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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: 18-59359129-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=59359129&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 59359129,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000251047.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "NM_005570.4",
"protein_id": "NP_005561.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 510,
"cds_start": 116,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 137,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": "ENST00000251047.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "ENST00000251047.6",
"protein_id": "ENSP00000251047.4",
"transcript_support_level": 1,
"aa_start": 39,
"aa_end": null,
"aa_length": 510,
"cds_start": 116,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 137,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": "NM_005570.4",
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "n.137T>C",
"hgvs_p": null,
"transcript": "ENST00000587561.1",
"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": 1181,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267677",
"gene_hgnc_id": null,
"hgvs_c": "n.233-27333A>G",
"hgvs_p": null,
"transcript": "ENST00000767578.1",
"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": 595,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267677",
"gene_hgnc_id": null,
"hgvs_c": "n.842+7327A>G",
"hgvs_p": null,
"transcript": "ENST00000767579.1",
"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": 1124,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267677",
"gene_hgnc_id": null,
"hgvs_c": "n.322+53A>G",
"hgvs_p": null,
"transcript": "ENST00000767580.1",
"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": 685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"dbsnp": "rs33926449",
"frequency_reference_population": 0.08347078,
"hom_count_reference_population": 6154,
"allele_count_reference_population": 134721,
"gnomad_exomes_af": 0.0824601,
"gnomad_genomes_af": 0.0931745,
"gnomad_exomes_ac": 120535,
"gnomad_genomes_ac": 14186,
"gnomad_exomes_homalt": 5357,
"gnomad_genomes_homalt": 797,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0016942322254180908,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.028,
"revel_prediction": "Benign",
"alphamissense_score": 0.0533,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.253,
"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": "ENST00000251047.6",
"gene_symbol": "LMAN1",
"hgnc_id": 6631,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000767578.1",
"gene_symbol": "ENSG00000267677",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.233-27333A>G",
"hgvs_p": null
}
],
"clinvar_disease": " combined deficiency of, type 1,Factor V and factor VIII,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|Factor V and factor VIII, combined deficiency of, type 1|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}