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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: 1-17266719-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=17266719&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 17266719,
"ref": "C",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_016233.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Arg137Arg",
"transcript": "NM_016233.2",
"protein_id": "NP_057317.2",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 664,
"cds_start": 409,
"cds_end": null,
"cds_length": 1995,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375460.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016233.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Arg137Arg",
"transcript": "ENST00000375460.3",
"protein_id": "ENSP00000364609.3",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 664,
"cds_start": 409,
"cds_end": null,
"cds_length": 1995,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016233.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375460.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"hgvs_c": "c.-129C>A",
"hgvs_p": null,
"transcript": "XM_017001463.2",
"protein_id": "XP_016856952.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 485,
"cds_start": null,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001463.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"hgvs_c": "c.295C>A",
"hgvs_p": "p.Arg99Arg",
"transcript": "XM_011541571.3",
"protein_id": "XP_011539873.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 626,
"cds_start": 295,
"cds_end": null,
"cds_length": 1881,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541571.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Arg137Arg",
"transcript": "XM_011541572.3",
"protein_id": "XP_011539874.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 421,
"cds_start": 409,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541572.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"hgvs_c": "c.-129C>A",
"hgvs_p": null,
"transcript": "XM_017001463.2",
"protein_id": "XP_016856952.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 485,
"cds_start": null,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001463.2"
}
],
"gene_symbol": "PADI3",
"gene_hgnc_id": 18337,
"dbsnp": "rs139823890",
"frequency_reference_population": 0.00054076983,
"hom_count_reference_population": 4,
"allele_count_reference_population": 872,
"gnomad_exomes_af": 0.000293098,
"gnomad_genomes_af": 0.00291614,
"gnomad_exomes_ac": 428,
"gnomad_genomes_ac": 444,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.27000001072883606,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.041999999433755875,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.107,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000204434838289809,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS1,BS2_Supporting",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS1",
"BS2_Supporting"
],
"verdict": "Benign",
"transcript": "NM_016233.2",
"gene_symbol": "PADI3",
"hgnc_id": 18337,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Arg137Arg"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}