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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: 1-17334002-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=17334002&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 17334002,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_012387.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "NM_012387.3",
"protein_id": "NP_036519.2",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 663,
"cds_start": 333,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "ENST00000375448.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "ENST00000375448.4",
"protein_id": "ENSP00000364597.4",
"transcript_support_level": 1,
"aa_start": 111,
"aa_end": null,
"aa_length": 663,
"cds_start": 333,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 2267,
"mane_select": "NM_012387.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.-87C>T",
"hgvs_p": null,
"transcript": "XM_011541152.1",
"protein_id": "XP_011539454.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 484,
"cds_start": -4,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "ENST00000375453.5",
"protein_id": "ENSP00000364602.1",
"transcript_support_level": 2,
"aa_start": 111,
"aa_end": null,
"aa_length": 127,
"cds_start": 333,
"cds_end": null,
"cds_length": 384,
"cdna_start": 361,
"cdna_end": null,
"cdna_length": 841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "XM_011541150.1",
"protein_id": "XP_011539452.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 601,
"cds_start": 333,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 2081,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "XM_011541151.2",
"protein_id": "XP_011539453.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 563,
"cds_start": 333,
"cds_end": null,
"cds_length": 1692,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "XM_011541153.2",
"protein_id": "XP_011539455.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 397,
"cds_start": 333,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "XM_011541154.3",
"protein_id": "XP_011539456.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 397,
"cds_start": 333,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "XM_011541155.2",
"protein_id": "XP_011539457.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 392,
"cds_start": 333,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr",
"transcript": "XM_011541156.2",
"protein_id": "XP_011539458.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 386,
"cds_start": 333,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"hgvs_c": "c.-87C>T",
"hgvs_p": null,
"transcript": "XM_011541152.1",
"protein_id": "XP_011539454.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 484,
"cds_start": -4,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PADI4",
"gene_hgnc_id": 18368,
"dbsnp": "rs141897176",
"frequency_reference_population": 0.00007902689,
"hom_count_reference_population": 0,
"allele_count_reference_population": 127,
"gnomad_exomes_af": 0.0000488035,
"gnomad_genomes_af": 0.000367855,
"gnomad_exomes_ac": 71,
"gnomad_genomes_ac": 56,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4099999964237213,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.859,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_012387.3",
"gene_symbol": "PADI4",
"hgnc_id": 18368,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Thr111Thr"
}
],
"clinvar_disease": "PADI4-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "PADI4-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}