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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: 1-21833345-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21833345&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21833345,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001291860.2",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 80,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11018T>G",
"hgvs_p": "p.Phe3673Cys",
"transcript": "NM_005529.7",
"protein_id": "NP_005520.4",
"transcript_support_level": null,
"aa_start": 3673,
"aa_end": null,
"aa_length": 4391,
"cds_start": 11018,
"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": "F",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 80,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11018T>G",
"hgvs_p": "p.Phe3673Cys",
"transcript": "ENST00000374695.8",
"protein_id": "ENSP00000363827.3",
"transcript_support_level": 1,
"aa_start": 3673,
"aa_end": null,
"aa_length": 4391,
"cds_start": 11018,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 80,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11021T>G",
"hgvs_p": "p.Phe3674Cys",
"transcript": "NM_001291860.2",
"protein_id": "NP_001278789.1",
"transcript_support_level": null,
"aa_start": 3674,
"aa_end": null,
"aa_length": 4392,
"cds_start": 11021,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.149T>G",
"hgvs_p": "p.Phe50Cys",
"transcript": "ENST00000635682.1",
"protein_id": "ENSP00000489161.1",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 305,
"cds_start": 149,
"cds_end": null,
"cds_length": 919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635682.1"
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 85,
"exon_rank_end": null,
"exon_count": 102,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11567T>G",
"hgvs_p": "p.Phe3856Cys",
"transcript": "XM_011541318.3",
"protein_id": "XP_011539620.1",
"transcript_support_level": null,
"aa_start": 3856,
"aa_end": null,
"aa_length": 4574,
"cds_start": 11567,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 84,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11516T>G",
"hgvs_p": "p.Phe3839Cys",
"transcript": "XM_047419080.1",
"protein_id": "XP_047275036.1",
"transcript_support_level": null,
"aa_start": 3839,
"aa_end": null,
"aa_length": 4557,
"cds_start": 11516,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 84,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11513T>G",
"hgvs_p": "p.Phe3838Cys",
"transcript": "XM_047419090.1",
"protein_id": "XP_047275046.1",
"transcript_support_level": null,
"aa_start": 3838,
"aa_end": null,
"aa_length": 4556,
"cds_start": 11513,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 81,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11213T>G",
"hgvs_p": "p.Phe3738Cys",
"transcript": "XM_017001120.1",
"protein_id": "XP_016856609.1",
"transcript_support_level": null,
"aa_start": 3738,
"aa_end": null,
"aa_length": 4456,
"cds_start": 11213,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 81,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11210T>G",
"hgvs_p": "p.Phe3737Cys",
"transcript": "XM_047419091.1",
"protein_id": "XP_047275047.1",
"transcript_support_level": null,
"aa_start": 3737,
"aa_end": null,
"aa_length": 4455,
"cds_start": 11210,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 80,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11162T>G",
"hgvs_p": "p.Phe3721Cys",
"transcript": "XM_017001121.1",
"protein_id": "XP_016856610.1",
"transcript_support_level": null,
"aa_start": 3721,
"aa_end": null,
"aa_length": 4439,
"cds_start": 11162,
"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": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 80,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.11159T>G",
"hgvs_p": "p.Phe3720Cys",
"transcript": "XM_017001122.1",
"protein_id": "XP_016856611.1",
"transcript_support_level": null,
"aa_start": 3720,
"aa_end": null,
"aa_length": 4438,
"cds_start": 11159,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "n.1373T>G",
"hgvs_p": null,
"transcript": "ENST00000471322.2",
"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": "ENST00000471322.2"
}
],
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"dbsnp": "rs147707402",
"frequency_reference_population": 0.000001368137,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136814,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7425183653831482,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.553,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7975,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.088,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001291860.2",
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.11021T>G",
"hgvs_p": "p.Phe3674Cys"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}