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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: 1-17356428-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=17356428&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 17356428,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000375448.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.1527C>A",
"hgvs_p": "p.His509Gln",
"transcript": "NM_012387.3",
"protein_id": "NP_036519.2",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 663,
"cds_start": 1527,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1553,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "ENST00000375448.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.1527C>A",
"hgvs_p": "p.His509Gln",
"transcript": "ENST00000375448.4",
"protein_id": "ENSP00000364597.4",
"transcript_support_level": 1,
"aa_start": 509,
"aa_end": null,
"aa_length": 663,
"cds_start": 1527,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 1553,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "NM_012387.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.1341C>A",
"hgvs_p": "p.His447Gln",
"transcript": "XM_011541150.1",
"protein_id": "XP_011539452.1",
"transcript_support_level": null,
"aa_start": 447,
"aa_end": null,
"aa_length": 601,
"cds_start": 1341,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 1367,
"cdna_end": null,
"cdna_length": 2081,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.1227C>A",
"hgvs_p": "p.His409Gln",
"transcript": "XM_011541151.2",
"protein_id": "XP_011539453.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 563,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1692,
"cdna_start": 1253,
"cdna_end": null,
"cdna_length": 1967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.990C>A",
"hgvs_p": "p.His330Gln",
"transcript": "XM_011541152.1",
"protein_id": "XP_011539454.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 484,
"cds_start": 990,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1087,
"cdna_end": null,
"cdna_length": 1801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.636C>A",
"hgvs_p": "p.His212Gln",
"transcript": "XM_047416610.1",
"protein_id": "XP_047272566.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 366,
"cds_start": 636,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 1499,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "n.428C>A",
"hgvs_p": null,
"transcript": "ENST00000467001.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 471,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "n.494C>A",
"hgvs_p": null,
"transcript": "ENST00000487048.5",
"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
}
],
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"dbsnp": "rs2301887",
"frequency_reference_population": 0.0000037213365,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000273947,
"gnomad_genomes_af": 0.0000131415,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4727531969547272,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.206,
"revel_prediction": "Benign",
"alphamissense_score": 0.188,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.016,
"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": "ENST00000375448.4",
"gene_symbol": "PADI4",
"hgnc_id": 18368,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1527C>A",
"hgvs_p": "p.His509Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}