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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: 3-52403825-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52403825&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 52403825,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000460680.6",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1320G>A",
"hgvs_p": "p.Leu440Leu",
"transcript": "NM_004656.4",
"protein_id": "NP_004647.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 729,
"cds_start": 1320,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": "ENST00000460680.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1320G>A",
"hgvs_p": "p.Leu440Leu",
"transcript": "ENST00000460680.6",
"protein_id": "ENSP00000417132.1",
"transcript_support_level": 1,
"aa_start": 440,
"aa_end": null,
"aa_length": 729,
"cds_start": 1320,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": "NM_004656.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.93G>A",
"hgvs_p": "p.Leu31Leu",
"transcript": "ENST00000469613.5",
"protein_id": "ENSP00000418320.1",
"transcript_support_level": 1,
"aa_start": 31,
"aa_end": null,
"aa_length": 128,
"cds_start": 93,
"cds_end": null,
"cds_length": 387,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 1654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Leu422Leu",
"transcript": "NM_001410772.1",
"protein_id": "NP_001397701.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 711,
"cds_start": 1266,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 3546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Leu422Leu",
"transcript": "ENST00000296288.9",
"protein_id": "ENSP00000296288.5",
"transcript_support_level": 5,
"aa_start": 422,
"aa_end": null,
"aa_length": 711,
"cds_start": 1266,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 3434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1320G>A",
"hgvs_p": "p.Leu440Leu",
"transcript": "XM_011534149.4",
"protein_id": "XP_011532451.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 752,
"cds_start": 1320,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 3669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1320G>A",
"hgvs_p": "p.Leu440Leu",
"transcript": "XM_011534150.4",
"protein_id": "XP_011532452.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 737,
"cds_start": 1320,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 3624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Leu422Leu",
"transcript": "XM_011534151.4",
"protein_id": "XP_011532453.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 734,
"cds_start": 1266,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 3615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1320G>A",
"hgvs_p": "p.Leu440Leu",
"transcript": "XM_011534152.3",
"protein_id": "XP_011532454.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 714,
"cds_start": 1320,
"cds_end": null,
"cds_length": 2145,
"cdna_start": 1450,
"cdna_end": null,
"cdna_length": 3555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Leu422Leu",
"transcript": "XM_047449044.1",
"protein_id": "XP_047305000.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 696,
"cds_start": 1266,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 1396,
"cdna_end": null,
"cdna_length": 3501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "n.748G>A",
"hgvs_p": null,
"transcript": "ENST00000490804.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.-178G>A",
"hgvs_p": null,
"transcript": "ENST00000478368.1",
"protein_id": "ENSP00000420647.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 253,
"cds_start": -4,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"dbsnp": "rs77722216",
"frequency_reference_population": 0.000118951444,
"hom_count_reference_population": 2,
"allele_count_reference_population": 192,
"gnomad_exomes_af": 0.000074564,
"gnomad_genomes_af": 0.000545077,
"gnomad_exomes_ac": 109,
"gnomad_genomes_ac": 83,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5329999923706055,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.533,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.453,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000460680.6",
"gene_symbol": "BAP1",
"hgnc_id": 950,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1320G>A",
"hgvs_p": "p.Leu440Leu"
}
],
"clinvar_disease": "BAP1-related tumor predisposition syndrome,Hereditary cancer-predisposing syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:4",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|not provided|BAP1-related tumor predisposition syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}