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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: 1-21878586-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21878586&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21878586,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001291860.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2549G>A",
"hgvs_p": "p.Arg850His",
"transcript": "NM_005529.7",
"protein_id": "NP_005520.4",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 4391,
"cds_start": 2549,
"cds_end": null,
"cds_length": 13176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374695.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005529.7"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2549G>A",
"hgvs_p": "p.Arg850His",
"transcript": "ENST00000374695.8",
"protein_id": "ENSP00000363827.3",
"transcript_support_level": 1,
"aa_start": 850,
"aa_end": null,
"aa_length": 4391,
"cds_start": 2549,
"cds_end": null,
"cds_length": 13176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005529.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374695.8"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2552G>A",
"hgvs_p": "p.Arg851His",
"transcript": "NM_001291860.2",
"protein_id": "NP_001278789.1",
"transcript_support_level": null,
"aa_start": 851,
"aa_end": null,
"aa_length": 4392,
"cds_start": 2552,
"cds_end": null,
"cds_length": 13179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291860.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 102,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2603G>A",
"hgvs_p": "p.Arg868His",
"transcript": "XM_011541318.3",
"protein_id": "XP_011539620.1",
"transcript_support_level": null,
"aa_start": 868,
"aa_end": null,
"aa_length": 4574,
"cds_start": 2603,
"cds_end": null,
"cds_length": 13725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541318.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2552G>A",
"hgvs_p": "p.Arg851His",
"transcript": "XM_047419080.1",
"protein_id": "XP_047275036.1",
"transcript_support_level": null,
"aa_start": 851,
"aa_end": null,
"aa_length": 4557,
"cds_start": 2552,
"cds_end": null,
"cds_length": 13674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419080.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2549G>A",
"hgvs_p": "p.Arg850His",
"transcript": "XM_047419090.1",
"protein_id": "XP_047275046.1",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 4556,
"cds_start": 2549,
"cds_end": null,
"cds_length": 13671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419090.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2744G>A",
"hgvs_p": "p.Arg915His",
"transcript": "XM_017001120.1",
"protein_id": "XP_016856609.1",
"transcript_support_level": null,
"aa_start": 915,
"aa_end": null,
"aa_length": 4456,
"cds_start": 2744,
"cds_end": null,
"cds_length": 13371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001120.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2741G>A",
"hgvs_p": "p.Arg914His",
"transcript": "XM_047419091.1",
"protein_id": "XP_047275047.1",
"transcript_support_level": null,
"aa_start": 914,
"aa_end": null,
"aa_length": 4455,
"cds_start": 2741,
"cds_end": null,
"cds_length": 13368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419091.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2693G>A",
"hgvs_p": "p.Arg898His",
"transcript": "XM_017001121.1",
"protein_id": "XP_016856610.1",
"transcript_support_level": null,
"aa_start": 898,
"aa_end": null,
"aa_length": 4439,
"cds_start": 2693,
"cds_end": null,
"cds_length": 13320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001121.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2690G>A",
"hgvs_p": "p.Arg897His",
"transcript": "XM_017001122.1",
"protein_id": "XP_016856611.1",
"transcript_support_level": null,
"aa_start": 897,
"aa_end": null,
"aa_length": 4438,
"cds_start": 2690,
"cds_end": null,
"cds_length": 13317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001122.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "n.159G>A",
"hgvs_p": null,
"transcript": "ENST00000480900.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000480900.1"
}
],
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"dbsnp": "rs140392638",
"frequency_reference_population": 0.00020073006,
"hom_count_reference_population": 2,
"allele_count_reference_population": 324,
"gnomad_exomes_af": 0.000155974,
"gnomad_genomes_af": 0.000630219,
"gnomad_exomes_ac": 228,
"gnomad_genomes_ac": 96,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13135981559753418,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.419,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2711,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.158,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001291860.2",
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2552G>A",
"hgvs_p": "p.Arg851His"
}
],
"clinvar_disease": "HSPG2-related disorder,Lethal Kniest-like syndrome,Schwartz-Jampel syndrome,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:6",
"phenotype_combined": "not specified|Schwartz-Jampel syndrome|Lethal Kniest-like syndrome|not provided|HSPG2-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}