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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: 2-169479580-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=169479580&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 169479580,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_152384.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "NM_152384.3",
"protein_id": "NP_689597.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 341,
"cds_start": 27,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295240.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152384.3"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000295240.8",
"protein_id": "ENSP00000295240.3",
"transcript_support_level": 1,
"aa_start": 9,
"aa_end": null,
"aa_length": 341,
"cds_start": 27,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152384.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295240.8"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251569",
"gene_hgnc_id": null,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000513963.1",
"protein_id": "ENSP00000424363.1",
"transcript_support_level": 2,
"aa_start": 9,
"aa_end": null,
"aa_length": 544,
"cds_start": 27,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513963.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000392663.6",
"protein_id": "ENSP00000376431.2",
"transcript_support_level": 1,
"aa_start": 9,
"aa_end": null,
"aa_length": 320,
"cds_start": 27,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392663.6"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000857799.1",
"protein_id": "ENSP00000527858.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 319,
"cds_start": 27,
"cds_end": null,
"cds_length": 960,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857799.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000950195.1",
"protein_id": "ENSP00000620254.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 298,
"cds_start": 27,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950195.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000950194.1",
"protein_id": "ENSP00000620253.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 288,
"cds_start": 27,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950194.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp",
"transcript": "ENST00000857800.1",
"protein_id": "ENSP00000527859.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 275,
"cds_start": 27,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857800.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "n.27G>C",
"hgvs_p": null,
"transcript": "ENST00000443151.1",
"protein_id": "ENSP00000406182.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000443151.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "n.101G>C",
"hgvs_p": null,
"transcript": "ENST00000469980.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000469980.1"
}
],
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"dbsnp": "rs1454907698",
"frequency_reference_population": 6.840685e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84068e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.637545645236969,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.613,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9366,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.15,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.61,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_152384.3",
"gene_symbol": "BBS5",
"hgnc_id": 970,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000513963.1",
"gene_symbol": "ENSG00000251569",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Glu9Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}