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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: 1-21861796-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21861796&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21861796,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000374695.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.4916C>T",
"hgvs_p": "p.Thr1639Met",
"transcript": "NM_005529.7",
"protein_id": "NP_005520.4",
"transcript_support_level": null,
"aa_start": 1639,
"aa_end": null,
"aa_length": 4391,
"cds_start": 4916,
"cds_end": null,
"cds_length": 13176,
"cdna_start": 5009,
"cdna_end": null,
"cdna_length": 14341,
"mane_select": "ENST00000374695.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.4916C>T",
"hgvs_p": "p.Thr1639Met",
"transcript": "ENST00000374695.8",
"protein_id": "ENSP00000363827.3",
"transcript_support_level": 1,
"aa_start": 1639,
"aa_end": null,
"aa_length": 4391,
"cds_start": 4916,
"cds_end": null,
"cds_length": 13176,
"cdna_start": 5009,
"cdna_end": null,
"cdna_length": 14341,
"mane_select": "NM_005529.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.4919C>T",
"hgvs_p": "p.Thr1640Met",
"transcript": "NM_001291860.2",
"protein_id": "NP_001278789.1",
"transcript_support_level": null,
"aa_start": 1640,
"aa_end": null,
"aa_length": 4392,
"cds_start": 4919,
"cds_end": null,
"cds_length": 13179,
"cdna_start": 5012,
"cdna_end": null,
"cdna_length": 14344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 102,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5465C>T",
"hgvs_p": "p.Thr1822Met",
"transcript": "XM_011541318.3",
"protein_id": "XP_011539620.1",
"transcript_support_level": null,
"aa_start": 1822,
"aa_end": null,
"aa_length": 4574,
"cds_start": 5465,
"cds_end": null,
"cds_length": 13725,
"cdna_start": 5558,
"cdna_end": null,
"cdna_length": 14890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5414C>T",
"hgvs_p": "p.Thr1805Met",
"transcript": "XM_047419080.1",
"protein_id": "XP_047275036.1",
"transcript_support_level": null,
"aa_start": 1805,
"aa_end": null,
"aa_length": 4557,
"cds_start": 5414,
"cds_end": null,
"cds_length": 13674,
"cdna_start": 5507,
"cdna_end": null,
"cdna_length": 14839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5411C>T",
"hgvs_p": "p.Thr1804Met",
"transcript": "XM_047419090.1",
"protein_id": "XP_047275046.1",
"transcript_support_level": null,
"aa_start": 1804,
"aa_end": null,
"aa_length": 4556,
"cds_start": 5411,
"cds_end": null,
"cds_length": 13671,
"cdna_start": 5504,
"cdna_end": null,
"cdna_length": 14836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5111C>T",
"hgvs_p": "p.Thr1704Met",
"transcript": "XM_017001120.1",
"protein_id": "XP_016856609.1",
"transcript_support_level": null,
"aa_start": 1704,
"aa_end": null,
"aa_length": 4456,
"cds_start": 5111,
"cds_end": null,
"cds_length": 13371,
"cdna_start": 5126,
"cdna_end": null,
"cdna_length": 14458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 40,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5108C>T",
"hgvs_p": "p.Thr1703Met",
"transcript": "XM_047419091.1",
"protein_id": "XP_047275047.1",
"transcript_support_level": null,
"aa_start": 1703,
"aa_end": null,
"aa_length": 4455,
"cds_start": 5108,
"cds_end": null,
"cds_length": 13368,
"cdna_start": 5123,
"cdna_end": null,
"cdna_length": 14455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5060C>T",
"hgvs_p": "p.Thr1687Met",
"transcript": "XM_017001121.1",
"protein_id": "XP_016856610.1",
"transcript_support_level": null,
"aa_start": 1687,
"aa_end": null,
"aa_length": 4439,
"cds_start": 5060,
"cds_end": null,
"cds_length": 13320,
"cdna_start": 5075,
"cdna_end": null,
"cdna_length": 14407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.5057C>T",
"hgvs_p": "p.Thr1686Met",
"transcript": "XM_017001122.1",
"protein_id": "XP_016856611.1",
"transcript_support_level": null,
"aa_start": 1686,
"aa_end": null,
"aa_length": 4438,
"cds_start": 5057,
"cds_end": null,
"cds_length": 13317,
"cdna_start": 5072,
"cdna_end": null,
"cdna_length": 14404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"dbsnp": "rs142433309",
"frequency_reference_population": 0.0030252405,
"hom_count_reference_population": 15,
"allele_count_reference_population": 4882,
"gnomad_exomes_af": 0.0031633,
"gnomad_genomes_af": 0.0017005,
"gnomad_exomes_ac": 4623,
"gnomad_genomes_ac": 259,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1667347252368927,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.417,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2388,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.136,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000374695.8",
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4916C>T",
"hgvs_p": "p.Thr1639Met"
}
],
"clinvar_disease": "HSPG2-related disorder,Intellectual disability,Lethal Kniest-like syndrome,Schwartz-Jampel syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:6 B:3",
"phenotype_combined": "not specified|Schwartz-Jampel syndrome|not provided|HSPG2-related disorder|Lethal Kniest-like syndrome|Intellectual disability",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}