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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: 12-54000490-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=54000490&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 54000490,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000303450.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC9",
"gene_hgnc_id": 5130,
"hgvs_c": "c.302C>G",
"hgvs_p": "p.Ser101Cys",
"transcript": "NM_006897.3",
"protein_id": "NP_008828.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 260,
"cds_start": 302,
"cds_end": null,
"cds_length": 783,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 1474,
"mane_select": "ENST00000303450.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC9",
"gene_hgnc_id": 5130,
"hgvs_c": "c.302C>G",
"hgvs_p": "p.Ser101Cys",
"transcript": "ENST00000303450.5",
"protein_id": "ENSP00000302836.4",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 260,
"cds_start": 302,
"cds_end": null,
"cds_length": 783,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 1474,
"mane_select": "NM_006897.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000273049",
"gene_hgnc_id": null,
"hgvs_c": "c.166+14480C>G",
"hgvs_p": null,
"transcript": "ENST00000513209.1",
"protein_id": "ENSP00000476742.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 126,
"cds_start": -4,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOXC9",
"gene_hgnc_id": 5130,
"hgvs_c": "c.302C>G",
"hgvs_p": "p.Ser101Cys",
"transcript": "ENST00000508190.1",
"protein_id": "ENSP00000423861.1",
"transcript_support_level": 3,
"aa_start": 101,
"aa_end": null,
"aa_length": 260,
"cds_start": 302,
"cds_end": null,
"cds_length": 783,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 1505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.-73+5474C>G",
"hgvs_p": null,
"transcript": "ENST00000509328.1",
"protein_id": "ENSP00000423898.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 70,
"cds_start": -4,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC6",
"gene_hgnc_id": 5128,
"hgvs_c": "c.-193+9676C>G",
"hgvs_p": null,
"transcript": "ENST00000504315.1",
"protein_id": "ENSP00000424124.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 50,
"cds_start": -4,
"cds_end": null,
"cds_length": 155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOXC9",
"gene_hgnc_id": 5130,
"hgvs_c": "n.123-1940C>G",
"hgvs_p": null,
"transcript": "ENST00000504557.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HOXC9",
"gene_hgnc_id": 5130,
"dbsnp": "rs200358721",
"frequency_reference_population": 0.000045633726,
"hom_count_reference_population": 0,
"allele_count_reference_population": 73,
"gnomad_exomes_af": 0.0000407616,
"gnomad_genomes_af": 0.0000919516,
"gnomad_exomes_ac": 59,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.43577611446380615,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.86,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1281,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.94,
"phylop100way_prediction": "Uncertain_significance",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000303450.5",
"gene_symbol": "HOXC9",
"hgnc_id": 5130,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.302C>G",
"hgvs_p": "p.Ser101Cys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000513209.1",
"gene_symbol": "ENSG00000273049",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.166+14480C>G",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000509328.1",
"gene_symbol": "HOXC6",
"hgnc_id": 5128,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-73+5474C>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}