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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: 1-10536284-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=10536284&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 10536284,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000356607.9",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"transcript": "NM_004565.3",
"protein_id": "NP_004556.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 377,
"cds_start": 156,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 173,
"cdna_end": null,
"cdna_length": 1922,
"mane_select": "ENST00000356607.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"transcript": "ENST00000356607.9",
"protein_id": "ENSP00000349016.4",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 377,
"cds_start": 156,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 173,
"cdna_end": null,
"cdna_length": 1922,
"mane_select": "NM_004565.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.141C>T",
"hgvs_p": "p.Phe47Phe",
"transcript": "ENST00000491661.2",
"protein_id": "ENSP00000465473.1",
"transcript_support_level": 2,
"aa_start": 47,
"aa_end": null,
"aa_length": 160,
"cds_start": 141,
"cds_end": null,
"cds_length": 483,
"cdna_start": 141,
"cdna_end": null,
"cdna_length": 637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.234C>T",
"hgvs_p": "p.Phe78Phe",
"transcript": "XM_047422544.1",
"protein_id": "XP_047278500.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 403,
"cds_start": 234,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 2000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.198C>T",
"hgvs_p": "p.Phe66Phe",
"transcript": "XM_011541577.3",
"protein_id": "XP_011539879.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 391,
"cds_start": 198,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 735,
"cdna_end": null,
"cdna_length": 2484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.234C>T",
"hgvs_p": "p.Phe78Phe",
"transcript": "XM_047422546.1",
"protein_id": "XP_047278502.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 360,
"cds_start": 234,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.99C>T",
"hgvs_p": "p.Phe33Phe",
"transcript": "XM_011541578.3",
"protein_id": "XP_011539880.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 358,
"cds_start": 99,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 774,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.99C>T",
"hgvs_p": "p.Phe33Phe",
"transcript": "XM_047422542.1",
"protein_id": "XP_047278498.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 358,
"cds_start": 99,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 4097,
"cdna_end": null,
"cdna_length": 5846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.99C>T",
"hgvs_p": "p.Phe33Phe",
"transcript": "XM_047422543.1",
"protein_id": "XP_047278499.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 358,
"cds_start": 99,
"cds_end": null,
"cds_length": 1077,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 2000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.198C>T",
"hgvs_p": "p.Phe66Phe",
"transcript": "XM_011541579.4",
"protein_id": "XP_011539881.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 348,
"cds_start": 198,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 743,
"cdna_end": null,
"cdna_length": 2363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe",
"transcript": "XM_011541580.2",
"protein_id": "XP_011539882.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 334,
"cds_start": 156,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 173,
"cdna_end": null,
"cdna_length": 1793,
"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": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "n.517C>T",
"hgvs_p": null,
"transcript": "ENST00000472851.1",
"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": 805,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "n.245C>T",
"hgvs_p": null,
"transcript": "ENST00000492696.1",
"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": 250,
"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": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"hgvs_c": "c.-37C>T",
"hgvs_p": null,
"transcript": "XM_047422545.1",
"protein_id": "XP_047278501.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 313,
"cds_start": -4,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PEX14",
"gene_hgnc_id": 8856,
"dbsnp": "rs12375",
"frequency_reference_population": 0.30503628,
"hom_count_reference_population": 77544,
"allele_count_reference_population": 487013,
"gnomad_exomes_af": 0.31005,
"gnomad_genomes_af": 0.257374,
"gnomad_exomes_ac": 447902,
"gnomad_genomes_ac": 39111,
"gnomad_exomes_homalt": 71803,
"gnomad_genomes_homalt": 5741,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3499999940395355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.381,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000356607.9",
"gene_symbol": "PEX14",
"hgnc_id": 8856,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Phe52Phe"
}
],
"clinvar_disease": " complementation group K,Peroxisome biogenesis disorder,Peroxisome biogenesis disorder 13A (Zellweger),not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "Peroxisome biogenesis disorder 13A (Zellweger)|not specified|not provided|Peroxisome biogenesis disorder, complementation group K",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}