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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: 1-235746388-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=235746388&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 235746388,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000389793.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala",
"transcript": "NM_000081.4",
"protein_id": "NP_000072.2",
"transcript_support_level": null,
"aa_start": 2640,
"aa_end": null,
"aa_length": 3801,
"cds_start": 7920,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 8081,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "ENST00000389793.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala",
"transcript": "ENST00000389793.7",
"protein_id": "ENSP00000374443.2",
"transcript_support_level": 5,
"aa_start": 2640,
"aa_end": null,
"aa_length": 3801,
"cds_start": 7920,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 8081,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "NM_000081.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala",
"transcript": "NM_001301365.1",
"protein_id": "NP_001288294.1",
"transcript_support_level": null,
"aa_start": 2640,
"aa_end": null,
"aa_length": 3801,
"cds_start": 7920,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 8539,
"cdna_end": null,
"cdna_length": 13934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.2400G>A",
"hgvs_p": "p.Ala800Ala",
"transcript": "ENST00000697241.1",
"protein_id": "ENSP00000513206.1",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 1407,
"cds_start": 2400,
"cds_end": null,
"cds_length": 4224,
"cdna_start": 2400,
"cdna_end": null,
"cdna_length": 4224,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.15G>A",
"hgvs_p": "p.Ala5Ala",
"transcript": "ENST00000475277.2",
"protein_id": "ENSP00000513164.1",
"transcript_support_level": 5,
"aa_start": 5,
"aa_end": null,
"aa_length": 629,
"cds_start": 15,
"cds_end": null,
"cds_length": 1890,
"cdna_start": 15,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_011544031.2",
"protein_id": "XP_011542333.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 3855,
"cds_start": 8082,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 8243,
"cdna_end": null,
"cdna_length": 13638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_011544032.2",
"protein_id": "XP_011542334.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 3855,
"cds_start": 8082,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 8706,
"cdna_end": null,
"cdna_length": 14101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_011544033.3",
"protein_id": "XP_011542335.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 3855,
"cds_start": 8082,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 10030,
"cdna_end": null,
"cdna_length": 15425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_047443026.1",
"protein_id": "XP_047298982.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 3855,
"cds_start": 8082,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 15122,
"cdna_end": null,
"cdna_length": 20517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_011544035.3",
"protein_id": "XP_011542337.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 3318,
"cds_start": 8082,
"cds_end": null,
"cds_length": 9957,
"cdna_start": 8243,
"cdna_end": null,
"cdna_length": 10323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala",
"transcript": "XM_047443027.1",
"protein_id": "XP_047298983.1",
"transcript_support_level": null,
"aa_start": 2640,
"aa_end": null,
"aa_length": 3264,
"cds_start": 7920,
"cds_end": null,
"cds_length": 9795,
"cdna_start": 8081,
"cdna_end": null,
"cdna_length": 10161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.5745G>A",
"hgvs_p": "p.Ala1915Ala",
"transcript": "XM_011544036.3",
"protein_id": "XP_011542338.1",
"transcript_support_level": null,
"aa_start": 1915,
"aa_end": null,
"aa_length": 3076,
"cds_start": 5745,
"cds_end": null,
"cds_length": 9231,
"cdna_start": 8175,
"cdna_end": null,
"cdna_length": 13570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.5583G>A",
"hgvs_p": "p.Ala1861Ala",
"transcript": "XM_047443034.1",
"protein_id": "XP_047298990.1",
"transcript_support_level": null,
"aa_start": 1861,
"aa_end": null,
"aa_length": 3022,
"cds_start": 5583,
"cds_end": null,
"cds_length": 9069,
"cdna_start": 8013,
"cdna_end": null,
"cdna_length": 13408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_011544037.3",
"protein_id": "XP_011542339.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 2876,
"cds_start": 8082,
"cds_end": null,
"cds_length": 8631,
"cdna_start": 8243,
"cdna_end": null,
"cdna_length": 13948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.8082G>A",
"hgvs_p": "p.Ala2694Ala",
"transcript": "XM_047443038.1",
"protein_id": "XP_047298994.1",
"transcript_support_level": null,
"aa_start": 2694,
"aa_end": null,
"aa_length": 2842,
"cds_start": 8082,
"cds_end": null,
"cds_length": 8529,
"cdna_start": 8243,
"cdna_end": null,
"cdna_length": 11881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala",
"transcript": "XM_047443040.1",
"protein_id": "XP_047298996.1",
"transcript_support_level": null,
"aa_start": 2640,
"aa_end": null,
"aa_length": 2822,
"cds_start": 7920,
"cds_end": null,
"cds_length": 8469,
"cdna_start": 8081,
"cdna_end": null,
"cdna_length": 13786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala",
"transcript": "XM_047443046.1",
"protein_id": "XP_047299002.1",
"transcript_support_level": null,
"aa_start": 2640,
"aa_end": null,
"aa_length": 2788,
"cds_start": 7920,
"cds_end": null,
"cds_length": 8367,
"cdna_start": 8081,
"cdna_end": null,
"cdna_length": 12632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.2595G>A",
"hgvs_p": null,
"transcript": "ENST00000461526.2",
"protein_id": "ENSP00000513165.1",
"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": 5771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.*3344G>A",
"hgvs_p": null,
"transcript": "ENST00000697178.1",
"protein_id": "ENSP00000513163.1",
"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": 13920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.1629G>A",
"hgvs_p": null,
"transcript": "ENST00000697236.1",
"protein_id": "ENSP00000513203.1",
"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": 6723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.54G>A",
"hgvs_p": null,
"transcript": "ENST00000697240.1",
"protein_id": "ENSP00000513205.1",
"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": 3784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.*3344G>A",
"hgvs_p": null,
"transcript": "ENST00000697178.1",
"protein_id": "ENSP00000513163.1",
"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": 13920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.*80G>A",
"hgvs_p": null,
"transcript": "ENST00000487530.2",
"protein_id": "ENSP00000417168.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": -4,
"cds_end": null,
"cds_length": 541,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"dbsnp": "rs778975523",
"frequency_reference_population": 0.000010534143,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.00000957799,
"gnomad_genomes_af": 0.0000197218,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8700000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.197,
"phylop100way_prediction": "Benign",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000389793.7",
"gene_symbol": "LYST",
"hgnc_id": 1968,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7920G>A",
"hgvs_p": "p.Ala2640Ala"
}
],
"clinvar_disease": "Chédiak-Higashi syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Chédiak-Higashi syndrome",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}