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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: 3-180654839-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=180654839&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 180654839,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000476379.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.853G>A",
"hgvs_p": "p.Val285Met",
"transcript": "NM_181426.2",
"protein_id": "NP_852091.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 941,
"cds_start": 853,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": "ENST00000476379.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.853G>A",
"hgvs_p": "p.Val285Met",
"transcript": "ENST00000476379.6",
"protein_id": "ENSP00000417960.2",
"transcript_support_level": 2,
"aa_start": 285,
"aa_end": null,
"aa_length": 941,
"cds_start": 853,
"cds_end": null,
"cds_length": 2826,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": "NM_181426.2",
"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": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1025G>A",
"hgvs_p": null,
"transcript": "ENST00000650889.1",
"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": 5052,
"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": 13,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000145075",
"gene_hgnc_id": null,
"hgvs_c": "n.1725G>A",
"hgvs_p": null,
"transcript": "ENST00000651576.1",
"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": 4451,
"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": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.990G>A",
"hgvs_p": null,
"transcript": "ENST00000652408.1",
"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": 2542,
"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": 19,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.739-2573G>A",
"hgvs_p": null,
"transcript": "ENST00000651046.1",
"protein_id": "ENSP00000499175.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 877,
"cds_start": -4,
"cds_end": null,
"cds_length": 2634,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3582,
"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": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.818-2573G>A",
"hgvs_p": null,
"transcript": "ENST00000650641.1",
"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": 2624,
"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": 12,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.881-2573G>A",
"hgvs_p": null,
"transcript": "ENST00000651818.1",
"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": 1732,
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.830-2573G>A",
"hgvs_p": null,
"transcript": "ENST00000652024.1",
"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": 4378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"dbsnp": "rs886038751",
"frequency_reference_population": 0.0000027435744,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000274357,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08482155203819275,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.044,
"revel_prediction": "Benign",
"alphamissense_score": 0.0891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.547,
"phylop100way_prediction": "Benign",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000476379.6",
"gene_symbol": "CCDC39",
"hgnc_id": 25244,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.853G>A",
"hgvs_p": "p.Val285Met"
},
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000651576.1",
"gene_symbol": "ENSG00000145075",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1725G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not specified|Primary ciliary dyskinesia",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}