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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: 3-52402360-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52402360&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 52402360,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000460680.6",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2118C>T",
"hgvs_p": "p.Ile706Ile",
"transcript": "NM_004656.4",
"protein_id": "NP_004647.1",
"transcript_support_level": null,
"aa_start": 706,
"aa_end": null,
"aa_length": 729,
"cds_start": 2118,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 2248,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": "ENST00000460680.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2118C>T",
"hgvs_p": "p.Ile706Ile",
"transcript": "ENST00000460680.6",
"protein_id": "ENSP00000417132.1",
"transcript_support_level": 1,
"aa_start": 706,
"aa_end": null,
"aa_length": 729,
"cds_start": 2118,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 2248,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": "NM_004656.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Ile230Ile",
"transcript": "ENST00000478368.1",
"protein_id": "ENSP00000420647.1",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 253,
"cds_start": 690,
"cds_end": null,
"cds_length": 762,
"cdna_start": 690,
"cdna_end": null,
"cdna_length": 1234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.315C>T",
"hgvs_p": "p.Ile105Ile",
"transcript": "ENST00000469613.5",
"protein_id": "ENSP00000418320.1",
"transcript_support_level": 1,
"aa_start": 105,
"aa_end": null,
"aa_length": 128,
"cds_start": 315,
"cds_end": null,
"cds_length": 387,
"cdna_start": 317,
"cdna_end": null,
"cdna_length": 1654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2064C>T",
"hgvs_p": "p.Ile688Ile",
"transcript": "NM_001410772.1",
"protein_id": "NP_001397701.1",
"transcript_support_level": null,
"aa_start": 688,
"aa_end": null,
"aa_length": 711,
"cds_start": 2064,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2194,
"cdna_end": null,
"cdna_length": 3546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2064C>T",
"hgvs_p": "p.Ile688Ile",
"transcript": "ENST00000296288.9",
"protein_id": "ENSP00000296288.5",
"transcript_support_level": 5,
"aa_start": 688,
"aa_end": null,
"aa_length": 711,
"cds_start": 2064,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2100,
"cdna_end": null,
"cdna_length": 3434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2187C>T",
"hgvs_p": "p.Ile729Ile",
"transcript": "XM_011534149.4",
"protein_id": "XP_011532451.1",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 752,
"cds_start": 2187,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 2317,
"cdna_end": null,
"cdna_length": 3669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2142C>T",
"hgvs_p": "p.Ile714Ile",
"transcript": "XM_011534150.4",
"protein_id": "XP_011532452.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 737,
"cds_start": 2142,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 2272,
"cdna_end": null,
"cdna_length": 3624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2133C>T",
"hgvs_p": "p.Ile711Ile",
"transcript": "XM_011534151.4",
"protein_id": "XP_011532453.1",
"transcript_support_level": null,
"aa_start": 711,
"aa_end": null,
"aa_length": 734,
"cds_start": 2133,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 2263,
"cdna_end": null,
"cdna_length": 3615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2073C>T",
"hgvs_p": "p.Ile691Ile",
"transcript": "XM_011534152.3",
"protein_id": "XP_011532454.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 714,
"cds_start": 2073,
"cds_end": null,
"cds_length": 2145,
"cdna_start": 2203,
"cdna_end": null,
"cdna_length": 3555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.2019C>T",
"hgvs_p": "p.Ile673Ile",
"transcript": "XM_047449044.1",
"protein_id": "XP_047305000.1",
"transcript_support_level": null,
"aa_start": 673,
"aa_end": null,
"aa_length": 696,
"cds_start": 2019,
"cds_end": null,
"cds_length": 2091,
"cdna_start": 2149,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "n.791C>T",
"hgvs_p": null,
"transcript": "ENST00000466093.1",
"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": 1127,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"hgvs_c": "c.-199C>T",
"hgvs_p": null,
"transcript": "ENST00000615113.1",
"protein_id": "ENSP00000482839.1",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 162,
"cds_start": -4,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BAP1",
"gene_hgnc_id": 950,
"dbsnp": "rs201122466",
"frequency_reference_population": 0.000013909366,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000146924,
"gnomad_genomes_af": 0.0000065634,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.39100000262260437,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.391,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.328,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000460680.6",
"gene_symbol": "BAP1",
"hgnc_id": 950,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2118C>T",
"hgvs_p": "p.Ile706Ile"
}
],
"clinvar_disease": "BAP1-related tumor predisposition syndrome,Hereditary cancer-predisposing syndrome",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|BAP1-related tumor predisposition syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}