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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: 18-62361793-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=62361793&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 62361793,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000586569.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Ala244Thr",
"transcript": "NM_003839.4",
"protein_id": "NP_003830.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 616,
"cds_start": 730,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 8148,
"mane_select": "ENST00000586569.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Ala244Thr",
"transcript": "ENST00000586569.3",
"protein_id": "ENSP00000465500.1",
"transcript_support_level": 1,
"aa_start": 244,
"aa_end": null,
"aa_length": 616,
"cds_start": 730,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 8148,
"mane_select": "NM_003839.4",
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.616+1744G>A",
"hgvs_p": null,
"transcript": "ENST00000269485.11",
"protein_id": "ENSP00000269485.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Ala230Thr",
"transcript": "NM_001278268.2",
"protein_id": "NP_001265197.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 602,
"cds_start": 688,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 8106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Gly244Arg",
"transcript": "NM_001270950.2",
"protein_id": "NP_001257879.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 337,
"cds_start": 730,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 7311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Ala244Thr",
"transcript": "NM_001270949.2",
"protein_id": "NP_001257878.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 263,
"cds_start": 730,
"cds_end": null,
"cds_length": 792,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 7364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.745G>A",
"hgvs_p": "p.Ala249Thr",
"transcript": "XM_011526244.3",
"protein_id": "XP_011524546.1",
"transcript_support_level": null,
"aa_start": 249,
"aa_end": null,
"aa_length": 621,
"cds_start": 745,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 788,
"cdna_end": null,
"cdna_length": 8163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Ala208Thr",
"transcript": "XM_011526245.3",
"protein_id": "XP_011524547.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 580,
"cds_start": 622,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 8232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Ala208Thr",
"transcript": "XM_017026064.2",
"protein_id": "XP_016881553.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 580,
"cds_start": 622,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1178,
"cdna_end": null,
"cdna_length": 8553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Ala194Thr",
"transcript": "XM_017026065.2",
"protein_id": "XP_016881554.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 566,
"cds_start": 580,
"cds_end": null,
"cds_length": 1701,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 8170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Ala174Thr",
"transcript": "XM_017026066.2",
"protein_id": "XP_016881555.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 546,
"cds_start": 520,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 790,
"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": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"hgvs_c": "c.616+1744G>A",
"hgvs_p": null,
"transcript": "NM_001270951.2",
"protein_id": "NP_001257880.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7197,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNFRSF11A",
"gene_hgnc_id": 11908,
"dbsnp": "rs121908658",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38996657729148865,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.222,
"revel_prediction": "Benign",
"alphamissense_score": 0.2293,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.664,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.97,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999992042933719,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000586569.3",
"gene_symbol": "TNFRSF11A",
"hgnc_id": 11908,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.730G>A",
"hgvs_p": "p.Ala244Thr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}