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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: 3-180650140-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=180650140&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 180650140,
"ref": "T",
"alt": "C",
"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": 9,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.1167+1261A>G",
"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": 9,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.1167+1261A>G",
"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": 8,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "c.975+1261A>G",
"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": 8,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1054+1261A>G",
"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": 10,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1558+1261A>G",
"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": 15,
"intron_rank_end": null,
"gene_symbol": "ENSG00000145075",
"gene_hgnc_id": null,
"hgvs_c": "n.2039+1261A>G",
"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": 9,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1117+1261A>G",
"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": 2,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.492+1261A>G",
"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": 8,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1066+1261A>G",
"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": 10,
"intron_rank_end": null,
"gene_symbol": "CCDC39",
"gene_hgnc_id": 25244,
"hgvs_c": "n.1304+1261A>G",
"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": "rs577069249",
"frequency_reference_population": 0.0004661974,
"hom_count_reference_population": 0,
"allele_count_reference_population": 71,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.000466197,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 71,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9599999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8199999928474426,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.96,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.131,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.82,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000476379.6",
"gene_symbol": "CCDC39",
"hgnc_id": 25244,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1167+1261A>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000651576.1",
"gene_symbol": "ENSG00000145075",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2039+1261A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 14,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:1",
"phenotype_combined": "Primary ciliary dyskinesia|not provided|Primary ciliary dyskinesia 14",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}