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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: 9-132264987-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=132264987&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 132264987,
"ref": "T",
"alt": "C",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "NM_015046.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7288-2A>G",
"hgvs_p": null,
"transcript": "NM_015046.7",
"protein_id": "NP_055861.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2677,
"cds_start": -4,
"cds_end": null,
"cds_length": 8034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11101,
"mane_select": "ENST00000224140.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7288-2A>G",
"hgvs_p": null,
"transcript": "ENST00000224140.6",
"protein_id": "ENSP00000224140.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2677,
"cds_start": -4,
"cds_end": null,
"cds_length": 8034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11101,
"mane_select": "NM_015046.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7375-2A>G",
"hgvs_p": null,
"transcript": "NM_001351528.2",
"protein_id": "NP_001338457.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2706,
"cds_start": -4,
"cds_end": null,
"cds_length": 8121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7288-2A>G",
"hgvs_p": null,
"transcript": "NM_001351527.2",
"protein_id": "NP_001338456.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2677,
"cds_start": -4,
"cds_end": null,
"cds_length": 8034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.2101-2A>G",
"hgvs_p": null,
"transcript": "ENST00000436441.5",
"protein_id": "ENSP00000409143.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 948,
"cds_start": -4,
"cds_end": null,
"cds_length": 2847,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "n.438-2A>G",
"hgvs_p": null,
"transcript": "ENST00000477049.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 4067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7375-2A>G",
"hgvs_p": null,
"transcript": "XM_005272172.4",
"protein_id": "XP_005272229.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2706,
"cds_start": -4,
"cds_end": null,
"cds_length": 8121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11304,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7375-2A>G",
"hgvs_p": null,
"transcript": "XM_005272173.4",
"protein_id": "XP_005272230.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2706,
"cds_start": -4,
"cds_end": null,
"cds_length": 8121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 27,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7375-2A>G",
"hgvs_p": null,
"transcript": "XM_011518404.4",
"protein_id": "XP_011516706.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2706,
"cds_start": -4,
"cds_end": null,
"cds_length": 8121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7375-2A>G",
"hgvs_p": null,
"transcript": "XM_011518405.4",
"protein_id": "XP_011516707.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2706,
"cds_start": -4,
"cds_end": null,
"cds_length": 8121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"hgvs_c": "c.7288-2A>G",
"hgvs_p": null,
"transcript": "XM_047423023.1",
"protein_id": "XP_047278979.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2677,
"cds_start": -4,
"cds_end": null,
"cds_length": 8034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SETX",
"gene_hgnc_id": 445,
"dbsnp": "rs1554801819",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23999999463558197,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9359999895095825,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.168,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.99,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999989917668626,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_015046.7",
"gene_symbol": "SETX",
"hgnc_id": 445,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.7288-2A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}