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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: 5-150117614-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=150117614&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 150117614,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000261799.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "PDGFRB",
"gene_hgnc_id": 8804,
"hgvs_c": "c.3137+4A>G",
"hgvs_p": null,
"transcript": "NM_002609.4",
"protein_id": "NP_002600.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1106,
"cds_start": -4,
"cds_end": null,
"cds_length": 3321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5700,
"mane_select": "ENST00000261799.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "PDGFRB",
"gene_hgnc_id": 8804,
"hgvs_c": "c.3137+4A>G",
"hgvs_p": null,
"transcript": "ENST00000261799.9",
"protein_id": "ENSP00000261799.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1106,
"cds_start": -4,
"cds_end": null,
"cds_length": 3321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5700,
"mane_select": "NM_002609.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "PDGFRB",
"gene_hgnc_id": 8804,
"hgvs_c": "n.*2451+4A>G",
"hgvs_p": null,
"transcript": "ENST00000520579.5",
"protein_id": "ENSP00000430026.1",
"transcript_support_level": 1,
"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": 3860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "PDGFRB",
"gene_hgnc_id": 8804,
"hgvs_c": "c.2945+4A>G",
"hgvs_p": null,
"transcript": "NM_001355016.2",
"protein_id": "NP_001341945.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1042,
"cds_start": -4,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "PDGFRB",
"gene_hgnc_id": 8804,
"hgvs_c": "c.2654+4A>G",
"hgvs_p": null,
"transcript": "NM_001355017.2",
"protein_id": "NP_001341946.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 945,
"cds_start": -4,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDGFRB",
"gene_hgnc_id": 8804,
"dbsnp": "rs246391",
"frequency_reference_population": 0.40295792,
"hom_count_reference_population": 131370,
"allele_count_reference_population": 627748,
"gnomad_exomes_af": 0.405792,
"gnomad_genomes_af": 0.376548,
"gnomad_exomes_ac": 570893,
"gnomad_genomes_ac": 56855,
"gnomad_exomes_homalt": 120262,
"gnomad_genomes_homalt": 11108,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.11400000005960464,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.43,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.08384833655732,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000261799.9",
"gene_symbol": "PDGFRB",
"hgnc_id": 8804,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3137+4A>G",
"hgvs_p": null
}
],
"clinvar_disease": " 1, 4, chronic, idiopathic, infantile, with eosinophilia,Acroosteolysis-keloid-like lesions-premature aging syndrome,Basal ganglia calcification,Infantile myofibromatosis,Myeloproliferative disorder,Myofibromatosis,Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome|not provided|Basal ganglia calcification, idiopathic, 4|Myeloproliferative disorder, chronic, with eosinophilia|Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome|Acroosteolysis-keloid-like lesions-premature aging syndrome|Myofibromatosis, infantile, 1",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}