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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: 1-36139776-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=36139776&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 36139776,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000373166.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Arg62Trp",
"transcript": "NM_014408.5",
"protein_id": "NP_055223.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 180,
"cds_start": 184,
"cds_end": null,
"cds_length": 543,
"cdna_start": 292,
"cdna_end": null,
"cdna_length": 1282,
"mane_select": "ENST00000373166.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Arg62Trp",
"transcript": "ENST00000373166.8",
"protein_id": "ENSP00000362261.3",
"transcript_support_level": 1,
"aa_start": 62,
"aa_end": null,
"aa_length": 180,
"cds_start": 184,
"cds_end": null,
"cds_length": 543,
"cdna_start": 292,
"cdna_end": null,
"cdna_length": 1282,
"mane_select": "NM_014408.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.208C>T",
"hgvs_p": "p.Arg70Trp",
"transcript": "NM_001270894.2",
"protein_id": "NP_001257823.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 188,
"cds_start": 208,
"cds_end": null,
"cds_length": 567,
"cdna_start": 316,
"cdna_end": null,
"cdna_length": 1306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.208C>T",
"hgvs_p": "p.Arg70Trp",
"transcript": "ENST00000616395.4",
"protein_id": "ENSP00000480332.1",
"transcript_support_level": 3,
"aa_start": 70,
"aa_end": null,
"aa_length": 188,
"cds_start": 208,
"cds_end": null,
"cds_length": 567,
"cdna_start": 344,
"cdna_end": null,
"cdna_length": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001270895.2",
"protein_id": "NP_001257824.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 134,
"cds_start": 46,
"cds_end": null,
"cds_length": 405,
"cdna_start": 313,
"cdna_end": null,
"cdna_length": 1303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001270896.2",
"protein_id": "NP_001257825.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 134,
"cds_start": 46,
"cds_end": null,
"cds_length": 405,
"cdna_start": 537,
"cdna_end": null,
"cdna_length": 1527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000373162.5",
"protein_id": "ENSP00000362256.1",
"transcript_support_level": 2,
"aa_start": 16,
"aa_end": null,
"aa_length": 134,
"cds_start": 46,
"cds_end": null,
"cds_length": 405,
"cdna_start": 548,
"cdna_end": null,
"cdna_length": 1056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000373163.5",
"protein_id": "ENSP00000362257.1",
"transcript_support_level": 3,
"aa_start": 16,
"aa_end": null,
"aa_length": 134,
"cds_start": 46,
"cds_end": null,
"cds_length": 405,
"cdna_start": 334,
"cdna_end": null,
"cdna_length": 951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000617904.4",
"protein_id": "ENSP00000480648.1",
"transcript_support_level": 2,
"aa_start": 16,
"aa_end": null,
"aa_length": 134,
"cds_start": 46,
"cds_end": null,
"cds_length": 405,
"cdna_start": 313,
"cdna_end": null,
"cdna_length": 1305,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Arg62Trp",
"transcript": "ENST00000373159.1",
"protein_id": "ENSP00000362253.1",
"transcript_support_level": 3,
"aa_start": 62,
"aa_end": null,
"aa_length": 118,
"cds_start": 184,
"cds_end": null,
"cds_length": 357,
"cdna_start": 302,
"cdna_end": null,
"cdna_length": 590,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "n.974C>T",
"hgvs_p": null,
"transcript": "ENST00000462715.1",
"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": 2428,
"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": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "n.338C>T",
"hgvs_p": null,
"transcript": "ENST00000497251.1",
"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": 715,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.43-1798C>T",
"hgvs_p": null,
"transcript": "NM_001270897.2",
"protein_id": "NP_001257826.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1084,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "c.43-1798C>T",
"hgvs_p": null,
"transcript": "ENST00000616074.4",
"protein_id": "ENSP00000482052.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "n.161-2454C>T",
"hgvs_p": null,
"transcript": "ENST00000469757.1",
"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": 221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "n.396-1798C>T",
"hgvs_p": null,
"transcript": "NR_073097.2",
"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": 1329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"hgvs_c": "n.151-2454C>T",
"hgvs_p": null,
"transcript": "NR_073098.2",
"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": 901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRAPPC3",
"gene_hgnc_id": 19942,
"dbsnp": "rs751375244",
"frequency_reference_population": 0.000016728976,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.000015049,
"gnomad_genomes_af": 0.0000328779,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8794050812721252,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.15000000596046448,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.519,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9017,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.741,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.15,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000373166.8",
"gene_symbol": "TRAPPC3",
"hgnc_id": 19942,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.184C>T",
"hgvs_p": "p.Arg62Trp"
}
],
"clinvar_disease": "Bardet-Biedl syndrome",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Bardet-Biedl syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}