.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016516.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "ENST00000272322.9",
"protein_id": "ENSP00000272322.4",
"transcript_support_level": 5,
"aa_start": 620,
"aa_end": null,
"aa_length": 977,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016516.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000272322.9"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1823C>T",
"hgvs_p": "p.Ser608Leu",
"transcript": "ENST00000409558.8",
"protein_id": "ENSP00000386980.3",
"transcript_support_level": 1,
"aa_start": 608,
"aa_end": null,
"aa_length": 965,
"cds_start": 1823,
"cds_end": null,
"cds_length": 2898,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409558.8"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1400C>T",
"hgvs_p": "p.Ser467Leu",
"transcript": "ENST00000354504.7",
"protein_id": "ENSP00000346499.3",
"transcript_support_level": 1,
"aa_start": 467,
"aa_end": null,
"aa_length": 824,
"cds_start": 1400,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000354504.7"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Ser628Leu",
"transcript": "ENST00000949097.1",
"protein_id": "ENSP00000619156.1",
"transcript_support_level": null,
"aa_start": 628,
"aa_end": null,
"aa_length": 985,
"cds_start": 1883,
"cds_end": null,
"cds_length": 2958,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949097.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "ENST00000949098.1",
"protein_id": "ENSP00000619157.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 977,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949098.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "ENST00000949099.1",
"protein_id": "ENSP00000619158.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 977,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949099.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "ENST00000949096.1",
"protein_id": "ENSP00000619155.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 975,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2928,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949096.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1823C>T",
"hgvs_p": "p.Ser608Leu",
"transcript": "NM_001005739.2",
"protein_id": "NP_001005739.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 965,
"cds_start": 1823,
"cds_end": null,
"cds_length": 2898,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001005739.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1823C>T",
"hgvs_p": "p.Ser608Leu",
"transcript": "ENST00000851817.1",
"protein_id": "ENSP00000521876.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 965,
"cds_start": 1823,
"cds_end": null,
"cds_length": 2898,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851817.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1817C>T",
"hgvs_p": "p.Ser606Leu",
"transcript": "ENST00000851818.1",
"protein_id": "ENSP00000521877.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 963,
"cds_start": 1817,
"cds_end": null,
"cds_length": 2892,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851818.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "ENST00000922500.1",
"protein_id": "ENSP00000592559.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 950,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2853,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922500.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1751C>T",
"hgvs_p": "p.Ser584Leu",
"transcript": "ENST00000922499.1",
"protein_id": "ENSP00000592558.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 941,
"cds_start": 1751,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922499.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1823C>T",
"hgvs_p": "p.Ser608Leu",
"transcript": "ENST00000949095.1",
"protein_id": "ENSP00000619154.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 938,
"cds_start": 1823,
"cds_end": null,
"cds_length": 2817,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949095.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1715C>T",
"hgvs_p": "p.Ser572Leu",
"transcript": "ENST00000851816.1",
"protein_id": "ENSP00000521875.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 929,
"cds_start": 1715,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851816.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "XM_047444727.1",
"protein_id": "XP_047300683.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 977,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444727.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu",
"transcript": "XM_047444728.1",
"protein_id": "XP_047300684.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 977,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444728.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1823C>T",
"hgvs_p": "p.Ser608Leu",
"transcript": "XM_047444729.1",
"protein_id": "XP_047300685.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 965,
"cds_start": 1823,
"cds_end": null,
"cds_length": 2898,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444729.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1505C>T",
"hgvs_p": "p.Ser502Leu",
"transcript": "XM_017004316.2",
"protein_id": "XP_016859805.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 859,
"cds_start": 1505,
"cds_end": null,
"cds_length": 2580,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004316.2"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.1505C>T",
"hgvs_p": "p.Ser502Leu",
"transcript": "XM_047444730.1",
"protein_id": "XP_047300686.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 859,
"cds_start": 1505,
"cds_end": null,
"cds_length": 2580,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444730.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "n.2370C>T",
"hgvs_p": null,
"transcript": "XR_007076389.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007076389.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"hgvs_c": "c.*168C>T",
"hgvs_p": null,
"transcript": "XM_047444731.1",
"protein_id": "XP_047300687.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 610,
"cds_start": null,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444731.1"
}
],
"gene_symbol": "VPS54",
"gene_hgnc_id": 18652,
"dbsnp": "rs928968871",
"frequency_reference_population": 0.0000037330055,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000137453,
"gnomad_genomes_af": 0.0000262736,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5114372372627258,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.131,
"revel_prediction": "Benign",
"alphamissense_score": 0.1355,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.369,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_016516.3",
"gene_symbol": "VPS54",
"hgnc_id": 18652,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Ser620Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}