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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: 20-58438817-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=58438817&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 58438817,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000475243.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.316-128G>A",
"hgvs_p": null,
"transcript": "NM_004738.5",
"protein_id": "NP_004729.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": -4,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7829,
"mane_select": "ENST00000475243.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.316-128G>A",
"hgvs_p": null,
"transcript": "ENST00000475243.6",
"protein_id": "ENSP00000417175.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": -4,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7829,
"mane_select": "NM_004738.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.212-5260G>A",
"hgvs_p": null,
"transcript": "ENST00000395802.7",
"protein_id": "ENSP00000379147.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 99,
"cds_start": -4,
"cds_end": null,
"cds_length": 300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1834,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "c.212-5260G>A",
"hgvs_p": null,
"transcript": "NM_001195677.2",
"protein_id": "NP_001182606.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 99,
"cds_start": -4,
"cds_end": null,
"cds_length": 300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7467,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.510-128G>A",
"hgvs_p": null,
"transcript": "ENST00000265619.6",
"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": 3596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.660-128G>A",
"hgvs_p": null,
"transcript": "ENST00000463370.5",
"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": 2393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.212-2090G>A",
"hgvs_p": null,
"transcript": "ENST00000520497.1",
"protein_id": "ENSP00000430426.1",
"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": 937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.443-2090G>A",
"hgvs_p": null,
"transcript": "NR_036633.2",
"protein_id": null,
"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": 7644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.547-128G>A",
"hgvs_p": null,
"transcript": "XR_001754433.3",
"protein_id": null,
"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": 968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"hgvs_c": "n.-160G>A",
"hgvs_p": null,
"transcript": "ENST00000476395.1",
"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": 3583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VAPB",
"gene_hgnc_id": 12649,
"dbsnp": "rs2234489",
"frequency_reference_population": 0.17126259,
"hom_count_reference_population": 12771,
"allele_count_reference_population": 128511,
"gnomad_exomes_af": 0.169344,
"gnomad_genomes_af": 0.178806,
"gnomad_exomes_ac": 101301,
"gnomad_genomes_ac": 27210,
"gnomad_exomes_homalt": 10091,
"gnomad_genomes_homalt": 2680,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.272,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000475243.6",
"gene_symbol": "VAPB",
"hgnc_id": 12649,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.316-128G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}