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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: 6-161973309-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=161973309&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 161973309,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000366898.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Asp243Asn",
"transcript": "NM_004562.3",
"protein_id": "NP_004553.2",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 465,
"cds_start": 727,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 4178,
"mane_select": "ENST00000366898.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Asp243Asn",
"transcript": "ENST00000366898.6",
"protein_id": "ENSP00000355865.1",
"transcript_support_level": 1,
"aa_start": 243,
"aa_end": null,
"aa_length": 465,
"cds_start": 727,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 4178,
"mane_select": "NM_004562.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Asp215Asn",
"transcript": "ENST00000366897.5",
"protein_id": "ENSP00000355863.1",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 437,
"cds_start": 643,
"cds_end": null,
"cds_length": 1314,
"cdna_start": 746,
"cdna_end": null,
"cdna_length": 2877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.280G>A",
"hgvs_p": "p.Asp94Asn",
"transcript": "ENST00000366896.5",
"protein_id": "ENSP00000355862.1",
"transcript_support_level": 1,
"aa_start": 94,
"aa_end": null,
"aa_length": 316,
"cds_start": 280,
"cds_end": null,
"cds_length": 951,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 2514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.*173G>A",
"hgvs_p": null,
"transcript": "ENST00000338468.8",
"protein_id": "ENSP00000343589.4",
"transcript_support_level": 1,
"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": 1276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.*173G>A",
"hgvs_p": null,
"transcript": "ENST00000338468.8",
"protein_id": "ENSP00000343589.4",
"transcript_support_level": 1,
"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": 1276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Asp215Asn",
"transcript": "NM_013987.3",
"protein_id": "NP_054642.2",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 437,
"cds_start": 643,
"cds_end": null,
"cds_length": 1314,
"cdna_start": 741,
"cdna_end": null,
"cdna_length": 4094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Asp243Asn",
"transcript": "ENST00000366892.5",
"protein_id": "ENSP00000355858.1",
"transcript_support_level": 5,
"aa_start": 243,
"aa_end": null,
"aa_length": 368,
"cds_start": 727,
"cds_end": null,
"cds_length": 1107,
"cdna_start": 823,
"cdna_end": null,
"cdna_length": 1505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.280G>A",
"hgvs_p": "p.Asp94Asn",
"transcript": "NM_013988.3",
"protein_id": "NP_054643.2",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 316,
"cds_start": 280,
"cds_end": null,
"cds_length": 951,
"cdna_start": 378,
"cdna_end": null,
"cdna_length": 3731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Asp281Asn",
"transcript": "XM_017010908.2",
"protein_id": "XP_016866397.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 503,
"cds_start": 841,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 1776,
"cdna_end": null,
"cdna_length": 5129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.724G>A",
"hgvs_p": "p.Asp242Asn",
"transcript": "XM_011535863.2",
"protein_id": "XP_011534165.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 464,
"cds_start": 724,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 822,
"cdna_end": null,
"cdna_length": 4175,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "c.490G>A",
"hgvs_p": "p.Asp164Asn",
"transcript": "XM_024446449.2",
"protein_id": "XP_024302217.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 386,
"cds_start": 490,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 661,
"cdna_end": null,
"cdna_length": 4014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.*198G>A",
"hgvs_p": null,
"transcript": "ENST00000366894.6",
"protein_id": "ENSP00000355860.2",
"transcript_support_level": 5,
"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": 1157,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.490G>A",
"hgvs_p": null,
"transcript": "ENST00000479615.5",
"protein_id": "ENSP00000434414.1",
"transcript_support_level": 5,
"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": 904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.721G>A",
"hgvs_p": null,
"transcript": "ENST00000673871.1",
"protein_id": "ENSP00000501207.1",
"transcript_support_level": null,
"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": 3971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.745G>A",
"hgvs_p": null,
"transcript": "ENST00000674232.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.363G>A",
"hgvs_p": null,
"transcript": "ENST00000674436.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.834G>A",
"hgvs_p": null,
"transcript": "ENST00000674501.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"hgvs_c": "n.*198G>A",
"hgvs_p": null,
"transcript": "ENST00000366894.6",
"protein_id": "ENSP00000355860.2",
"transcript_support_level": 5,
"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": 1157,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRKN",
"gene_hgnc_id": 8607,
"dbsnp": "rs146173584",
"frequency_reference_population": 0.00017620058,
"hom_count_reference_population": 4,
"allele_count_reference_population": 283,
"gnomad_exomes_af": 0.000183648,
"gnomad_genomes_af": 0.000105085,
"gnomad_exomes_ac": 267,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2951540946960449,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.427,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2728,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.561,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,BP4,BS2_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4",
"BS2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000366898.6",
"gene_symbol": "PRKN",
"hgnc_id": 8607,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.727G>A",
"hgvs_p": "p.Asp243Asn"
}
],
"clinvar_disease": "Autosomal recessive juvenile Parkinson disease 2,Lung cancer,Ovarian cancer,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "not specified|not provided|Autosomal recessive juvenile Parkinson disease 2|Autosomal recessive juvenile Parkinson disease 2;Ovarian cancer;Lung cancer",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}