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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: 17-72122749-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=72122749&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 72122749,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000245479.3",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOX9",
"gene_hgnc_id": 11204,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Phe154Phe",
"transcript": "NM_000346.4",
"protein_id": "NP_000337.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 509,
"cds_start": 462,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 834,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "ENST00000245479.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOX9",
"gene_hgnc_id": 11204,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Phe154Phe",
"transcript": "ENST00000245479.3",
"protein_id": "ENSP00000245479.2",
"transcript_support_level": 1,
"aa_start": 154,
"aa_end": null,
"aa_length": 509,
"cds_start": 462,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 834,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "NM_000346.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SOX9-AS1",
"gene_hgnc_id": 49321,
"hgvs_c": "n.96+18936G>A",
"hgvs_p": null,
"transcript": "ENST00000414600.1",
"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": 742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288605",
"gene_hgnc_id": null,
"hgvs_c": "n.147-37704G>A",
"hgvs_p": null,
"transcript": "ENST00000628742.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288605",
"gene_hgnc_id": null,
"hgvs_c": "n.304-77225G>A",
"hgvs_p": null,
"transcript": "ENST00000674828.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SOX9-AS1",
"gene_hgnc_id": 49321,
"hgvs_c": "n.511-37704G>A",
"hgvs_p": null,
"transcript": "ENST00000715469.1",
"protein_id": null,
"transcript_support_level": null,
"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": 999,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SOX9",
"gene_hgnc_id": 11204,
"dbsnp": "rs137853129",
"frequency_reference_population": 0.000004104388,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410439,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.27000001072883606,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.374,
"phylop100way_prediction": "Benign",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000245479.3",
"gene_symbol": "SOX9",
"hgnc_id": 11204,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Phe154Phe"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000414600.1",
"gene_symbol": "SOX9-AS1",
"hgnc_id": 49321,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.96+18936G>A",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000674828.1",
"gene_symbol": "ENSG00000288605",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.304-77225G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}