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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: X-9746119-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=9746119&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 9746119,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000467482.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR143",
"gene_hgnc_id": 20145,
"hgvs_c": "c.583T>C",
"hgvs_p": "p.Tyr195His",
"transcript": "NM_000273.3",
"protein_id": "NP_000264.2",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 404,
"cds_start": 583,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 1645,
"mane_select": "ENST00000467482.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR143",
"gene_hgnc_id": 20145,
"hgvs_c": "c.583T>C",
"hgvs_p": "p.Tyr195His",
"transcript": "ENST00000467482.6",
"protein_id": "ENSP00000417161.1",
"transcript_support_level": 1,
"aa_start": 195,
"aa_end": null,
"aa_length": 404,
"cds_start": 583,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 1645,
"mane_select": "NM_000273.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR143",
"gene_hgnc_id": 20145,
"hgvs_c": "c.583T>C",
"hgvs_p": "p.Tyr195His",
"transcript": "NM_001440781.1",
"protein_id": "NP_001427710.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 386,
"cds_start": 583,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 1781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR143",
"gene_hgnc_id": 20145,
"hgvs_c": "c.331T>C",
"hgvs_p": "p.Tyr111His",
"transcript": "ENST00000447366.5",
"protein_id": "ENSP00000390546.2",
"transcript_support_level": 3,
"aa_start": 111,
"aa_end": null,
"aa_length": 266,
"cds_start": 331,
"cds_end": null,
"cds_length": 801,
"cdna_start": 389,
"cdna_end": null,
"cdna_length": 859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"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": "GPR143",
"gene_hgnc_id": 20145,
"hgvs_c": "c.331T>C",
"hgvs_p": "p.Tyr111His",
"transcript": "ENST00000431126.1",
"protein_id": "ENSP00000406138.1",
"transcript_support_level": 3,
"aa_start": 111,
"aa_end": null,
"aa_length": 170,
"cds_start": 331,
"cds_end": null,
"cds_length": 515,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPR143",
"gene_hgnc_id": 20145,
"hgvs_c": "c.331T>C",
"hgvs_p": "p.Tyr111His",
"transcript": "XM_024452388.2",
"protein_id": "XP_024308156.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 320,
"cds_start": 331,
"cds_end": null,
"cds_length": 963,
"cdna_start": 358,
"cdna_end": null,
"cdna_length": 1390,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GPR143",
"gene_hgnc_id": 20145,
"dbsnp": "rs1555914719",
"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": 0.9750353693962097,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.93,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5357,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.67,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.759,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000467482.6",
"gene_symbol": "GPR143",
"hgnc_id": 20145,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.583T>C",
"hgvs_p": "p.Tyr195His"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}