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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: 3-149129774-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149129774&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 149129774,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_032383.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "NM_032383.5",
"protein_id": "NP_115759.2",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 1004,
"cds_start": 51,
"cds_end": null,
"cds_length": 3015,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296051.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032383.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000296051.7",
"protein_id": "ENSP00000296051.2",
"transcript_support_level": 1,
"aa_start": 17,
"aa_end": null,
"aa_length": 1004,
"cds_start": 51,
"cds_end": null,
"cds_length": 3015,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032383.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296051.7"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000870872.1",
"protein_id": "ENSP00000540931.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 999,
"cds_start": 51,
"cds_end": null,
"cds_length": 3000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870872.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000870871.1",
"protein_id": "ENSP00000540930.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 986,
"cds_start": 51,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870871.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000960205.1",
"protein_id": "ENSP00000630264.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 962,
"cds_start": 51,
"cds_end": null,
"cds_length": 2889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960205.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000870869.1",
"protein_id": "ENSP00000540928.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 935,
"cds_start": 51,
"cds_end": null,
"cds_length": 2808,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870869.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000870868.1",
"protein_id": "ENSP00000540927.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 926,
"cds_start": 51,
"cds_end": null,
"cds_length": 2781,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870868.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000940665.1",
"protein_id": "ENSP00000610724.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 921,
"cds_start": 51,
"cds_end": null,
"cds_length": 2766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940665.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000870870.1",
"protein_id": "ENSP00000540929.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 874,
"cds_start": 51,
"cds_end": null,
"cds_length": 2625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870870.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "NM_001308258.2",
"protein_id": "NP_001295187.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 839,
"cds_start": 51,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308258.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000460120.5",
"protein_id": "ENSP00000418230.1",
"transcript_support_level": 2,
"aa_start": 17,
"aa_end": null,
"aa_length": 839,
"cds_start": 51,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000460120.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000940666.1",
"protein_id": "ENSP00000610725.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 805,
"cds_start": 51,
"cds_end": null,
"cds_length": 2418,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940666.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000960204.1",
"protein_id": "ENSP00000630263.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 770,
"cds_start": 51,
"cds_end": null,
"cds_length": 2313,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960204.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000940664.1",
"protein_id": "ENSP00000610723.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 761,
"cds_start": 51,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940664.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "ENST00000940667.1",
"protein_id": "ENSP00000610726.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 753,
"cds_start": 51,
"cds_end": null,
"cds_length": 2262,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940667.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "XM_047449064.1",
"protein_id": "XP_047305020.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 942,
"cds_start": 51,
"cds_end": null,
"cds_length": 2829,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449064.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro",
"transcript": "XM_005247834.5",
"protein_id": "XP_005247891.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 763,
"cds_start": 51,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247834.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "n.137C>T",
"hgvs_p": null,
"transcript": "ENST00000462030.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000462030.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "n.84C>T",
"hgvs_p": null,
"transcript": "ENST00000486530.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000486530.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "n.136C>T",
"hgvs_p": null,
"transcript": "ENST00000494327.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000494327.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "n.137C>T",
"hgvs_p": null,
"transcript": "XR_001740328.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001740328.3"
}
],
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"dbsnp": "rs141883346",
"frequency_reference_population": 0.0011605688,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1867,
"gnomad_exomes_af": 0.00118788,
"gnomad_genomes_af": 0.00089947,
"gnomad_exomes_ac": 1730,
"gnomad_genomes_ac": 137,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.28999999165534973,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.103,
"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": -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_032383.5",
"gene_symbol": "HPS3",
"hgnc_id": 15597,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.51C>T",
"hgvs_p": "p.Pro17Pro"
}
],
"clinvar_disease": "Hermansky-Pudlak syndrome,Hermansky-Pudlak syndrome 3,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3 B:1",
"phenotype_combined": "not specified|Hermansky-Pudlak syndrome 3|not provided|Hermansky-Pudlak syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}