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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: 1-94041249-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=94041249&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 94041249,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000370225.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.3482G>A",
"hgvs_p": "p.Arg1161His",
"transcript": "NM_000350.3",
"protein_id": "NP_000341.2",
"transcript_support_level": null,
"aa_start": 1161,
"aa_end": null,
"aa_length": 2273,
"cds_start": 3482,
"cds_end": null,
"cds_length": 6822,
"cdna_start": 3585,
"cdna_end": null,
"cdna_length": 7328,
"mane_select": "ENST00000370225.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.3482G>A",
"hgvs_p": "p.Arg1161His",
"transcript": "ENST00000370225.4",
"protein_id": "ENSP00000359245.3",
"transcript_support_level": 1,
"aa_start": 1161,
"aa_end": null,
"aa_length": 2273,
"cds_start": 3482,
"cds_end": null,
"cds_length": 6822,
"cdna_start": 3585,
"cdna_end": null,
"cdna_length": 7328,
"mane_select": "NM_000350.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.3260G>A",
"hgvs_p": "p.Arg1087His",
"transcript": "NM_001425324.1",
"protein_id": "NP_001412253.1",
"transcript_support_level": null,
"aa_start": 1087,
"aa_end": null,
"aa_length": 2199,
"cds_start": 3260,
"cds_end": null,
"cds_length": 6600,
"cdna_start": 3363,
"cdna_end": null,
"cdna_length": 7106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"dbsnp": "rs768278935",
"frequency_reference_population": 0.000011771718,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000123129,
"gnomad_genomes_af": 0.00000657229,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9118541479110718,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.76,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4286,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.75,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM5",
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000370225.4",
"gene_symbol": "ABCA4",
"hgnc_id": 34,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3482G>A",
"hgvs_p": "p.Arg1161His"
}
],
"clinvar_disease": "Age related macular degeneration 2,Autosomal recessive retinitis pigmentosa,Cone-rod dystrophy,Cone-rod dystrophy 3,Retinal dystrophy,Retinitis pigmentosa 19,Severe early-childhood-onset retinal dystrophy,Stargardt disease,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:3",
"phenotype_combined": "Severe early-childhood-onset retinal dystrophy|not provided|Autosomal recessive retinitis pigmentosa|Stargardt disease|Retinal dystrophy|Cone-rod dystrophy|Age related macular degeneration 2;Severe early-childhood-onset retinal dystrophy;Cone-rod dystrophy 3;Retinitis pigmentosa 19",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}