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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: 1-21842350-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21842350&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21842350,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000374695.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 68,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.8941G>T",
"hgvs_p": "p.Val2981Phe",
"transcript": "NM_005529.7",
"protein_id": "NP_005520.4",
"transcript_support_level": null,
"aa_start": 2981,
"aa_end": null,
"aa_length": 4391,
"cds_start": 8941,
"cds_end": null,
"cds_length": 13176,
"cdna_start": 9034,
"cdna_end": null,
"cdna_length": 14341,
"mane_select": "ENST00000374695.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 68,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.8941G>T",
"hgvs_p": "p.Val2981Phe",
"transcript": "ENST00000374695.8",
"protein_id": "ENSP00000363827.3",
"transcript_support_level": 1,
"aa_start": 2981,
"aa_end": null,
"aa_length": 4391,
"cds_start": 8941,
"cds_end": null,
"cds_length": 13176,
"cdna_start": 9034,
"cdna_end": null,
"cdna_length": 14341,
"mane_select": "NM_005529.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 68,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.8944G>T",
"hgvs_p": "p.Val2982Phe",
"transcript": "NM_001291860.2",
"protein_id": "NP_001278789.1",
"transcript_support_level": null,
"aa_start": 2982,
"aa_end": null,
"aa_length": 4392,
"cds_start": 8944,
"cds_end": null,
"cds_length": 13179,
"cdna_start": 9037,
"cdna_end": null,
"cdna_length": 14344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 73,
"exon_rank_end": null,
"exon_count": 102,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9490G>T",
"hgvs_p": "p.Val3164Phe",
"transcript": "XM_011541318.3",
"protein_id": "XP_011539620.1",
"transcript_support_level": null,
"aa_start": 3164,
"aa_end": null,
"aa_length": 4574,
"cds_start": 9490,
"cds_end": null,
"cds_length": 13725,
"cdna_start": 9583,
"cdna_end": null,
"cdna_length": 14890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9439G>T",
"hgvs_p": "p.Val3147Phe",
"transcript": "XM_047419080.1",
"protein_id": "XP_047275036.1",
"transcript_support_level": null,
"aa_start": 3147,
"aa_end": null,
"aa_length": 4557,
"cds_start": 9439,
"cds_end": null,
"cds_length": 13674,
"cdna_start": 9532,
"cdna_end": null,
"cdna_length": 14839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 72,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9436G>T",
"hgvs_p": "p.Val3146Phe",
"transcript": "XM_047419090.1",
"protein_id": "XP_047275046.1",
"transcript_support_level": null,
"aa_start": 3146,
"aa_end": null,
"aa_length": 4556,
"cds_start": 9436,
"cds_end": null,
"cds_length": 13671,
"cdna_start": 9529,
"cdna_end": null,
"cdna_length": 14836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 69,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9136G>T",
"hgvs_p": "p.Val3046Phe",
"transcript": "XM_017001120.1",
"protein_id": "XP_016856609.1",
"transcript_support_level": null,
"aa_start": 3046,
"aa_end": null,
"aa_length": 4456,
"cds_start": 9136,
"cds_end": null,
"cds_length": 13371,
"cdna_start": 9151,
"cdna_end": null,
"cdna_length": 14458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 69,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9133G>T",
"hgvs_p": "p.Val3045Phe",
"transcript": "XM_047419091.1",
"protein_id": "XP_047275047.1",
"transcript_support_level": null,
"aa_start": 3045,
"aa_end": null,
"aa_length": 4455,
"cds_start": 9133,
"cds_end": null,
"cds_length": 13368,
"cdna_start": 9148,
"cdna_end": null,
"cdna_length": 14455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 68,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9085G>T",
"hgvs_p": "p.Val3029Phe",
"transcript": "XM_017001121.1",
"protein_id": "XP_016856610.1",
"transcript_support_level": null,
"aa_start": 3029,
"aa_end": null,
"aa_length": 4439,
"cds_start": 9085,
"cds_end": null,
"cds_length": 13320,
"cdna_start": 9100,
"cdna_end": null,
"cdna_length": 14407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 68,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.9082G>T",
"hgvs_p": "p.Val3028Phe",
"transcript": "XM_017001122.1",
"protein_id": "XP_016856611.1",
"transcript_support_level": null,
"aa_start": 3028,
"aa_end": null,
"aa_length": 4438,
"cds_start": 9082,
"cds_end": null,
"cds_length": 13317,
"cdna_start": 9097,
"cdna_end": null,
"cdna_length": 14404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"dbsnp": "rs2229490",
"frequency_reference_population": 0.0000018635693,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000137209,
"gnomad_genomes_af": 0.00000657108,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20073473453521729,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.123,
"revel_prediction": "Benign",
"alphamissense_score": 0.2605,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.849,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.13,
"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": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000374695.8",
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8941G>T",
"hgvs_p": "p.Val2981Phe"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}