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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: 11-72243787-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=72243787&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 72243787,
"ref": "C",
"alt": "T",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_001425096.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PHOX2A",
"gene_hgnc_id": 691,
"hgvs_c": "c.217+1G>A",
"hgvs_p": null,
"transcript": "NM_005169.4",
"protein_id": "NP_005160.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 284,
"cds_start": null,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000298231.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005169.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PHOX2A",
"gene_hgnc_id": 691,
"hgvs_c": "c.217+1G>A",
"hgvs_p": null,
"transcript": "ENST00000298231.5",
"protein_id": "ENSP00000298231.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 284,
"cds_start": null,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005169.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298231.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PHOX2A",
"gene_hgnc_id": 691,
"hgvs_c": "c.217+1G>A",
"hgvs_p": null,
"transcript": "NM_001425096.1",
"protein_id": "NP_001412025.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 312,
"cds_start": null,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001425096.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PHOX2A",
"gene_hgnc_id": 691,
"hgvs_c": "c.217+1G>A",
"hgvs_p": null,
"transcript": "NM_001425097.1",
"protein_id": "NP_001412026.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 292,
"cds_start": null,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001425097.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PHOX2A",
"gene_hgnc_id": 691,
"hgvs_c": "c.217+1G>A",
"hgvs_p": null,
"transcript": "NM_001425098.1",
"protein_id": "NP_001412027.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 182,
"cds_start": null,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001425098.1"
},
{
"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": "PHOX2A",
"gene_hgnc_id": 691,
"hgvs_c": "n.85+1793G>A",
"hgvs_p": null,
"transcript": "ENST00000544057.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000544057.1"
}
],
"gene_symbol": "PHOX2A",
"gene_hgnc_id": 691,
"dbsnp": "rs1590729541",
"frequency_reference_population": 0.0000018273084,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000182731,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3100000023841858,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9259999990463257,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.125,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.99,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999986675681007,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001425096.1",
"gene_symbol": "PHOX2A",
"hgnc_id": 691,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.217+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 2, congenital,Fibrosis of extraocular muscles",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Fibrosis of extraocular muscles, congenital, 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}