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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: 18-62360008-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=62360008&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 62360008,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000586569.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val",
"transcript": "NM_003839.4",
"protein_id": "NP_003830.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 616,
"cds_start": 575,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 8148,
"mane_select": "ENST00000586569.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val",
"transcript": "ENST00000586569.3",
"protein_id": "ENSP00000465500.1",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 616,
"cds_start": 575,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 8148,
"mane_select": "NM_003839.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val",
"transcript": "ENST00000269485.11",
"protein_id": "ENSP00000269485.7",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 299,
"cds_start": 575,
"cds_end": null,
"cds_length": 900,
"cdna_start": 641,
"cdna_end": null,
"cdna_length": 3591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ala178Val",
"transcript": "NM_001278268.2",
"protein_id": "NP_001265197.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 602,
"cds_start": 533,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 8106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val",
"transcript": "NM_001270950.2",
"protein_id": "NP_001257879.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 337,
"cds_start": 575,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 7311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val",
"transcript": "NM_001270951.2",
"protein_id": "NP_001257880.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 299,
"cds_start": 575,
"cds_end": null,
"cds_length": 900,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 7197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val",
"transcript": "NM_001270949.2",
"protein_id": "NP_001257878.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 263,
"cds_start": 575,
"cds_end": null,
"cds_length": 792,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 7364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.590C>T",
"hgvs_p": "p.Ala197Val",
"transcript": "XM_011526244.3",
"protein_id": "XP_011524546.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 621,
"cds_start": 590,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 633,
"cdna_end": null,
"cdna_length": 8163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.467C>T",
"hgvs_p": "p.Ala156Val",
"transcript": "XM_011526245.3",
"protein_id": "XP_011524547.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 580,
"cds_start": 467,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 8232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.467C>T",
"hgvs_p": "p.Ala156Val",
"transcript": "XM_017026064.2",
"protein_id": "XP_016881553.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 580,
"cds_start": 467,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1023,
"cdna_end": null,
"cdna_length": 8553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.425C>T",
"hgvs_p": "p.Ala142Val",
"transcript": "XM_017026065.2",
"protein_id": "XP_016881554.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 566,
"cds_start": 425,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 8170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.365C>T",
"hgvs_p": "p.Ala122Val",
"transcript": "XM_017026066.2",
"protein_id": "XP_016881555.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 546,
"cds_start": 365,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 635,
"cdna_end": null,
"cdna_length": 8165,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "n.493C>T",
"hgvs_p": null,
"transcript": "ENST00000587697.1",
"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": 528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"dbsnp": "rs1805034",
"frequency_reference_population": 0.5206174,
"hom_count_reference_population": 221917,
"allele_count_reference_population": 839505,
"gnomad_exomes_af": 0.516143,
"gnomad_genomes_af": 0.563619,
"gnomad_exomes_ac": 753844,
"gnomad_genomes_ac": 85661,
"gnomad_exomes_homalt": 197394,
"gnomad_genomes_homalt": 24523,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00000593056620346033,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.047,
"revel_prediction": "Benign",
"alphamissense_score": 0.0556,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.391,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000586569.3",
"gene_symbol": "TNFRSF11A",
"hgnc_id": 11908,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.575C>T",
"hgvs_p": "p.Ala192Val"
}
],
"clinvar_disease": "Bone Paget disease,Increased bone mineral density,Osteopetrosis,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:5",
"phenotype_combined": "not specified|Osteopetrosis|Bone Paget disease|not provided|Increased bone mineral density",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}