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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: 3-49682366-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49682366&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49682366,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000296456.10",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Thr541Lys",
"transcript": "NM_001640.4",
"protein_id": "NP_001631.3",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 732,
"cds_start": 1622,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 1673,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": "ENST00000296456.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Thr541Lys",
"transcript": "ENST00000296456.10",
"protein_id": "ENSP00000296456.5",
"transcript_support_level": 1,
"aa_start": 541,
"aa_end": null,
"aa_length": 732,
"cds_start": 1622,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 1673,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": "NM_001640.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Thr541Lys",
"transcript": "ENST00000438011.5",
"protein_id": "ENSP00000415862.1",
"transcript_support_level": 1,
"aa_start": 541,
"aa_end": null,
"aa_length": 737,
"cds_start": 1622,
"cds_end": null,
"cds_length": 2214,
"cdna_start": 1657,
"cdna_end": null,
"cdna_length": 2249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1757C>A",
"hgvs_p": "p.Thr586Lys",
"transcript": "XM_011533658.4",
"protein_id": "XP_011531960.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 777,
"cds_start": 1757,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 1782,
"cdna_end": null,
"cdna_length": 2988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1706C>A",
"hgvs_p": "p.Thr569Lys",
"transcript": "XM_047448065.1",
"protein_id": "XP_047304021.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 760,
"cds_start": 1706,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1798,
"cdna_end": null,
"cdna_length": 3004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1619C>A",
"hgvs_p": "p.Thr540Lys",
"transcript": "XM_017006285.2",
"protein_id": "XP_016861774.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 731,
"cds_start": 1619,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 1644,
"cdna_end": null,
"cdna_length": 2850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1484C>A",
"hgvs_p": "p.Thr495Lys",
"transcript": "XM_005265097.3",
"protein_id": "XP_005265154.1",
"transcript_support_level": null,
"aa_start": 495,
"aa_end": null,
"aa_length": 686,
"cds_start": 1484,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 1535,
"cdna_end": null,
"cdna_length": 2741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "c.1037C>A",
"hgvs_p": "p.Thr346Lys",
"transcript": "XM_047448066.1",
"protein_id": "XP_047304022.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 537,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1185,
"cdna_end": null,
"cdna_length": 2391,
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "n.*322C>A",
"hgvs_p": null,
"transcript": "ENST00000469362.6",
"protein_id": "ENSP00000438180.1",
"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": 830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "n.*322C>A",
"hgvs_p": null,
"transcript": "ENST00000469362.6",
"protein_id": "ENSP00000438180.1",
"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": 830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"hgvs_c": "n.-235C>A",
"hgvs_p": null,
"transcript": "ENST00000480772.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 703,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APEH",
"gene_hgnc_id": 586,
"dbsnp": "rs3816877",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5541529059410095,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.351,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6212,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.923,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000296456.10",
"gene_symbol": "APEH",
"hgnc_id": 586,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Thr541Lys"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}