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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: 1-1211711-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1211711&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 1211711,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_003327.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Lys252Lys",
"transcript": "NM_003327.4",
"protein_id": "NP_003318.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 277,
"cds_start": 756,
"cds_end": null,
"cds_length": 834,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 1075,
"mane_select": "ENST00000379236.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Lys252Lys",
"transcript": "ENST00000379236.4",
"protein_id": "ENSP00000368538.3",
"transcript_support_level": 1,
"aa_start": 252,
"aa_end": null,
"aa_length": 277,
"cds_start": 756,
"cds_end": null,
"cds_length": 834,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 1075,
"mane_select": "NM_003327.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"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.865G>A",
"hgvs_p": "p.Ala289Thr",
"transcript": "ENST00000699971.1",
"protein_id": "ENSP00000514728.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 355,
"cds_start": 865,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 891,
"cdna_end": null,
"cdna_length": 1184,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"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.559G>A",
"hgvs_p": "p.Ala187Thr",
"transcript": "ENST00000699976.1",
"protein_id": "ENSP00000514732.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 253,
"cds_start": 559,
"cds_end": null,
"cds_length": 762,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Lys252Lys",
"transcript": "NM_001410709.1",
"protein_id": "NP_001397638.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 303,
"cds_start": 756,
"cds_end": null,
"cds_length": 912,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 1153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Lys252Lys",
"transcript": "ENST00000699974.1",
"protein_id": "ENSP00000514730.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 303,
"cds_start": 756,
"cds_end": null,
"cds_length": 912,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 1153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.819G>A",
"hgvs_p": "p.Lys273Lys",
"transcript": "ENST00000699969.1",
"protein_id": "ENSP00000514726.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 298,
"cds_start": 819,
"cds_end": null,
"cds_length": 897,
"cdna_start": 845,
"cdna_end": null,
"cdna_length": 1152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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": "c.492G>A",
"hgvs_p": "p.Lys164Lys",
"transcript": "ENST00000699975.1",
"protein_id": "ENSP00000514731.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 189,
"cds_start": 492,
"cds_end": null,
"cds_length": 570,
"cdna_start": 518,
"cdna_end": null,
"cdna_length": 811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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": "c.768G>A",
"hgvs_p": "p.Lys256Lys",
"transcript": "XM_011542074.3",
"protein_id": "XP_011540376.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 307,
"cds_start": 768,
"cds_end": null,
"cds_length": 924,
"cdna_start": 1145,
"cdna_end": null,
"cdna_length": 1516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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": "c.768G>A",
"hgvs_p": "p.Lys256Lys",
"transcript": "XM_011542076.3",
"protein_id": "XP_011540378.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 281,
"cds_start": 768,
"cds_end": null,
"cds_length": 846,
"cdna_start": 1145,
"cdna_end": null,
"cdna_length": 1438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "XM_011542077.3",
"protein_id": "XP_011540379.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 203,
"cds_start": 456,
"cds_end": null,
"cds_length": 612,
"cdna_start": 583,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.1336G>A",
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.713G>A",
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.1351G>A",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.*136G>A",
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.644G>A",
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.689G>A",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "n.*136G>A",
"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": 5,
"intron_rank_end": null,
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"hgvs_c": "c.635-86G>A",
"hgvs_p": null,
"transcript": "ENST00000699977.1",
"protein_id": "ENSP00000514733.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": -4,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNFRSF4",
"gene_hgnc_id": 11918,
"dbsnp": "rs1649118689",
"frequency_reference_population": 0.0000065751406,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657514,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"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": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.755,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_003327.4",
"gene_symbol": "TNFRSF4",
"hgnc_id": 11918,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.756G>A",
"hgvs_p": "p.Lys252Lys"
}
],
"clinvar_disease": "Combined immunodeficiency due to OX40 deficiency",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Combined immunodeficiency due to OX40 deficiency",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}