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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: 3-180647255-TA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=180647255&ref=TA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 180647255,
"ref": "TA",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000476379.6",
"consequences": [
{
"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": 20,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.1363-13delT",
"hgvs_p": null,
"transcript": "NM_181426.2",
"protein_id": "NP_852091.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 941,
"cds_start": -4,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3848,
"mane_select": "ENST00000476379.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.1363-13delT",
"hgvs_p": null,
"transcript": "ENST00000476379.6",
"protein_id": "ENSP00000417960.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 941,
"cds_start": -4,
"cds_end": null,
"cds_length": 2826,
"cdna_start": null,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.1171-13delT",
"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": 9,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1250-13delT",
"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": 11,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1754-13delT",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "ENSG00000145075",
"gene_hgnc_id": null,
"hgvs_c": "n.2235-13delT",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1313-13delT",
"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": 13,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.688-13delT",
"hgvs_p": null,
"transcript": "ENST00000651922.1",
"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": 2828,
"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": 9,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1262-13delT",
"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
},
{
"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": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1500-13delT",
"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
}
],
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"dbsnp": "rs374074877",
"frequency_reference_population": 0.027843062,
"hom_count_reference_population": 5,
"allele_count_reference_population": 32082,
"gnomad_exomes_af": 0.0313026,
"gnomad_genomes_af": 0.00369791,
"gnomad_exomes_ac": 31548,
"gnomad_genomes_ac": 534,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.273,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000476379.6",
"gene_symbol": "CCDC39",
"hgnc_id": 25244,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1363-13delT",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000651576.1",
"gene_symbol": "ENSG00000145075",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2235-13delT",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 14",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Primary ciliary dyskinesia|Primary ciliary dyskinesia 14",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}