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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: 5-55233170-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=55233170&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 55233170,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000282572.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"hgvs_c": "c.354G>A",
"hgvs_p": "p.Pro118Pro",
"transcript": "NM_021147.5",
"protein_id": "NP_066970.3",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 350,
"cds_start": 354,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 1361,
"mane_select": "ENST00000282572.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"hgvs_c": "c.354G>A",
"hgvs_p": "p.Pro118Pro",
"transcript": "ENST00000282572.5",
"protein_id": "ENSP00000282572.4",
"transcript_support_level": 1,
"aa_start": 118,
"aa_end": null,
"aa_length": 350,
"cds_start": 354,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 1361,
"mane_select": "NM_021147.5",
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"hgvs_c": "n.354G>A",
"hgvs_p": null,
"transcript": "ENST00000501463.2",
"protein_id": "ENSP00000422485.1",
"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": 1726,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO-DT",
"gene_hgnc_id": 55543,
"hgvs_c": "n.121C>T",
"hgvs_p": null,
"transcript": "ENST00000749853.1",
"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": 500,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"hgvs_c": "n.439G>A",
"hgvs_p": null,
"transcript": "NR_125346.2",
"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": 1737,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"hgvs_c": "n.439G>A",
"hgvs_p": null,
"transcript": "NR_125347.2",
"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": 1366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"hgvs_c": "n.-179G>A",
"hgvs_p": null,
"transcript": "NR_125348.1",
"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": 1340,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCNO",
"gene_hgnc_id": 18576,
"dbsnp": "rs368155527",
"frequency_reference_population": 0.00022497275,
"hom_count_reference_population": 0,
"allele_count_reference_population": 348,
"gnomad_exomes_af": 0.000111125,
"gnomad_genomes_af": 0.00126952,
"gnomad_exomes_ac": 155,
"gnomad_genomes_ac": 193,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.2800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.085,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000282572.5",
"gene_symbol": "CCNO",
"hgnc_id": 18576,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.354G>A",
"hgvs_p": "p.Pro118Pro"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000749853.1",
"gene_symbol": "CCNO-DT",
"hgnc_id": 55543,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.121C>T",
"hgvs_p": null
}
],
"clinvar_disease": "CCNO-related disorder,Primary ciliary dyskinesia",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Primary ciliary dyskinesia|CCNO-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}