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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: 3-10142063-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=10142063&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 10142063,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000256474.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "NM_000551.4",
"protein_id": "NP_000542.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 213,
"cds_start": 216,
"cds_end": null,
"cds_length": 642,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4414,
"mane_select": "ENST00000256474.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000256474.3",
"protein_id": "ENSP00000256474.3",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 213,
"cds_start": 216,
"cds_end": null,
"cds_length": 642,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4414,
"mane_select": "NM_000551.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000345392.3",
"protein_id": "ENSP00000344757.2",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 172,
"cds_start": 216,
"cds_end": null,
"cds_length": 519,
"cdna_start": 276,
"cdna_end": null,
"cdna_length": 4281,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.262C>T",
"hgvs_p": null,
"transcript": "ENST00000477538.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 5224,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000696153.2",
"protein_id": "ENSP00000512444.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 250,
"cds_start": 216,
"cds_end": null,
"cds_length": 753,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000713811.1",
"protein_id": "ENSP00000519117.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 210,
"cds_start": 216,
"cds_end": null,
"cds_length": 633,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "NM_001354723.2",
"protein_id": "NP_001341652.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 193,
"cds_start": 216,
"cds_end": null,
"cds_length": 582,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000696143.2",
"protein_id": "ENSP00000512435.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 193,
"cds_start": 216,
"cds_end": null,
"cds_length": 582,
"cdna_start": 248,
"cdna_end": null,
"cdna_length": 4512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "NM_198156.3",
"protein_id": "NP_937799.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 172,
"cds_start": 216,
"cds_end": null,
"cds_length": 519,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4291,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000713982.1",
"protein_id": "ENSP00000519273.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 140,
"cds_start": 216,
"cds_end": null,
"cds_length": 423,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 4319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser",
"transcript": "ENST00000713812.1",
"protein_id": "ENSP00000519118.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 117,
"cds_start": 216,
"cds_end": null,
"cds_length": 354,
"cdna_start": 278,
"cdna_end": null,
"cdna_length": 4285,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.216C>T",
"hgvs_p": null,
"transcript": "ENST00000696142.2",
"protein_id": "ENSP00000512434.1",
"transcript_support_level": null,
"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": 4665,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.277C>T",
"hgvs_p": null,
"transcript": "ENST00000713813.1",
"protein_id": null,
"transcript_support_level": null,
"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": 5116,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.216C>T",
"hgvs_p": null,
"transcript": "ENST00000713814.1",
"protein_id": "ENSP00000519119.1",
"transcript_support_level": null,
"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": 4462,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.286C>T",
"hgvs_p": null,
"transcript": "NR_176335.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.36+180C>T",
"hgvs_p": null,
"transcript": "ENST00000713815.1",
"protein_id": "ENSP00000519120.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 56,
"cds_start": -4,
"cds_end": null,
"cds_length": 171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.84+180C>T",
"hgvs_p": null,
"transcript": "ENST00000713816.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"dbsnp": "rs774557051",
"frequency_reference_population": 0.000001244363,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.8727e-7,
"gnomad_genomes_af": 0.00000656961,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.20000000298023224,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.589,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6,BP7",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000256474.3",
"gene_symbol": "VHL",
"hgnc_id": 12687,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Ser72Ser"
}
],
"clinvar_disease": "Chuvash polycythemia,Hereditary cancer-predisposing syndrome,Von Hippel-Lindau syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:2 B:1",
"phenotype_combined": "Chuvash polycythemia;Von Hippel-Lindau syndrome|Hereditary cancer-predisposing syndrome|Von Hippel-Lindau syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}