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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: 1-41580942-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=41580942&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 41580942,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000372583.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIVEP3",
"gene_hgnc_id": 13561,
"hgvs_c": "c.3856C>T",
"hgvs_p": "p.Arg1286Trp",
"transcript": "NM_024503.5",
"protein_id": "NP_078779.2",
"transcript_support_level": null,
"aa_start": 1286,
"aa_end": null,
"aa_length": 2406,
"cds_start": 3856,
"cds_end": null,
"cds_length": 7221,
"cdna_start": 5166,
"cdna_end": null,
"cdna_length": 12617,
"mane_select": "ENST00000372583.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIVEP3",
"gene_hgnc_id": 13561,
"hgvs_c": "c.3856C>T",
"hgvs_p": "p.Arg1286Trp",
"transcript": "ENST00000372583.6",
"protein_id": "ENSP00000361664.1",
"transcript_support_level": 1,
"aa_start": 1286,
"aa_end": null,
"aa_length": 2406,
"cds_start": 3856,
"cds_end": null,
"cds_length": 7221,
"cdna_start": 5166,
"cdna_end": null,
"cdna_length": 12617,
"mane_select": "NM_024503.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIVEP3",
"gene_hgnc_id": 13561,
"hgvs_c": "c.3856C>T",
"hgvs_p": "p.Arg1286Trp",
"transcript": "ENST00000372584.5",
"protein_id": "ENSP00000361665.1",
"transcript_support_level": 1,
"aa_start": 1286,
"aa_end": null,
"aa_length": 2405,
"cds_start": 3856,
"cds_end": null,
"cds_length": 7218,
"cdna_start": 4871,
"cdna_end": null,
"cdna_length": 12319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIVEP3",
"gene_hgnc_id": 13561,
"hgvs_c": "c.3856C>T",
"hgvs_p": "p.Arg1286Trp",
"transcript": "NM_001127714.3",
"protein_id": "NP_001121186.1",
"transcript_support_level": null,
"aa_start": 1286,
"aa_end": null,
"aa_length": 2405,
"cds_start": 3856,
"cds_end": null,
"cds_length": 7218,
"cdna_start": 5086,
"cdna_end": null,
"cdna_length": 12534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIVEP3",
"gene_hgnc_id": 13561,
"hgvs_c": "c.3856C>T",
"hgvs_p": "p.Arg1286Trp",
"transcript": "ENST00000643665.1",
"protein_id": "ENSP00000494598.1",
"transcript_support_level": null,
"aa_start": 1286,
"aa_end": null,
"aa_length": 2405,
"cds_start": 3856,
"cds_end": null,
"cds_length": 7218,
"cdna_start": 4768,
"cdna_end": null,
"cdna_length": 12216,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HIVEP3",
"gene_hgnc_id": 13561,
"dbsnp": "rs12132697",
"frequency_reference_population": 0.00002047596,
"hom_count_reference_population": 1,
"allele_count_reference_population": 33,
"gnomad_exomes_af": 0.0000219259,
"gnomad_genomes_af": 0.00000657091,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14497312903404236,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.122,
"revel_prediction": "Benign",
"alphamissense_score": 0.0963,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.829,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000372583.6",
"gene_symbol": "HIVEP3",
"hgnc_id": 13561,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.3856C>T",
"hgvs_p": "p.Arg1286Trp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}