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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: 1-17225868-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=17225868&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 17225868,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000375471.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly",
"transcript": "NM_013358.3",
"protein_id": "NP_037490.2",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 663,
"cds_start": 466,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 3846,
"mane_select": "ENST00000375471.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly",
"transcript": "ENST00000375471.5",
"protein_id": "ENSP00000364620.4",
"transcript_support_level": 1,
"aa_start": 156,
"aa_end": null,
"aa_length": 663,
"cds_start": 466,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 3846,
"mane_select": "NM_013358.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.313C>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "XM_017001101.2",
"protein_id": "XP_016856590.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 612,
"cds_start": 313,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 3751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.313C>G",
"hgvs_p": "p.Arg105Gly",
"transcript": "XM_017001102.2",
"protein_id": "XP_016856591.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 612,
"cds_start": 313,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 3751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly",
"transcript": "XM_017001103.3",
"protein_id": "XP_016856592.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 594,
"cds_start": 466,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 2457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly",
"transcript": "XM_047418756.1",
"protein_id": "XP_047274712.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 547,
"cds_start": 466,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 1825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly",
"transcript": "XM_047418757.1",
"protein_id": "XP_047274713.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 542,
"cds_start": 466,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly",
"transcript": "XM_011541307.3",
"protein_id": "XP_011539609.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 471,
"cds_start": 466,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 1589,
"mane_select": null,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "n.327C>G",
"hgvs_p": null,
"transcript": "ENST00000483501.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 513,
"mane_select": null,
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "n.556C>G",
"hgvs_p": null,
"transcript": "XR_007059265.1",
"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": 1597,
"mane_select": null,
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"hgvs_c": "n.556C>G",
"hgvs_p": null,
"transcript": "XR_946619.3",
"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": 1648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PADI1",
"gene_hgnc_id": 18367,
"dbsnp": "rs763031946",
"frequency_reference_population": 0.0000013681481,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136815,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6585580706596375,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.258,
"revel_prediction": "Benign",
"alphamissense_score": 0.1598,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.819,
"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": 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": "ENST00000375471.5",
"gene_symbol": "PADI1",
"hgnc_id": 18367,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.466C>G",
"hgvs_p": "p.Arg156Gly"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}