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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: 1-1212082-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1212082&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 1212082,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000379236.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr",
"transcript": "NM_003327.4",
"protein_id": "NP_003318.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 277,
"cds_start": 494,
"cds_end": null,
"cds_length": 834,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1075,
"mane_select": "ENST00000379236.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr",
"transcript": "ENST00000379236.4",
"protein_id": "ENSP00000368538.3",
"transcript_support_level": 1,
"aa_start": 165,
"aa_end": null,
"aa_length": 277,
"cds_start": 494,
"cds_end": null,
"cds_length": 834,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1075,
"mane_select": "NM_003327.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr",
"transcript": "ENST00000699971.1",
"protein_id": "ENSP00000514728.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 355,
"cds_start": 494,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1184,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr",
"transcript": "NM_001410709.1",
"protein_id": "NP_001397638.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 303,
"cds_start": 494,
"cds_end": null,
"cds_length": 912,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr",
"transcript": "ENST00000699974.1",
"protein_id": "ENSP00000514730.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 303,
"cds_start": 494,
"cds_end": null,
"cds_length": 912,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "ENST00000699969.1",
"protein_id": "ENSP00000514726.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 298,
"cds_start": 557,
"cds_end": null,
"cds_length": 897,
"cdna_start": 583,
"cdna_end": null,
"cdna_length": 1152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr",
"transcript": "ENST00000699977.1",
"protein_id": "ENSP00000514733.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 234,
"cds_start": 494,
"cds_end": null,
"cds_length": 705,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"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": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.506T>C",
"hgvs_p": "p.Ile169Thr",
"transcript": "XM_011542074.3",
"protein_id": "XP_011540376.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 307,
"cds_start": 506,
"cds_end": null,
"cds_length": 924,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 1516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.506T>C",
"hgvs_p": "p.Ile169Thr",
"transcript": "XM_011542076.3",
"protein_id": "XP_011540378.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 281,
"cds_start": 506,
"cds_end": null,
"cds_length": 846,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 1438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"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": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.194T>C",
"hgvs_p": "p.Ile65Thr",
"transcript": "XM_011542077.3",
"protein_id": "XP_011540379.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 203,
"cds_start": 194,
"cds_end": null,
"cds_length": 612,
"cdna_start": 321,
"cdna_end": null,
"cdna_length": 954,
"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": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.330T>C",
"hgvs_p": null,
"transcript": "ENST00000453580.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 393,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.1074T>C",
"hgvs_p": null,
"transcript": "ENST00000497869.5",
"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": 1707,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.451T>C",
"hgvs_p": null,
"transcript": "ENST00000699970.1",
"protein_id": "ENSP00000514727.1",
"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": 1012,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.1089T>C",
"hgvs_p": null,
"transcript": "ENST00000699972.1",
"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": 1644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.*12T>C",
"hgvs_p": null,
"transcript": "ENST00000699973.1",
"protein_id": "ENSP00000514729.1",
"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": 1067,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.382T>C",
"hgvs_p": null,
"transcript": "ENST00000699978.1",
"protein_id": "ENSP00000514734.1",
"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": 959,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.427T>C",
"hgvs_p": null,
"transcript": "ENST00000699979.1",
"protein_id": "ENSP00000514735.1",
"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": 1002,
"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": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.1022T>C",
"hgvs_p": null,
"transcript": "XR_007063145.1",
"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": 1048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.*12T>C",
"hgvs_p": null,
"transcript": "ENST00000699973.1",
"protein_id": "ENSP00000514729.1",
"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": 1067,
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.438-250T>C",
"hgvs_p": null,
"transcript": "ENST00000699976.1",
"protein_id": "ENSP00000514732.1",
"transcript_support_level": null,
"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": 878,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.371-250T>C",
"hgvs_p": null,
"transcript": "ENST00000699975.1",
"protein_id": "ENSP00000514731.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": -4,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"dbsnp": "rs150407012",
"frequency_reference_population": 0.0010226724,
"hom_count_reference_population": 8,
"allele_count_reference_population": 1649,
"gnomad_exomes_af": 0.00103957,
"gnomad_genomes_af": 0.000860563,
"gnomad_exomes_ac": 1518,
"gnomad_genomes_ac": 131,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.035802245140075684,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.099,
"revel_prediction": "Benign",
"alphamissense_score": 0.2169,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.207,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000379236.4",
"gene_symbol": "TNFRSF4",
"hgnc_id": 11918,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Ile165Thr"
}
],
"clinvar_disease": "Combined immunodeficiency due to OX40 deficiency,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Combined immunodeficiency due to OX40 deficiency|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}