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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: 17-63961242-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=63961242&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 63961242,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000435607.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN4A",
"gene_hgnc_id": 10591,
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.His599Arg",
"transcript": "NM_000334.4",
"protein_id": "NP_000325.4",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 1836,
"cds_start": 1796,
"cds_end": null,
"cds_length": 5511,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 7805,
"mane_select": "ENST00000435607.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN4A",
"gene_hgnc_id": 10591,
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.His599Arg",
"transcript": "ENST00000435607.3",
"protein_id": "ENSP00000396320.1",
"transcript_support_level": 1,
"aa_start": 599,
"aa_end": null,
"aa_length": 1836,
"cds_start": 1796,
"cds_end": null,
"cds_length": 5511,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 7805,
"mane_select": "NM_000334.4",
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN4A",
"gene_hgnc_id": 10591,
"hgvs_c": "n.452A>G",
"hgvs_p": null,
"transcript": "ENST00000581514.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105371858",
"gene_hgnc_id": null,
"hgvs_c": "n.68+520T>C",
"hgvs_p": null,
"transcript": "XR_001752969.2",
"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": 414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105371858",
"gene_hgnc_id": null,
"hgvs_c": "n.68+520T>C",
"hgvs_p": null,
"transcript": "XR_934910.3",
"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": 289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN4A",
"gene_hgnc_id": 10591,
"dbsnp": "rs187401185",
"frequency_reference_population": 0.004125831,
"hom_count_reference_population": 25,
"allele_count_reference_population": 6148,
"gnomad_exomes_af": 0.00421227,
"gnomad_genomes_af": 0.00328924,
"gnomad_exomes_ac": 5689,
"gnomad_genomes_ac": 459,
"gnomad_exomes_homalt": 23,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10639506578445435,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.925,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9514,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.015,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,PP3,BP4_Moderate,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 11,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP3",
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000435607.3",
"gene_symbol": "SCN4A",
"hgnc_id": 10591,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1796A>G",
"hgvs_p": "p.His599Arg"
},
{
"score": -6,
"benign_score": 7,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Moderate",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "XR_934910.3",
"gene_symbol": "LOC105371858",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.68+520T>C",
"hgvs_p": null
}
],
"clinvar_disease": " type 2,Congenital myasthenic syndrome 16,Familial hyperkalemic periodic paralysis,Hypokalemic periodic paralysis,Paramyotonia congenita of Von Eulenburg,Potassium-aggravated myotonia,SCN4A-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:4 B:5",
"phenotype_combined": "Potassium-aggravated myotonia|Hypokalemic periodic paralysis, type 2|Congenital myasthenic syndrome 16|not provided|Paramyotonia congenita of Von Eulenburg|SCN4A-related disorder|Familial hyperkalemic periodic paralysis|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}