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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: 1-21865303-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21865303&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"hgvs_c": "c.4380C>T",
"hgvs_p": "p.Tyr1460Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -5,
"transcript": "NM_001291860.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_score": -5,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.69,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6899999976158142,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "Y",
"aa_start": 1459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 4470,
"cds_end": null,
"cds_length": 13176,
"cds_start": 4377,
"consequences": [
"synonymous_variant"
],
"exon_count": 97,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_005529.7",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4377C>T",
"hgvs_p": "p.Tyr1459Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374695.8",
"protein_coding": true,
"protein_id": "NP_005520.4",
"strand": false,
"transcript": "NM_005529.7",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "Y",
"aa_start": 1459,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 4470,
"cds_end": null,
"cds_length": 13176,
"cds_start": 4377,
"consequences": [
"synonymous_variant"
],
"exon_count": 97,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000374695.8",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4377C>T",
"hgvs_p": "p.Tyr1459Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005529.7",
"protein_coding": true,
"protein_id": "ENSP00000363827.3",
"strand": false,
"transcript": "ENST00000374695.8",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4392,
"aa_ref": "Y",
"aa_start": 1460,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14344,
"cdna_start": 4473,
"cds_end": null,
"cds_length": 13179,
"cds_start": 4380,
"consequences": [
"synonymous_variant"
],
"exon_count": 97,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_001291860.2",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4380C>T",
"hgvs_p": "p.Tyr1460Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278789.1",
"strand": false,
"transcript": "NM_001291860.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4574,
"aa_ref": "Y",
"aa_start": 1642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14890,
"cdna_start": 5019,
"cds_end": null,
"cds_length": 13725,
"cds_start": 4926,
"consequences": [
"synonymous_variant"
],
"exon_count": 102,
"exon_rank": 40,
"exon_rank_end": null,
"feature": "XM_011541318.3",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4926C>T",
"hgvs_p": "p.Tyr1642Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539620.1",
"strand": false,
"transcript": "XM_011541318.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4557,
"aa_ref": "Y",
"aa_start": 1625,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14839,
"cdna_start": 4968,
"cds_end": null,
"cds_length": 13674,
"cds_start": 4875,
"consequences": [
"synonymous_variant"
],
"exon_count": 101,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "XM_047419080.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4875C>T",
"hgvs_p": "p.Tyr1625Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275036.1",
"strand": false,
"transcript": "XM_047419080.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4556,
"aa_ref": "Y",
"aa_start": 1624,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14836,
"cdna_start": 4965,
"cds_end": null,
"cds_length": 13671,
"cds_start": 4872,
"consequences": [
"synonymous_variant"
],
"exon_count": 101,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "XM_047419090.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4872C>T",
"hgvs_p": "p.Tyr1624Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275046.1",
"strand": false,
"transcript": "XM_047419090.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4456,
"aa_ref": "Y",
"aa_start": 1524,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14458,
"cdna_start": 4587,
"cds_end": null,
"cds_length": 13371,
"cds_start": 4572,
"consequences": [
"synonymous_variant"
],
"exon_count": 98,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "XM_017001120.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4572C>T",
"hgvs_p": "p.Tyr1524Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856609.1",
"strand": false,
"transcript": "XM_017001120.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4455,
"aa_ref": "Y",
"aa_start": 1523,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14455,
"cdna_start": 4584,
"cds_end": null,
"cds_length": 13368,
"cds_start": 4569,
"consequences": [
"synonymous_variant"
],
"exon_count": 98,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "XM_047419091.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4569C>T",
"hgvs_p": "p.Tyr1523Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275047.1",
"strand": false,
"transcript": "XM_047419091.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4439,
"aa_ref": "Y",
"aa_start": 1507,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14407,
"cdna_start": 4536,
"cds_end": null,
"cds_length": 13320,
"cds_start": 4521,
"consequences": [
"synonymous_variant"
],
"exon_count": 97,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_017001121.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4521C>T",
"hgvs_p": "p.Tyr1507Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856610.1",
"strand": false,
"transcript": "XM_017001121.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 4438,
"aa_ref": "Y",
"aa_start": 1506,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14404,
"cdna_start": 4533,
"cds_end": null,
"cds_length": 13317,
"cds_start": 4518,
"consequences": [
"synonymous_variant"
],
"exon_count": 97,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_017001122.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.4518C>T",
"hgvs_p": "p.Tyr1506Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856611.1",
"strand": false,
"transcript": "XM_017001122.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs779605727",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000218901,
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"gnomad_exomes_ac": 32,
"gnomad_exomes_af": 0.0000218901,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.526,
"pos": 21865303,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001291860.2"
}
]
}