← Back to variant description
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: 1-94043413-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=94043413&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 94043413,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000370225.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.3113C>T",
"hgvs_p": "p.Ala1038Val",
"transcript": "NM_000350.3",
"protein_id": "NP_000341.2",
"transcript_support_level": null,
"aa_start": 1038,
"aa_end": null,
"aa_length": 2273,
"cds_start": 3113,
"cds_end": null,
"cds_length": 6822,
"cdna_start": 3216,
"cdna_end": null,
"cdna_length": 7328,
"mane_select": "ENST00000370225.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.3113C>T",
"hgvs_p": "p.Ala1038Val",
"transcript": "ENST00000370225.4",
"protein_id": "ENSP00000359245.3",
"transcript_support_level": 1,
"aa_start": 1038,
"aa_end": null,
"aa_length": 2273,
"cds_start": 3113,
"cds_end": null,
"cds_length": 6822,
"cdna_start": 3216,
"cdna_end": null,
"cdna_length": 7328,
"mane_select": "NM_000350.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.2891C>T",
"hgvs_p": "p.Ala964Val",
"transcript": "NM_001425324.1",
"protein_id": "NP_001412253.1",
"transcript_support_level": null,
"aa_start": 964,
"aa_end": null,
"aa_length": 2199,
"cds_start": 2891,
"cds_end": null,
"cds_length": 6600,
"cdna_start": 2994,
"cdna_end": null,
"cdna_length": 7106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"dbsnp": "rs61751374",
"frequency_reference_population": 0.0018480383,
"hom_count_reference_population": 7,
"allele_count_reference_population": 2983,
"gnomad_exomes_af": 0.00187018,
"gnomad_genomes_af": 0.0016354,
"gnomad_exomes_ac": 2734,
"gnomad_genomes_ac": 249,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.023493528366088867,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.533,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1637,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.785,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PP2,PP5_Very_Strong,BP4,BS2_Supporting",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 2,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PP2",
"PP5_Very_Strong",
"BP4",
"BS2_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000370225.4",
"gene_symbol": "ABCA4",
"hgnc_id": 34,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3113C>T",
"hgvs_p": "p.Ala1038Val"
}
],
"clinvar_disease": "ABCA4-related disorder,Age related macular degeneration 2,Cone-rod dystrophy 3,Macular dystrophy,Optic atrophy,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 19,Severe early-childhood-onset retinal dystrophy,Stargardt disease,not provided,not specified",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:23 LP:4 O:1",
"phenotype_combined": "Cone-rod dystrophy 3|Severe early-childhood-onset retinal dystrophy|not provided|Retinal dystrophy|Severe early-childhood-onset retinal dystrophy;Retinitis pigmentosa 19;Age related macular degeneration 2;Cone-rod dystrophy 3|Macular dystrophy|Stargardt disease|Retinitis pigmentosa|ABCA4-related disorder|not specified|Age related macular degeneration 2|Optic atrophy|Retinitis pigmentosa 19;Cone-rod dystrophy 3",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}