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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: 1-158619331-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=158619331&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 158619331,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000643759.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.6421C>A",
"hgvs_p": "p.Arg2141Arg",
"transcript": "NM_003126.4",
"protein_id": "NP_003117.2",
"transcript_support_level": null,
"aa_start": 2141,
"aa_end": null,
"aa_length": 2419,
"cds_start": 6421,
"cds_end": null,
"cds_length": 7260,
"cdna_start": 6619,
"cdna_end": null,
"cdna_length": 8018,
"mane_select": "ENST00000643759.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.6421C>A",
"hgvs_p": "p.Arg2141Arg",
"transcript": "ENST00000643759.2",
"protein_id": "ENSP00000495214.1",
"transcript_support_level": null,
"aa_start": 2141,
"aa_end": null,
"aa_length": 2419,
"cds_start": 6421,
"cds_end": null,
"cds_length": 7260,
"cdna_start": 6619,
"cdna_end": null,
"cdna_length": 8018,
"mane_select": "NM_003126.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.6421C>A",
"hgvs_p": "p.Arg2141Arg",
"transcript": "XM_011509916.3",
"protein_id": "XP_011508218.1",
"transcript_support_level": null,
"aa_start": 2141,
"aa_end": null,
"aa_length": 2419,
"cds_start": 6421,
"cds_end": null,
"cds_length": 7260,
"cdna_start": 6502,
"cdna_end": null,
"cdna_length": 7901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.6421C>A",
"hgvs_p": "p.Arg2141Arg",
"transcript": "XM_011509917.4",
"protein_id": "XP_011508219.1",
"transcript_support_level": null,
"aa_start": 2141,
"aa_end": null,
"aa_length": 2413,
"cds_start": 6421,
"cds_end": null,
"cds_length": 7242,
"cdna_start": 6619,
"cdna_end": null,
"cdna_length": 8000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.6100C>A",
"hgvs_p": "p.Arg2034Arg",
"transcript": "XM_047428883.1",
"protein_id": "XP_047284839.1",
"transcript_support_level": null,
"aa_start": 2034,
"aa_end": null,
"aa_length": 2312,
"cds_start": 6100,
"cds_end": null,
"cds_length": 6939,
"cdna_start": 6456,
"cdna_end": null,
"cdna_length": 7855,
"mane_select": null,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "n.624C>A",
"hgvs_p": null,
"transcript": "ENST00000484520.1",
"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": 769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"dbsnp": "rs41273519",
"frequency_reference_population": 0.00002325976,
"hom_count_reference_population": 0,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000232598,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"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": 0.4099999964237213,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.037,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.41,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000643759.2",
"gene_symbol": "SPTA1",
"hgnc_id": 11272,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.6421C>A",
"hgvs_p": "p.Arg2141Arg"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}