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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: 1-94078693-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=94078693&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 94078693,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000370225.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.1253T>G",
"hgvs_p": "p.Phe418Cys",
"transcript": "NM_000350.3",
"protein_id": "NP_000341.2",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 2273,
"cds_start": 1253,
"cds_end": null,
"cds_length": 6822,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 7328,
"mane_select": "ENST00000370225.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.1253T>G",
"hgvs_p": "p.Phe418Cys",
"transcript": "ENST00000370225.4",
"protein_id": "ENSP00000359245.3",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 2273,
"cds_start": 1253,
"cds_end": null,
"cds_length": 6822,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 7328,
"mane_select": "NM_000350.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.1253T>G",
"hgvs_p": "p.Phe418Cys",
"transcript": "NM_001425324.1",
"protein_id": "NP_001412253.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 2199,
"cds_start": 1253,
"cds_end": null,
"cds_length": 6600,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 7106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"hgvs_c": "c.1253T>G",
"hgvs_p": "p.Phe418Cys",
"transcript": "ENST00000649773.1",
"protein_id": "ENSP00000496882.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 979,
"cds_start": 1253,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 1333,
"cdna_end": null,
"cdna_length": 3105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124904222",
"gene_hgnc_id": null,
"hgvs_c": "n.203-5036A>C",
"hgvs_p": null,
"transcript": "XR_007066231.1",
"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": 1908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCA4",
"gene_hgnc_id": 34,
"dbsnp": "rs794726979",
"frequency_reference_population": 6.843109e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84311e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9069716930389404,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.932,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9444,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.947,
"phylop100way_prediction": "Pathogenic",
"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,PM2,PM5,PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000370225.4",
"gene_symbol": "ABCA4",
"hgnc_id": 34,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1253T>G",
"hgvs_p": "p.Phe418Cys"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007066231.1",
"gene_symbol": "LOC124904222",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.203-5036A>C",
"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
}