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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: 3-149139464-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149139464&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "HPS3",
"hgnc_id": 15597,
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_032383.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 25236,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.8,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1004,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4611,
"cdna_start": null,
"cds_end": null,
"cds_length": 3015,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_032383.5",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000296051.7",
"protein_coding": true,
"protein_id": "NP_115759.2",
"strand": true,
"transcript": "NM_032383.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1004,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4611,
"cdna_start": null,
"cds_end": null,
"cds_length": 3015,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000296051.7",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032383.5",
"protein_coding": true,
"protein_id": "ENSP00000296051.2",
"strand": true,
"transcript": "ENST00000296051.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 999,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3787,
"cdna_start": null,
"cds_end": null,
"cds_length": 3000,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000870872.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540931.1",
"strand": true,
"transcript": "ENST00000870872.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 986,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3756,
"cdna_start": null,
"cds_end": null,
"cds_length": 2961,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000870871.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540930.1",
"strand": true,
"transcript": "ENST00000870871.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 962,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3708,
"cdna_start": null,
"cds_end": null,
"cds_length": 2889,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000960205.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630264.1",
"strand": true,
"transcript": "ENST00000960205.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 935,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3633,
"cdna_start": null,
"cds_end": null,
"cds_length": 2808,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000870869.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540928.1",
"strand": true,
"transcript": "ENST00000870869.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 926,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3624,
"cdna_start": null,
"cds_end": null,
"cds_length": 2781,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000870868.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540927.1",
"strand": true,
"transcript": "ENST00000870868.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 921,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3559,
"cdna_start": null,
"cds_end": null,
"cds_length": 2766,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000940665.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610724.1",
"strand": true,
"transcript": "ENST00000940665.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 874,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3423,
"cdna_start": null,
"cds_end": null,
"cds_length": 2625,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000870870.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-930C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000540929.1",
"strand": true,
"transcript": "ENST00000870870.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 839,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4116,
"cdna_start": null,
"cds_end": null,
"cds_length": 2520,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001308258.2",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-1553C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001295187.1",
"strand": true,
"transcript": "NM_001308258.2",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": 839,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2745,
"cdna_start": null,
"cds_end": null,
"cds_length": 2520,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000460120.5",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-1553C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418230.1",
"strand": true,
"transcript": "ENST00000460120.5",
"transcript_support_level": 2
},
{
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"aa_length": 805,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3203,
"cdna_start": null,
"cds_end": null,
"cds_length": 2418,
"cds_start": null,
"consequences": [
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],
"exon_count": 14,
"exon_rank": null,
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"feature": "ENST00000940666.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000610725.1",
"strand": true,
"transcript": "ENST00000940666.1",
"transcript_support_level": null
},
{
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"canonical": false,
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"cdna_length": 3135,
"cdna_start": null,
"cds_end": null,
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"consequences": [
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],
"exon_count": 15,
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"feature": "ENST00000960204.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
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"intron_rank": 1,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000630263.1",
"strand": true,
"transcript": "ENST00000960204.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": null,
"cds_end": null,
"cds_length": 2286,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000940664.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-1553C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610723.1",
"strand": true,
"transcript": "ENST00000940664.1",
"transcript_support_level": null
},
{
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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": 14,
"exon_rank": null,
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"feature": "ENST00000940667.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-5890C>T",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610726.1",
"strand": true,
"transcript": "ENST00000940667.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2977,
"cdna_start": null,
"cds_end": null,
"cds_length": 2829,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047449064.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047305020.1",
"strand": true,
"transcript": "XM_047449064.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2455,
"cdna_start": null,
"cds_end": null,
"cds_length": 2292,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005247834.5",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "c.218-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_005247891.1",
"strand": true,
"transcript": "XM_005247834.5",
"transcript_support_level": null
},
{
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"biotype": "retained_intron",
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"cdna_end": null,
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"cds_end": null,
"cds_length": null,
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"consequences": [
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],
"exon_count": 7,
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"feature": "ENST00000462030.5",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "n.817-540C>T",
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"protein_id": null,
"strand": true,
"transcript": "ENST00000462030.5",
"transcript_support_level": 2
},
{
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"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
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"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000486530.1",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "n.251-540C>T",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000486530.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
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"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 16,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001740328.3",
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"hgvs_c": "n.304-540C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001740328.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs16861514",
"effect": "intron_variant",
"frequency_reference_population": 0.16592152,
"gene_hgnc_id": 15597,
"gene_symbol": "HPS3",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 25236,
"gnomad_genomes_af": 0.165922,
"gnomad_genomes_homalt": 2174,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2174,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.295,
"pos": 149139464,
"ref": "C",
"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_032383.5"
}
]
}