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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: 3-187733551-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=187733551&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 187733551,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000406870.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "NM_001706.5",
"protein_id": "NP_001697.2",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 706,
"cds_start": 143,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 3306,
"mane_select": "ENST00000406870.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "ENST00000406870.7",
"protein_id": "ENSP00000384371.2",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 706,
"cds_start": 143,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 3306,
"mane_select": "NM_001706.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "ENST00000232014.8",
"protein_id": "ENSP00000232014.4",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 706,
"cds_start": 143,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 672,
"cdna_end": null,
"cdna_length": 2710,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "ENST00000450123.6",
"protein_id": "ENSP00000413122.2",
"transcript_support_level": 1,
"aa_start": 48,
"aa_end": null,
"aa_length": 650,
"cds_start": 143,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 167,
"cdna_end": null,
"cdna_length": 2003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "NM_001130845.2",
"protein_id": "NP_001124317.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 706,
"cds_start": 143,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 3659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "NM_001134738.2",
"protein_id": "NP_001128210.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 650,
"cds_start": 143,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 3138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "ENST00000621333.4",
"protein_id": "ENSP00000479784.1",
"transcript_support_level": 5,
"aa_start": 48,
"aa_end": null,
"aa_length": 650,
"cds_start": 143,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 3399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "ENST00000430339.5",
"protein_id": "ENSP00000415574.1",
"transcript_support_level": 2,
"aa_start": 48,
"aa_end": null,
"aa_length": 120,
"cds_start": 143,
"cds_end": null,
"cds_length": 365,
"cdna_start": 232,
"cdna_end": null,
"cdna_length": 454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "ENST00000438077.1",
"protein_id": "ENSP00000414455.1",
"transcript_support_level": 3,
"aa_start": 48,
"aa_end": null,
"aa_length": 103,
"cds_start": 143,
"cds_end": null,
"cds_length": 312,
"cdna_start": 540,
"cdna_end": null,
"cdna_length": 709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "XM_005247694.5",
"protein_id": "XP_005247751.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 706,
"cds_start": 143,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 501,
"cdna_end": null,
"cdna_length": 3560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met",
"transcript": "XM_047448655.1",
"protein_id": "XP_047304611.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 706,
"cds_start": 143,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1758,
"cdna_end": null,
"cdna_length": 4817,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "n.143C>T",
"hgvs_p": null,
"transcript": "ENST00000419510.6",
"protein_id": "ENSP00000398014.2",
"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": 4178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ENSG00000228804",
"gene_hgnc_id": null,
"hgvs_c": "n.596G>A",
"hgvs_p": null,
"transcript": "ENST00000437407.2",
"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": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ENSG00000228804",
"gene_hgnc_id": null,
"hgvs_c": "n.374G>A",
"hgvs_p": null,
"transcript": "ENST00000449623.6",
"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": 679,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"hgvs_c": "n.220C>T",
"hgvs_p": null,
"transcript": "ENST00000480458.5",
"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": 342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BCL6",
"gene_hgnc_id": 1001,
"dbsnp": "rs200263685",
"frequency_reference_population": 0.00006754194,
"hom_count_reference_population": 0,
"allele_count_reference_population": 109,
"gnomad_exomes_af": 0.0000643049,
"gnomad_genomes_af": 0.0000986673,
"gnomad_exomes_ac": 94,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2192898392677307,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.437,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7899,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.362,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000406870.7",
"gene_symbol": "BCL6",
"hgnc_id": 1001,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.143C>T",
"hgvs_p": "p.Thr48Met"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000437407.2",
"gene_symbol": "ENSG00000228804",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.596G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "not provided",
"clinvar_review_status": "no classification provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "not provided",
"custom_annotations": null
}
],
"message": null
}