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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: 11-88312569-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=88312569&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CTSC",
"hgnc_id": 2528,
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"inheritance_mode": "Unknown,AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_001814.6",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 11326,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "11",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " aggressive 1,Haim-Munk syndrome,Papillon-Lefèvre syndrome,Periodontitis,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8199999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 463,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1870,
"cdna_start": null,
"cds_end": null,
"cds_length": 1392,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001814.6",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000227266.10",
"protein_coding": true,
"protein_id": "NP_001805.4",
"strand": false,
"transcript": "NM_001814.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 463,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1870,
"cdna_start": null,
"cds_end": null,
"cds_length": 1392,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000227266.10",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001814.6",
"protein_coding": true,
"protein_id": "ENSP00000227266.4",
"strand": false,
"transcript": "ENST00000227266.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 463,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1908,
"cdna_start": null,
"cds_end": null,
"cds_length": 1392,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880823.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550882.1",
"strand": false,
"transcript": "ENST00000880823.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 459,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1853,
"cdna_start": null,
"cds_end": null,
"cds_length": 1380,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880825.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550884.1",
"strand": false,
"transcript": "ENST00000880825.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 452,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1667,
"cdna_start": null,
"cds_end": null,
"cds_length": 1359,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000678464.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000503046.1",
"strand": false,
"transcript": "ENST00000678464.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 452,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1881,
"cdna_start": null,
"cds_end": null,
"cds_length": 1359,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000934339.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604398.1",
"strand": false,
"transcript": "ENST00000934339.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 450,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1867,
"cdna_start": null,
"cds_end": null,
"cds_length": 1353,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000678506.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000503580.1",
"strand": false,
"transcript": "ENST00000678506.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 448,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1820,
"cdna_start": null,
"cds_end": null,
"cds_length": 1347,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000934341.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604400.1",
"strand": false,
"transcript": "ENST00000934341.1",
"transcript_support_level": null
},
{
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"aa_length": 425,
"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1785,
"cdna_start": null,
"cds_end": null,
"cds_length": 1278,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000934340.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000604399.1",
"strand": false,
"transcript": "ENST00000934340.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
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"cdna_end": null,
"cdna_length": 1431,
"cdna_start": null,
"cds_end": null,
"cds_length": 1260,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000678915.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
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"intron_rank": 2,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000504805.1",
"strand": false,
"transcript": "ENST00000678915.1",
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},
{
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"biotype": "protein_coding",
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"cdna_start": null,
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"consequences": [
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],
"exon_count": 6,
"exon_rank": null,
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"feature": "ENST00000880824.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "c.319-15C>T",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000550883.1",
"strand": false,
"transcript": "ENST00000880824.1",
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},
{
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"consequences": [
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],
"exon_count": 7,
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"feature": "ENST00000679224.1",
"gene_hgnc_id": 2528,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000504475.1",
"strand": false,
"transcript": "ENST00000679224.1",
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},
{
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],
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"feature": "ENST00000527018.6",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000432556.2",
"strand": false,
"transcript": "ENST00000527018.6",
"transcript_support_level": 5
},
{
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"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
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"cds_end": null,
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"consequences": [
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],
"exon_count": 6,
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"feature": "ENST00000533897.2",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "n.367-15C>T",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": false,
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"transcript": "ENST00000533897.2",
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},
{
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"biotype": "nonsense_mediated_decay",
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],
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"feature": "ENST00000676612.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "n.*126-15C>T",
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"mane_plus": null,
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"protein_coding": false,
"protein_id": "ENSP00000504440.1",
"strand": false,
"transcript": "ENST00000676612.1",
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},
{
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"biotype": "nonsense_mediated_decay",
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"consequences": [
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],
"exon_count": 6,
"exon_rank": null,
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"feature": "ENST00000677208.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "n.319-3251C>T",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": "ENSP00000504347.1",
"strand": false,
"transcript": "ENST00000677208.1",
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},
{
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"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2468,
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"cds_end": null,
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"consequences": [
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],
"exon_count": 10,
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"feature": "ENST00000677661.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "n.404-15C>T",
"hgvs_p": null,
"intron_rank": 5,
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"protein_id": "ENSP00000503323.1",
"strand": false,
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},
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],
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},
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],
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"feature": "ENST00000678395.1",
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},
{
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"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
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"feature": "ENST00000678520.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "n.*126-15C>T",
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000503361.1",
"strand": false,
"transcript": "ENST00000678520.1",
"transcript_support_level": null
},
{
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"biotype": "nonsense_mediated_decay",
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"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
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"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
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"feature": "ENST00000678554.1",
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"hgvs_c": "n.319-15C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000504541.1",
"strand": false,
"transcript": "ENST00000678554.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs45539936",
"effect": "intron_variant",
"frequency_reference_population": 0.007018279,
"gene_hgnc_id": 2528,
"gene_symbol": "CTSC",
"gnomad_exomes_ac": 10525,
"gnomad_exomes_af": 0.00720128,
"gnomad_exomes_homalt": 58,
"gnomad_genomes_ac": 801,
"gnomad_genomes_af": 0.00526143,
"gnomad_genomes_homalt": 3,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 61,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Haim-Munk syndrome|Papillon-Lefèvre syndrome|Haim-Munk syndrome;Periodontitis, aggressive 1;Papillon-Lefèvre syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.172,
"pos": 88312569,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001814.6"
}
]
}