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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: 12-112013490-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=112013490&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 112013490,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006817.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"hgvs_c": "c.25G>T",
"hgvs_p": "p.Ala9Ser",
"transcript": "NM_006817.4",
"protein_id": "NP_006808.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 261,
"cds_start": 25,
"cds_end": null,
"cds_length": 786,
"cdna_start": 65,
"cdna_end": null,
"cdna_length": 1623,
"mane_select": "ENST00000261735.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"hgvs_c": "c.25G>T",
"hgvs_p": "p.Ala9Ser",
"transcript": "ENST00000261735.4",
"protein_id": "ENSP00000261735.3",
"transcript_support_level": 1,
"aa_start": 9,
"aa_end": null,
"aa_length": 261,
"cds_start": 25,
"cds_end": null,
"cds_length": 786,
"cdna_start": 65,
"cdna_end": null,
"cdna_length": 1623,
"mane_select": "NM_006817.4",
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"hgvs_c": "n.62G>T",
"hgvs_p": null,
"transcript": "ENST00000553161.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM116",
"gene_hgnc_id": 25084,
"hgvs_c": "c.303C>A",
"hgvs_p": "p.Cys101*",
"transcript": "ENST00000716768.1",
"protein_id": "ENSP00000520598.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 465,
"cds_start": 303,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 377,
"cdna_end": null,
"cdna_length": 1795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"hgvs_c": "c.25G>T",
"hgvs_p": "p.Ala9Ser",
"transcript": "NM_001034025.2",
"protein_id": "NP_001029197.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 53,
"cds_start": 25,
"cds_end": null,
"cds_length": 162,
"cdna_start": 65,
"cdna_end": null,
"cdna_length": 1484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"hgvs_c": "c.25G>T",
"hgvs_p": "p.Ala9Ser",
"transcript": "ENST00000455836.1",
"protein_id": "ENSP00000412083.1",
"transcript_support_level": 2,
"aa_start": 9,
"aa_end": null,
"aa_length": 53,
"cds_start": 25,
"cds_end": null,
"cds_length": 162,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 1333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMEM116",
"gene_hgnc_id": 25084,
"hgvs_c": "c.4C>A",
"hgvs_p": "p.Arg2Arg",
"transcript": "ENST00000716727.1",
"protein_id": "ENSP00000520597.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 344,
"cds_start": 4,
"cds_end": null,
"cds_length": 1035,
"cdna_start": 377,
"cdna_end": null,
"cdna_length": 1731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"hgvs_c": "c.9G>T",
"hgvs_p": "p.Pro3Pro",
"transcript": "ENST00000552052.1",
"protein_id": "ENSP00000447472.1",
"transcript_support_level": 3,
"aa_start": 3,
"aa_end": null,
"aa_length": 93,
"cds_start": 9,
"cds_end": null,
"cds_length": 282,
"cdna_start": 11,
"cdna_end": null,
"cdna_length": 284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ERP29",
"gene_hgnc_id": 13799,
"dbsnp": "rs141517360",
"frequency_reference_population": 0.00001488361,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.0000102718,
"gnomad_genomes_af": 0.0000591327,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.040158987045288086,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.008,
"revel_prediction": "Benign",
"alphamissense_score": 0.0869,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.564,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_006817.4",
"gene_symbol": "ERP29",
"hgnc_id": 13799,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.25G>T",
"hgvs_p": "p.Ala9Ser"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000716768.1",
"gene_symbol": "TMEM116",
"hgnc_id": 25084,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.303C>A",
"hgvs_p": "p.Cys101*"
}
],
"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
}