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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: 4-121854739-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121854739&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 121854739,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000264499.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.683G>T",
"hgvs_p": "p.Arg228Leu",
"transcript": "NM_176824.3",
"protein_id": "NP_789794.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 715,
"cds_start": 683,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 844,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": "ENST00000264499.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.683G>T",
"hgvs_p": "p.Arg228Leu",
"transcript": "ENST00000264499.9",
"protein_id": "ENSP00000264499.4",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 715,
"cds_start": 683,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 844,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": "NM_176824.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.683G>T",
"hgvs_p": "p.Arg228Leu",
"transcript": "ENST00000506636.1",
"protein_id": "ENSP00000423626.1",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 672,
"cds_start": 683,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 820,
"cdna_end": null,
"cdna_length": 2570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.683G>T",
"hgvs_p": "p.Arg228Leu",
"transcript": "NM_018190.4",
"protein_id": "NP_060660.2",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 672,
"cds_start": 683,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 844,
"cdna_end": null,
"cdna_length": 2594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.731G>T",
"hgvs_p": "p.Arg244Leu",
"transcript": "XM_011532079.4",
"protein_id": "XP_011530381.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 731,
"cds_start": 731,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 3888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.728G>T",
"hgvs_p": "p.Arg243Leu",
"transcript": "XM_011532080.4",
"protein_id": "XP_011530382.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 730,
"cds_start": 728,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 889,
"cdna_end": null,
"cdna_length": 3885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.686G>T",
"hgvs_p": "p.Arg229Leu",
"transcript": "XM_005263106.5",
"protein_id": "XP_005263163.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 716,
"cds_start": 686,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 3843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.731G>T",
"hgvs_p": "p.Arg244Leu",
"transcript": "XM_011532081.4",
"protein_id": "XP_011530383.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 676,
"cds_start": 731,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 3723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.728G>T",
"hgvs_p": "p.Arg243Leu",
"transcript": "XM_047415889.1",
"protein_id": "XP_047271845.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 675,
"cds_start": 728,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 889,
"cdna_end": null,
"cdna_length": 3720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.686G>T",
"hgvs_p": "p.Arg229Leu",
"transcript": "XM_047415890.1",
"protein_id": "XP_047271846.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 661,
"cds_start": 686,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 3678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.683G>T",
"hgvs_p": "p.Arg228Leu",
"transcript": "XM_017008357.3",
"protein_id": "XP_016863846.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 660,
"cds_start": 683,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 844,
"cdna_end": null,
"cdna_length": 3675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"dbsnp": "rs369866009",
"frequency_reference_population": 0.0000013698649,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136986,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12099036574363708,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.164,
"revel_prediction": "Benign",
"alphamissense_score": 0.0883,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.564,
"phylop100way_prediction": "Benign",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000264499.9",
"gene_symbol": "BBS7",
"hgnc_id": 18758,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.683G>T",
"hgvs_p": "p.Arg228Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}