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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: 1-9245189-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=9245189&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 9245189,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_004285.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Ser85Ser",
"transcript": "NM_004285.4",
"protein_id": "NP_004276.2",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 791,
"cds_start": 255,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 9147,
"mane_select": "ENST00000377403.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Ser85Ser",
"transcript": "ENST00000377403.7",
"protein_id": "ENSP00000366620.2",
"transcript_support_level": 1,
"aa_start": 85,
"aa_end": null,
"aa_length": 791,
"cds_start": 255,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 9147,
"mane_select": "NM_004285.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.288C>T",
"hgvs_p": "p.Ser96Ser",
"transcript": "ENST00000602477.1",
"protein_id": "ENSP00000473348.1",
"transcript_support_level": 1,
"aa_start": 96,
"aa_end": null,
"aa_length": 802,
"cds_start": 288,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 440,
"cdna_end": null,
"cdna_length": 5590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.288C>T",
"hgvs_p": "p.Ser96Ser",
"transcript": "NM_001282587.2",
"protein_id": "NP_001269516.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 802,
"cds_start": 288,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 9026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.288C>T",
"hgvs_p": "p.Ser96Ser",
"transcript": "XM_047435002.1",
"protein_id": "XP_047290958.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 802,
"cds_start": 288,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 762,
"cdna_end": null,
"cdna_length": 9351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.282C>T",
"hgvs_p": "p.Ser94Ser",
"transcript": "XM_005263540.6",
"protein_id": "XP_005263597.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 800,
"cds_start": 282,
"cds_end": null,
"cds_length": 2403,
"cdna_start": 413,
"cdna_end": null,
"cdna_length": 9002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.276C>T",
"hgvs_p": "p.Ser92Ser",
"transcript": "XM_047435003.1",
"protein_id": "XP_047290959.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 798,
"cds_start": 276,
"cds_end": null,
"cds_length": 2397,
"cdna_start": 407,
"cdna_end": null,
"cdna_length": 8996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Ser85Ser",
"transcript": "XM_006711052.5",
"protein_id": "XP_006711115.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 791,
"cds_start": 255,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 9139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Ser85Ser",
"transcript": "XM_017002865.3",
"protein_id": "XP_016858354.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 791,
"cds_start": 255,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 9018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Ser85Ser",
"transcript": "XM_047435005.1",
"protein_id": "XP_047290961.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 791,
"cds_start": 255,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 9016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"dbsnp": "rs138775586",
"frequency_reference_population": 0.0026278556,
"hom_count_reference_population": 29,
"allele_count_reference_population": 4242,
"gnomad_exomes_af": 0.00269651,
"gnomad_genomes_af": 0.0019691,
"gnomad_exomes_ac": 3942,
"gnomad_genomes_ac": 300,
"gnomad_exomes_homalt": 27,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.2800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.765,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004285.4",
"gene_symbol": "H6PD",
"hgnc_id": 4795,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Ser85Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}