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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: 9-101429858-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=101429858&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 101429858,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000647789.2",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr",
"transcript": "NM_000035.4",
"protein_id": "NP_000026.2",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 364,
"cds_start": 221,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 2420,
"mane_select": "ENST00000647789.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr",
"transcript": "ENST00000647789.2",
"protein_id": "ENSP00000497767.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 364,
"cds_start": 221,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 2420,
"mane_select": "NM_000035.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr",
"transcript": "ENST00000648064.1",
"protein_id": "ENSP00000497990.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 364,
"cds_start": 221,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 368,
"cdna_end": null,
"cdna_length": 1612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr",
"transcript": "ENST00000648758.1",
"protein_id": "ENSP00000497731.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 364,
"cds_start": 221,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 395,
"cdna_end": null,
"cdna_length": 1444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr",
"transcript": "ENST00000649902.1",
"protein_id": "ENSP00000497216.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 342,
"cds_start": 221,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 241,
"cdna_end": null,
"cdna_length": 1408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr",
"transcript": "ENST00000648423.1",
"protein_id": "ENSP00000497985.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 74,
"cds_start": 221,
"cds_end": null,
"cds_length": 225,
"cdna_start": 410,
"cdna_end": null,
"cdna_length": 414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "n.18T>C",
"hgvs_p": null,
"transcript": "ENST00000468981.3",
"protein_id": null,
"transcript_support_level": 5,
"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": 218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "n.391T>C",
"hgvs_p": null,
"transcript": "ENST00000648906.1",
"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": 1109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"hgvs_c": "n.297T>C",
"hgvs_p": null,
"transcript": "ENST00000650613.1",
"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": 1034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALDOB",
"gene_hgnc_id": 417,
"dbsnp": "rs781023784",
"frequency_reference_population": 0.0000034202253,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342023,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9845362901687622,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.933,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5549,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.325,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000647789.2",
"gene_symbol": "ALDOB",
"hgnc_id": 417,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.221T>C",
"hgvs_p": "p.Ile74Thr"
}
],
"clinvar_disease": "Hereditary fructosuria",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Hereditary fructosuria",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}