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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: 4-121833309-TCTGGAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=121833309&ref=TCTGGAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 121833309,
"ref": "TCTGGAA",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000264499.9",
"consequences": [
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1592_1597delTTCCAG",
"hgvs_p": "p.Val531_Pro532del",
"transcript": "NM_176824.3",
"protein_id": "NP_789794.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 715,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": "ENST00000264499.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1592_1597delTTCCAG",
"hgvs_p": "p.Val531_Pro532del",
"transcript": "ENST00000264499.9",
"protein_id": "ENSP00000264499.4",
"transcript_support_level": 1,
"aa_start": 531,
"aa_end": null,
"aa_length": 715,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": "NM_176824.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1592_1597delTTCCAG",
"hgvs_p": "p.Val531_Pro532del",
"transcript": "ENST00000506636.1",
"protein_id": "ENSP00000423626.1",
"transcript_support_level": 1,
"aa_start": 531,
"aa_end": null,
"aa_length": 672,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 1734,
"cdna_end": null,
"cdna_length": 2570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1592_1597delTTCCAG",
"hgvs_p": "p.Val531_Pro532del",
"transcript": "NM_018190.4",
"protein_id": "NP_060660.2",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 672,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 2594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1640_1645delTTCCAG",
"hgvs_p": "p.Val547_Pro548del",
"transcript": "XM_011532079.4",
"protein_id": "XP_011530381.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 731,
"cds_start": 1640,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 1806,
"cdna_end": null,
"cdna_length": 3888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1637_1642delTTCCAG",
"hgvs_p": "p.Val546_Pro547del",
"transcript": "XM_011532080.4",
"protein_id": "XP_011530382.1",
"transcript_support_level": null,
"aa_start": 546,
"aa_end": null,
"aa_length": 730,
"cds_start": 1637,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 1803,
"cdna_end": null,
"cdna_length": 3885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VPE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1595_1600delTTCCAG",
"hgvs_p": "p.Val532_Pro533del",
"transcript": "XM_005263106.5",
"protein_id": "XP_005263163.1",
"transcript_support_level": null,
"aa_start": 532,
"aa_end": null,
"aa_length": 716,
"cds_start": 1595,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 1761,
"cdna_end": null,
"cdna_length": 3843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1559+1829_1559+1834delTTCCAG",
"hgvs_p": null,
"transcript": "XM_011532081.4",
"protein_id": "XP_011530383.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 676,
"cds_start": -4,
"cds_end": null,
"cds_length": 2031,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1556+1829_1556+1834delTTCCAG",
"hgvs_p": null,
"transcript": "XM_047415889.1",
"protein_id": "XP_047271845.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 675,
"cds_start": -4,
"cds_end": null,
"cds_length": 2028,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1514+1829_1514+1834delTTCCAG",
"hgvs_p": null,
"transcript": "XM_047415890.1",
"protein_id": "XP_047271846.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 661,
"cds_start": -4,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"hgvs_c": "c.1511+1829_1511+1834delTTCCAG",
"hgvs_p": null,
"transcript": "XM_017008357.3",
"protein_id": "XP_016863846.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 660,
"cds_start": -4,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BBS7",
"gene_hgnc_id": 18758,
"dbsnp": "rs587777836",
"frequency_reference_population": 0.00000867451,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000889367,
"gnomad_genomes_af": 0.00000656987,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.802,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM4,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PM2",
"PM4",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000264499.9",
"gene_symbol": "BBS7",
"hgnc_id": 18758,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1592_1597delTTCCAG",
"hgvs_p": "p.Val531_Pro532del"
}
],
"clinvar_disease": "Bardet-Biedl syndrome,Bardet-Biedl syndrome 7",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"phenotype_combined": "Bardet-Biedl syndrome 7|Bardet-Biedl syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}