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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: 3-52763618-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52763618&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 52763618,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000233027.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "NM_003157.6",
"protein_id": "NP_003148.2",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 841,
"cds_start": 673,
"cds_end": null,
"cds_length": 2526,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 6053,
"mane_select": "ENST00000233027.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "ENST00000233027.10",
"protein_id": "ENSP00000233027.5",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 841,
"cds_start": 673,
"cds_end": null,
"cds_length": 2526,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 6053,
"mane_select": "NM_003157.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "ENST00000383721.8",
"protein_id": "ENSP00000373227.4",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 781,
"cds_start": 673,
"cds_end": null,
"cds_length": 2346,
"cdna_start": 866,
"cdna_end": null,
"cdna_length": 2576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "NM_001348412.2",
"protein_id": "NP_001335341.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 795,
"cds_start": 673,
"cds_end": null,
"cds_length": 2388,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 5915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "NM_001348413.2",
"protein_id": "NP_001335342.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 781,
"cds_start": 673,
"cds_end": null,
"cds_length": 2346,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.427C>T",
"hgvs_p": "p.Pro143Ser",
"transcript": "NM_001348414.2",
"protein_id": "NP_001335343.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 759,
"cds_start": 427,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 829,
"cdna_end": null,
"cdna_length": 6015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.406C>T",
"hgvs_p": "p.Pro136Ser",
"transcript": "NM_001193533.3",
"protein_id": "NP_001180462.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 752,
"cds_start": 406,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 600,
"cdna_end": null,
"cdna_length": 5786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.406C>T",
"hgvs_p": "p.Pro136Ser",
"transcript": "ENST00000535191.5",
"protein_id": "ENSP00000437703.1",
"transcript_support_level": 2,
"aa_start": 136,
"aa_end": null,
"aa_length": 752,
"cds_start": 406,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 2452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.406C>T",
"hgvs_p": "p.Pro136Ser",
"transcript": "ENST00000461689.5",
"protein_id": "ENSP00000419666.1",
"transcript_support_level": 5,
"aa_start": 136,
"aa_end": null,
"aa_length": 721,
"cds_start": 406,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 516,
"cdna_end": null,
"cdna_length": 2276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "XM_017007085.2",
"protein_id": "XP_016862574.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 870,
"cds_start": 673,
"cds_end": null,
"cds_length": 2613,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 4441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "XM_011534039.4",
"protein_id": "XP_011532341.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 842,
"cds_start": 673,
"cds_end": null,
"cds_length": 2529,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 2941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "XM_017007086.2",
"protein_id": "XP_016862575.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 824,
"cds_start": 673,
"cds_end": null,
"cds_length": 2475,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 4303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "XM_047448772.1",
"protein_id": "XP_047304728.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 796,
"cds_start": 673,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 3362,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "XM_011534040.4",
"protein_id": "XP_011532342.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 671,
"cds_start": 673,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 2875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser",
"transcript": "XM_047448774.1",
"protein_id": "XP_047304730.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 625,
"cds_start": 673,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 867,
"cdna_end": null,
"cdna_length": 2737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NEK4",
"gene_hgnc_id": 11399,
"dbsnp": "rs1029871",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5527277588844299,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.151,
"revel_prediction": "Benign",
"alphamissense_score": 0.1775,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.649,
"phylop100way_prediction": "Pathogenic",
"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": 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": "ENST00000233027.10",
"gene_symbol": "NEK4",
"hgnc_id": 11399,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.673C>T",
"hgvs_p": "p.Pro225Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}