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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: 1-235809132-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=235809132&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 235809132,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000389793.7",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "NM_000081.4",
"protein_id": "NP_000072.2",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3801,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "ENST00000389793.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "ENST00000389793.7",
"protein_id": "ENSP00000374443.2",
"transcript_support_level": 5,
"aa_start": 562,
"aa_end": null,
"aa_length": 3801,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "NM_000081.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.2237G>C",
"hgvs_p": null,
"transcript": "ENST00000465349.5",
"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": 5220,
"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": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.1686G>C",
"hgvs_p": null,
"transcript": "ENST00000489585.5",
"protein_id": "ENSP00000513166.1",
"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": 7069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "NM_001301365.1",
"protein_id": "NP_001288294.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3801,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 2305,
"cdna_end": null,
"cdna_length": 13934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1089G>C",
"hgvs_p": "p.Gln363His",
"transcript": "ENST00000697242.1",
"protein_id": "ENSP00000513207.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 1265,
"cds_start": 1089,
"cds_end": null,
"cds_length": 3798,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 3938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_011544031.2",
"protein_id": "XP_011542333.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3855,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 13638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_011544032.2",
"protein_id": "XP_011542334.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3855,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 2310,
"cdna_end": null,
"cdna_length": 14101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_011544033.3",
"protein_id": "XP_011542335.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3855,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 3634,
"cdna_end": null,
"cdna_length": 15425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_047443026.1",
"protein_id": "XP_047298982.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3855,
"cds_start": 1686,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 8726,
"cdna_end": null,
"cdna_length": 20517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_011544035.3",
"protein_id": "XP_011542337.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3318,
"cds_start": 1686,
"cds_end": null,
"cds_length": 9957,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 10323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_047443027.1",
"protein_id": "XP_047298983.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 3264,
"cds_start": 1686,
"cds_end": null,
"cds_length": 9795,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 10161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_011544037.3",
"protein_id": "XP_011542339.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 2876,
"cds_start": 1686,
"cds_end": null,
"cds_length": 8631,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 13948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_047443038.1",
"protein_id": "XP_047298994.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 2842,
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"cdna_start": 1847,
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"cdna_length": 11881,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_047443040.1",
"protein_id": "XP_047298996.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 2822,
"cds_start": 1686,
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"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 13786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_047443046.1",
"protein_id": "XP_047299002.1",
"transcript_support_level": null,
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"cds_start": 1686,
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"mane_select": null,
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"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_011544039.3",
"protein_id": "XP_011542341.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 2555,
"cds_start": 1686,
"cds_end": null,
"cds_length": 7668,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 7939,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His",
"transcript": "XM_047443064.1",
"protein_id": "XP_047299020.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 2009,
"cds_start": 1686,
"cds_end": null,
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"cdna_start": 1847,
"cdna_end": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.1686G>C",
"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,
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"cdna_start": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.-1028G>C",
"hgvs_p": null,
"transcript": "XM_011544036.3",
"protein_id": "XP_011542338.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3076,
"cds_start": -4,
"cds_end": null,
"cds_length": 9231,
"cdna_start": null,
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"cdna_length": 13570,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.-1028G>C",
"hgvs_p": null,
"transcript": "XM_047443034.1",
"protein_id": "XP_047298990.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3022,
"cds_start": -4,
"cds_end": null,
"cds_length": 9069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"dbsnp": "rs77091385",
"frequency_reference_population": 0.005710239,
"hom_count_reference_population": 35,
"allele_count_reference_population": 9217,
"gnomad_exomes_af": 0.00591325,
"gnomad_genomes_af": 0.00376192,
"gnomad_exomes_ac": 8644,
"gnomad_genomes_ac": 573,
"gnomad_exomes_homalt": 35,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0099392831325531,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.096,
"revel_prediction": "Benign",
"alphamissense_score": 0.253,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.008,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000389793.7",
"gene_symbol": "LYST",
"hgnc_id": 1968,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1686G>C",
"hgvs_p": "p.Gln562His"
}
],
"clinvar_disease": "Autoinflammatory syndrome,Chédiak-Higashi syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:6 B:1",
"phenotype_combined": "not specified|Chédiak-Higashi syndrome|not provided|Autoinflammatory syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}