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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: 6-32858490-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=32858490&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 32858490,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000374859.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Arg173Cys",
"transcript": "NM_002800.5",
"protein_id": "NP_002791.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 219,
"cds_start": 517,
"cds_end": null,
"cds_length": 660,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 1017,
"mane_select": "ENST00000374859.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Arg173Cys",
"transcript": "ENST00000374859.3",
"protein_id": "ENSP00000363993.2",
"transcript_support_level": 1,
"aa_start": 173,
"aa_end": null,
"aa_length": 219,
"cds_start": 517,
"cds_end": null,
"cds_length": 660,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 1017,
"mane_select": "NM_002800.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"hgvs_c": "c.448C>T",
"hgvs_p": "p.Arg150Cys",
"transcript": "ENST00000395330.6",
"protein_id": "ENSP00000378739.1",
"transcript_support_level": 3,
"aa_start": 150,
"aa_end": null,
"aa_length": 196,
"cds_start": 448,
"cds_end": null,
"cds_length": 591,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 1941,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"hgvs_c": "n.2266C>T",
"hgvs_p": null,
"transcript": "ENST00000464863.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2676,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"hgvs_c": "n.498C>T",
"hgvs_p": null,
"transcript": "ENST00000467593.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"hgvs_c": "c.*53C>T",
"hgvs_p": null,
"transcript": "ENST00000414474.5",
"protein_id": "ENSP00000394363.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 130,
"cds_start": -4,
"cds_end": null,
"cds_length": 395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PSMB9",
"gene_hgnc_id": 9546,
"dbsnp": "rs17213861",
"frequency_reference_population": 0.004610892,
"hom_count_reference_population": 23,
"allele_count_reference_population": 7437,
"gnomad_exomes_af": 0.00478324,
"gnomad_genomes_af": 0.00295671,
"gnomad_exomes_ac": 6987,
"gnomad_genomes_ac": 450,
"gnomad_exomes_homalt": 21,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01070868968963623,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.4300000071525574,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.165,
"revel_prediction": "Benign",
"alphamissense_score": 0.1312,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.657,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.43,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP6_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000374859.3",
"gene_symbol": "PSMB9",
"hgnc_id": 9546,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.517C>T",
"hgvs_p": "p.Arg173Cys"
}
],
"clinvar_disease": "PSMB9-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "PSMB9-related disorder|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}