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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: 1-12335710-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=12335710&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 12335710,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000620676.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "c.8434T>C",
"hgvs_p": "p.Tyr2812His",
"transcript": "NM_015378.4",
"protein_id": "NP_056193.2",
"transcript_support_level": null,
"aa_start": 2812,
"aa_end": null,
"aa_length": 4388,
"cds_start": 8434,
"cds_end": null,
"cds_length": 13167,
"cdna_start": 8601,
"cdna_end": null,
"cdna_length": 16357,
"mane_select": "ENST00000620676.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "c.8434T>C",
"hgvs_p": "p.Tyr2812His",
"transcript": "ENST00000620676.6",
"protein_id": "ENSP00000478104.1",
"transcript_support_level": 1,
"aa_start": 2812,
"aa_end": null,
"aa_length": 4388,
"cds_start": 8434,
"cds_end": null,
"cds_length": 13167,
"cdna_start": 8601,
"cdna_end": null,
"cdna_length": 16357,
"mane_select": "NM_015378.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "c.8434T>C",
"hgvs_p": "p.Tyr2812His",
"transcript": "ENST00000613099.4",
"protein_id": "ENSP00000482233.1",
"transcript_support_level": 1,
"aa_start": 2812,
"aa_end": null,
"aa_length": 4363,
"cds_start": 8434,
"cds_end": null,
"cds_length": 13092,
"cdna_start": 8564,
"cdna_end": null,
"cdna_length": 16245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "c.4900T>C",
"hgvs_p": "p.Tyr1634His",
"transcript": "ENST00000011700.10",
"protein_id": "ENSP00000011700.6",
"transcript_support_level": 1,
"aa_start": 1634,
"aa_end": null,
"aa_length": 3209,
"cds_start": 4900,
"cds_end": null,
"cds_length": 9630,
"cdna_start": 4902,
"cdna_end": null,
"cdna_length": 10969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "c.8434T>C",
"hgvs_p": "p.Tyr2812His",
"transcript": "NM_018156.4",
"protein_id": "NP_060626.2",
"transcript_support_level": null,
"aa_start": 2812,
"aa_end": null,
"aa_length": 4363,
"cds_start": 8434,
"cds_end": null,
"cds_length": 13092,
"cdna_start": 8601,
"cdna_end": null,
"cdna_length": 16282,
"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": 15,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "n.2322T>C",
"hgvs_p": null,
"transcript": "ENST00000460333.5",
"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": 4910,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "n.1712T>C",
"hgvs_p": null,
"transcript": "ENST00000487188.1",
"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": 3990,
"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": 19,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"hgvs_c": "n.3100T>C",
"hgvs_p": null,
"transcript": "ENST00000646917.1",
"protein_id": "ENSP00000494348.1",
"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": 5369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VPS13D",
"gene_hgnc_id": 23595,
"dbsnp": "rs774443148",
"frequency_reference_population": 0.000017979479,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000171144,
"gnomad_genomes_af": 0.0000262833,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7375935316085815,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.293,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7291,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.608,
"phylop100way_prediction": "Pathogenic",
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000620676.6",
"gene_symbol": "VPS13D",
"hgnc_id": 23595,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8434T>C",
"hgvs_p": "p.Tyr2812His"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}