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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: 20-35134805-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=35134805&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 35134805,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000374492.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDEM2",
"gene_hgnc_id": 15877,
"hgvs_c": "c.635C>T",
"hgvs_p": "p.Pro212Leu",
"transcript": "NM_018217.3",
"protein_id": "NP_060687.2",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 578,
"cds_start": 635,
"cds_end": null,
"cds_length": 1737,
"cdna_start": 713,
"cdna_end": null,
"cdna_length": 1884,
"mane_select": "ENST00000374492.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDEM2",
"gene_hgnc_id": 15877,
"hgvs_c": "c.635C>T",
"hgvs_p": "p.Pro212Leu",
"transcript": "ENST00000374492.8",
"protein_id": "ENSP00000363616.3",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 578,
"cds_start": 635,
"cds_end": null,
"cds_length": 1737,
"cdna_start": 713,
"cdna_end": null,
"cdna_length": 1884,
"mane_select": "NM_018217.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDEM2",
"gene_hgnc_id": 15877,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Pro175Leu",
"transcript": "ENST00000374491.3",
"protein_id": "ENSP00000363615.2",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 541,
"cds_start": 524,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 1756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDEM2",
"gene_hgnc_id": 15877,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Pro175Leu",
"transcript": "NM_001145025.2",
"protein_id": "NP_001138497.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 541,
"cds_start": 524,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 602,
"cdna_end": null,
"cdna_length": 1773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP24-AS1-EDEM2",
"gene_hgnc_id": null,
"hgvs_c": "c.512C>T",
"hgvs_p": "p.Pro171Leu",
"transcript": "NM_001355008.2",
"protein_id": "NP_001341937.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 537,
"cds_start": 512,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 2363,
"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": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EDEM2",
"gene_hgnc_id": 15877,
"hgvs_c": "n.929C>T",
"hgvs_p": null,
"transcript": "NR_026728.2",
"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": 2100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EDEM2",
"gene_hgnc_id": 15877,
"dbsnp": "rs759514733",
"frequency_reference_population": 0.00001094523,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.0000109452,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.498178094625473,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.31,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1109,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.493,
"phylop100way_prediction": "Uncertain_significance",
"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": "ENST00000374492.8",
"gene_symbol": "EDEM2",
"hgnc_id": 15877,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.635C>T",
"hgvs_p": "p.Pro212Leu"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001355008.2",
"gene_symbol": "MMP24-AS1-EDEM2",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.512C>T",
"hgvs_p": "p.Pro171Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}