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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: 6-116632389-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=116632389&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 116632389,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000229554.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "c.2099C>T",
"hgvs_p": "p.Ala700Val",
"transcript": "NM_001010892.3",
"protein_id": "NP_001010892.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 716,
"cds_start": 2099,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 2244,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "ENST00000229554.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "c.2099C>T",
"hgvs_p": "p.Ala700Val",
"transcript": "ENST00000229554.10",
"protein_id": "ENSP00000229554.5",
"transcript_support_level": 1,
"aa_start": 700,
"aa_end": null,
"aa_length": 716,
"cds_start": 2099,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 2244,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "NM_001010892.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "c.*160C>T",
"hgvs_p": null,
"transcript": "ENST00000368581.8",
"protein_id": "ENSP00000357570.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 600,
"cds_start": -4,
"cds_end": null,
"cds_length": 1803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Ala453Val",
"transcript": "ENST00000368580.4",
"protein_id": "ENSP00000357569.4",
"transcript_support_level": 5,
"aa_start": 453,
"aa_end": null,
"aa_length": 469,
"cds_start": 1358,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1358,
"cdna_end": null,
"cdna_length": 1410,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "n.2494C>T",
"hgvs_p": null,
"transcript": "XR_007059261.1",
"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": 3090,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "n.2454C>T",
"hgvs_p": null,
"transcript": "XR_007059262.1",
"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": 3050,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "n.2358C>T",
"hgvs_p": null,
"transcript": "XR_007059263.1",
"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": 2954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "c.*160C>T",
"hgvs_p": null,
"transcript": "NM_001161664.2",
"protein_id": "NP_001155136.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 600,
"cds_start": -4,
"cds_end": null,
"cds_length": 1803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"hgvs_c": "c.*160C>T",
"hgvs_p": null,
"transcript": "XM_047418725.1",
"protein_id": "XP_047274681.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 632,
"cds_start": -4,
"cds_end": null,
"cds_length": 1899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2800,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124901386",
"gene_hgnc_id": null,
"hgvs_c": "n.459+1416G>A",
"hgvs_p": null,
"transcript": "XR_007059721.1",
"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": 1991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RSPH4A",
"gene_hgnc_id": 21558,
"dbsnp": "rs9488992",
"frequency_reference_population": 0.005219481,
"hom_count_reference_population": 378,
"allele_count_reference_population": 8423,
"gnomad_exomes_af": 0.00289797,
"gnomad_genomes_af": 0.0275374,
"gnomad_exomes_ac": 4236,
"gnomad_genomes_ac": 4187,
"gnomad_exomes_homalt": 182,
"gnomad_genomes_homalt": 196,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001731276512145996,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.156,
"revel_prediction": "Benign",
"alphamissense_score": 0.1067,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.129,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000229554.10",
"gene_symbol": "RSPH4A",
"hgnc_id": 21558,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2099C>T",
"hgvs_p": "p.Ala700Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_007059721.1",
"gene_symbol": "LOC124901386",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.459+1416G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 11,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Primary ciliary dyskinesia|not provided|Primary ciliary dyskinesia 11",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}