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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: 3-46021442-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46021442&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46021442,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005283.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr",
"transcript": "NM_001024644.2",
"protein_id": "NP_001019815.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 333,
"cds_start": 506,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 5039,
"mane_select": "ENST00000309285.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001024644.2"
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr",
"transcript": "ENST00000309285.4",
"protein_id": "ENSP00000310405.3",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 333,
"cds_start": 506,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 5039,
"mane_select": "NM_001024644.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000309285.4"
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr",
"transcript": "ENST00000395946.3",
"protein_id": "ENSP00000379277.3",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 333,
"cds_start": 506,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395946.3"
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr",
"transcript": "NM_001381860.1",
"protein_id": "NP_001368789.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 333,
"cds_start": 506,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 819,
"cdna_end": null,
"cdna_length": 5254,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001381860.1"
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr",
"transcript": "NM_005283.3",
"protein_id": "NP_005274.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 333,
"cds_start": 506,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 726,
"cdna_end": null,
"cdna_length": 5161,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005283.3"
},
{
"aa_ref": "K",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr",
"transcript": "ENST00000683768.1",
"protein_id": "ENSP00000507745.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 333,
"cds_start": 506,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 5504,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000683768.1"
}
],
"gene_symbol": "XCR1",
"gene_hgnc_id": 1625,
"dbsnp": "rs1708144736",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09088504314422607,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.15,
"revel_prediction": "Benign",
"alphamissense_score": 0.116,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.799,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005283.3",
"gene_symbol": "XCR1",
"hgnc_id": 1625,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.506A>C",
"hgvs_p": "p.Lys169Thr"
}
],
"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
}