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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: 1-21839541-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21839541&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"hgvs_c": "c.9722C>A",
"hgvs_p": "p.Ala3241Glu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001291860.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 7,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0849,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.11436727643013,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "A",
"aa_start": 3240,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 9812,
"cds_end": null,
"cds_length": 13176,
"cds_start": 9719,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 73,
"exon_rank_end": null,
"feature": "NM_005529.7",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9719C>A",
"hgvs_p": "p.Ala3240Glu",
"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": "E",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "A",
"aa_start": 3240,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 9812,
"cds_end": null,
"cds_length": 13176,
"cds_start": 9719,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 73,
"exon_rank_end": null,
"feature": "ENST00000374695.8",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9719C>A",
"hgvs_p": "p.Ala3240Glu",
"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": "E",
"aa_end": null,
"aa_length": 4392,
"aa_ref": "A",
"aa_start": 3241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14344,
"cdna_start": 9815,
"cds_end": null,
"cds_length": 13179,
"cds_start": 9722,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 73,
"exon_rank_end": null,
"feature": "NM_001291860.2",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9722C>A",
"hgvs_p": "p.Ala3241Glu",
"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": "E",
"aa_end": null,
"aa_length": 4574,
"aa_ref": "A",
"aa_start": 3423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14890,
"cdna_start": 10361,
"cds_end": null,
"cds_length": 13725,
"cds_start": 10268,
"consequences": [
"missense_variant"
],
"exon_count": 102,
"exon_rank": 78,
"exon_rank_end": null,
"feature": "XM_011541318.3",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.10268C>A",
"hgvs_p": "p.Ala3423Glu",
"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": "E",
"aa_end": null,
"aa_length": 4557,
"aa_ref": "A",
"aa_start": 3406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14839,
"cdna_start": 10310,
"cds_end": null,
"cds_length": 13674,
"cds_start": 10217,
"consequences": [
"missense_variant"
],
"exon_count": 101,
"exon_rank": 77,
"exon_rank_end": null,
"feature": "XM_047419080.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.10217C>A",
"hgvs_p": "p.Ala3406Glu",
"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": "E",
"aa_end": null,
"aa_length": 4556,
"aa_ref": "A",
"aa_start": 3405,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14836,
"cdna_start": 10307,
"cds_end": null,
"cds_length": 13671,
"cds_start": 10214,
"consequences": [
"missense_variant"
],
"exon_count": 101,
"exon_rank": 77,
"exon_rank_end": null,
"feature": "XM_047419090.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.10214C>A",
"hgvs_p": "p.Ala3405Glu",
"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": "E",
"aa_end": null,
"aa_length": 4456,
"aa_ref": "A",
"aa_start": 3305,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14458,
"cdna_start": 9929,
"cds_end": null,
"cds_length": 13371,
"cds_start": 9914,
"consequences": [
"missense_variant"
],
"exon_count": 98,
"exon_rank": 74,
"exon_rank_end": null,
"feature": "XM_017001120.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9914C>A",
"hgvs_p": "p.Ala3305Glu",
"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": "E",
"aa_end": null,
"aa_length": 4455,
"aa_ref": "A",
"aa_start": 3304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14455,
"cdna_start": 9926,
"cds_end": null,
"cds_length": 13368,
"cds_start": 9911,
"consequences": [
"missense_variant"
],
"exon_count": 98,
"exon_rank": 74,
"exon_rank_end": null,
"feature": "XM_047419091.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9911C>A",
"hgvs_p": "p.Ala3304Glu",
"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": "E",
"aa_end": null,
"aa_length": 4439,
"aa_ref": "A",
"aa_start": 3288,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14407,
"cdna_start": 9878,
"cds_end": null,
"cds_length": 13320,
"cds_start": 9863,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 73,
"exon_rank_end": null,
"feature": "XM_017001121.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9863C>A",
"hgvs_p": "p.Ala3288Glu",
"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": "E",
"aa_end": null,
"aa_length": 4438,
"aa_ref": "A",
"aa_start": 3287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14404,
"cdna_start": 9875,
"cds_end": null,
"cds_length": 13317,
"cds_start": 9860,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": 73,
"exon_rank_end": null,
"feature": "XM_017001122.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.9860C>A",
"hgvs_p": "p.Ala3287Glu",
"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": "rs62642505",
"effect": "missense_variant",
"frequency_reference_population": 0.0000043378086,
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000410511,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657358,
"gnomad_genomes_homalt": 0,
"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": 0.104,
"pos": 21839541,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.052,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_001291860.2"
}
]
}