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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: 14-36657575-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=36657575&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 36657575,
"ref": "C",
"alt": "T",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "NM_006194.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"hgvs_c": "c.-719C>T",
"hgvs_p": null,
"transcript": "NM_006194.4",
"protein_id": "NP_006185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4662,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006194.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"hgvs_c": "c.-719C>T",
"hgvs_p": null,
"transcript": "ENST00000402703.6",
"protein_id": "ENSP00000384817.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3104,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402703.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"hgvs_c": "c.-719C>T",
"hgvs_p": null,
"transcript": "NM_006194.4",
"protein_id": "NP_006185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4662,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006194.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"hgvs_c": "c.-719C>T",
"hgvs_p": null,
"transcript": "ENST00000402703.6",
"protein_id": "ENSP00000384817.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 341,
"cds_start": null,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3104,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402703.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"hgvs_c": "n.8C>T",
"hgvs_p": null,
"transcript": "ENST00000553267.4",
"protein_id": null,
"transcript_support_level": 4,
"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": 645,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000553267.4"
},
{
"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": "ENSG00000258661",
"gene_hgnc_id": null,
"hgvs_c": "n.258+969G>A",
"hgvs_p": null,
"transcript": "ENST00000555107.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 2613,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000555107.1"
},
{
"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": "ENSG00000258661",
"gene_hgnc_id": null,
"hgvs_c": "n.535-2117G>A",
"hgvs_p": null,
"transcript": "ENST00000729136.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1112,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000729136.1"
},
{
"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": "ENSG00000258661",
"gene_hgnc_id": null,
"hgvs_c": "n.207+969G>A",
"hgvs_p": null,
"transcript": "ENST00000729137.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1874,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000729137.1"
},
{
"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": "LOC105370455",
"gene_hgnc_id": null,
"hgvs_c": "n.206+969G>A",
"hgvs_p": null,
"transcript": "XR_943758.3",
"protein_id": null,
"transcript_support_level": null,
"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": 1873,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_943758.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"hgvs_c": "c.-398C>T",
"hgvs_p": null,
"transcript": "ENST00000555639.2",
"protein_id": "ENSP00000501203.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 82,
"cds_start": null,
"cds_end": null,
"cds_length": 251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 553,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000555639.2"
}
],
"gene_symbol": "PAX9",
"gene_hgnc_id": 8623,
"dbsnp": "rs147254306",
"frequency_reference_population": 0.00055177487,
"hom_count_reference_population": 0,
"allele_count_reference_population": 84,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.000551775,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 84,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3700000047683716,
"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": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.091,
"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,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_006194.4",
"gene_symbol": "PAX9",
"hgnc_id": 8623,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-719C>T",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000555107.1",
"gene_symbol": "ENSG00000258661",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.258+969G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XR_943758.3",
"gene_symbol": "LOC105370455",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.206+969G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 3, selective,Tooth agenesis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Tooth agenesis, selective, 3",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}