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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: 4-166003471-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=166003471&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 166003471,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000061240.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "c.713T>C",
"hgvs_p": "p.Val238Ala",
"transcript": "NM_012464.5",
"protein_id": "NP_036596.3",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 1013,
"cds_start": 713,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 7291,
"mane_select": "ENST00000061240.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "c.713T>C",
"hgvs_p": "p.Val238Ala",
"transcript": "ENST00000061240.7",
"protein_id": "ENSP00000061240.2",
"transcript_support_level": 1,
"aa_start": 238,
"aa_end": null,
"aa_length": 1013,
"cds_start": 713,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 7291,
"mane_select": "NM_012464.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "c.713T>C",
"hgvs_p": "p.Val238Ala",
"transcript": "ENST00000507499.5",
"protein_id": "ENSP00000426082.1",
"transcript_support_level": 1,
"aa_start": 238,
"aa_end": null,
"aa_length": 1036,
"cds_start": 713,
"cds_end": null,
"cds_length": 3111,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 4818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"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": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "c.713T>C",
"hgvs_p": "p.Val238Ala",
"transcript": "ENST00000513213.5",
"protein_id": "ENSP00000422937.1",
"transcript_support_level": 1,
"aa_start": 238,
"aa_end": null,
"aa_length": 392,
"cds_start": 713,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 878,
"cdna_end": null,
"cdna_length": 1829,
"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": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "n.*358T>C",
"hgvs_p": null,
"transcript": "ENST00000509505.5",
"protein_id": "ENSP00000422692.1",
"transcript_support_level": 1,
"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": 4787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "n.*358T>C",
"hgvs_p": null,
"transcript": "ENST00000509505.5",
"protein_id": "ENSP00000422692.1",
"transcript_support_level": 1,
"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": 4787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"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": "TLL1",
"gene_hgnc_id": 11843,
"hgvs_c": "c.713T>C",
"hgvs_p": "p.Val238Ala",
"transcript": "NM_001204760.2",
"protein_id": "NP_001191689.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 392,
"cds_start": 713,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 2333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TLL1",
"gene_hgnc_id": 11843,
"dbsnp": "rs137852952",
"frequency_reference_population": 0.0003971347,
"hom_count_reference_population": 0,
"allele_count_reference_population": 641,
"gnomad_exomes_af": 0.000413193,
"gnomad_genomes_af": 0.000242983,
"gnomad_exomes_ac": 604,
"gnomad_genomes_ac": 37,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7273228168487549,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.633,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9306,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000061240.7",
"gene_symbol": "TLL1",
"hgnc_id": 11843,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.713T>C",
"hgvs_p": "p.Val238Ala"
}
],
"clinvar_disease": "Atrial septal defect 6,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Atrial septal defect 6|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}