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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: 17-80050062-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=80050062&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 80050062,
"ref": "A",
"alt": "G",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "ENST00000397545.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "NM_017950.4",
"protein_id": "NP_060420.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1142,
"cds_start": -4,
"cds_end": null,
"cds_length": 3429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4288,
"mane_select": "ENST00000397545.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "ENST00000397545.9",
"protein_id": "ENSP00000380679.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1142,
"cds_start": -4,
"cds_end": null,
"cds_length": 3429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4288,
"mane_select": "NM_017950.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "ENST00000374876.4",
"protein_id": "ENSP00000364010.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 478,
"cds_start": -4,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "n.477-2A>G",
"hgvs_p": null,
"transcript": "ENST00000574799.5",
"protein_id": null,
"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": 3795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "NM_001243342.2",
"protein_id": "NP_001230271.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "ENST00000374877.7",
"protein_id": "ENSP00000364011.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1030,
"cds_start": -4,
"cds_end": null,
"cds_length": 3093,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "NM_001330508.2",
"protein_id": "NP_001317437.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "c.940-2A>G",
"hgvs_p": null,
"transcript": "ENST00000269318.9",
"protein_id": "ENSP00000269318.5",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"hgvs_c": "n.*137-2A>G",
"hgvs_p": null,
"transcript": "ENST00000573474.5",
"protein_id": "ENSP00000460432.1",
"transcript_support_level": 4,
"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": 554,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289689",
"gene_hgnc_id": null,
"hgvs_c": "n.984-2543T>C",
"hgvs_p": null,
"transcript": "ENST00000695610.1",
"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": 1055,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289689",
"gene_hgnc_id": null,
"hgvs_c": "n.1432-2543T>C",
"hgvs_p": null,
"transcript": "ENST00000695611.1",
"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": 1503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCDC40",
"gene_hgnc_id": 26090,
"dbsnp": "rs750708201",
"frequency_reference_population": 0.000024167251,
"hom_count_reference_population": 0,
"allele_count_reference_population": 39,
"gnomad_exomes_af": 0.0000259945,
"gnomad_genomes_af": 0.00000658302,
"gnomad_exomes_ac": 38,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.30000001192092896,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9300000071525574,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.593,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999984298712381,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000397545.9",
"gene_symbol": "CCDC40",
"hgnc_id": 26090,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.940-2A>G",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000695610.1",
"gene_symbol": "ENSG00000289689",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.984-2543T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Primary ciliary dyskinesia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}