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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: 1-40310265-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40310265&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40310265,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000372748.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.737C>G",
"hgvs_p": "p.Thr246Arg",
"transcript": "NM_001852.4",
"protein_id": "NP_001843.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 689,
"cds_start": 737,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 826,
"cdna_end": null,
"cdna_length": 2852,
"mane_select": "ENST00000372748.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.737C>G",
"hgvs_p": "p.Thr246Arg",
"transcript": "ENST00000372748.8",
"protein_id": "ENSP00000361834.3",
"transcript_support_level": 1,
"aa_start": 246,
"aa_end": null,
"aa_length": 689,
"cds_start": 737,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 826,
"cdna_end": null,
"cdna_length": 2852,
"mane_select": "NM_001852.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "n.1040C>G",
"hgvs_p": null,
"transcript": "ENST00000482722.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.749C>G",
"hgvs_p": "p.Thr250Arg",
"transcript": "XM_017000332.2",
"protein_id": "XP_016855821.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 693,
"cds_start": 749,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 838,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.467C>G",
"hgvs_p": "p.Thr156Arg",
"transcript": "XM_011540715.3",
"protein_id": "XP_011539017.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 599,
"cds_start": 467,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 932,
"cdna_end": null,
"cdna_length": 2958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.467C>G",
"hgvs_p": "p.Thr156Arg",
"transcript": "XM_011540716.3",
"protein_id": "XP_011539018.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 599,
"cds_start": 467,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 778,
"cdna_end": null,
"cdna_length": 2804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.455C>G",
"hgvs_p": "p.Thr152Arg",
"transcript": "XM_017000333.2",
"protein_id": "XP_016855822.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 595,
"cds_start": 455,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 2792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.749C>G",
"hgvs_p": "p.Thr250Arg",
"transcript": "XM_047446392.1",
"protein_id": "XP_047302348.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 395,
"cds_start": 749,
"cds_end": null,
"cds_length": 1188,
"cdna_start": 838,
"cdna_end": null,
"cdna_length": 1365,
"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_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "n.788C>G",
"hgvs_p": null,
"transcript": "ENST00000488463.6",
"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": 843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.*25C>G",
"hgvs_p": null,
"transcript": "ENST00000417105.6",
"protein_id": "ENSP00000388493.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 142,
"cds_start": -4,
"cds_end": null,
"cds_length": 430,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"dbsnp": "rs2228565",
"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": 0.1323339343070984,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.024000000208616257,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.207,
"revel_prediction": "Benign",
"alphamissense_score": 0.0806,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.167,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000112967564628213,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000372748.8",
"gene_symbol": "COL9A2",
"hgnc_id": 2218,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.737C>G",
"hgvs_p": "p.Thr246Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}