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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: 4-52077011-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=52077011&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 52077011,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000295213.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.991G>A",
"hgvs_p": "p.Val331Ile",
"transcript": "NM_145263.4",
"protein_id": "NP_660306.1",
"transcript_support_level": null,
"aa_start": 331,
"aa_end": null,
"aa_length": 538,
"cds_start": 991,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 1392,
"cdna_end": null,
"cdna_length": 4430,
"mane_select": "ENST00000295213.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.991G>A",
"hgvs_p": "p.Val331Ile",
"transcript": "ENST00000295213.9",
"protein_id": "ENSP00000295213.4",
"transcript_support_level": 1,
"aa_start": 331,
"aa_end": null,
"aa_length": 538,
"cds_start": 991,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 1392,
"cdna_end": null,
"cdna_length": 4430,
"mane_select": "NM_145263.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.895G>A",
"hgvs_p": "p.Val299Ile",
"transcript": "NM_001297608.2",
"protein_id": "NP_001284537.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 506,
"cds_start": 895,
"cds_end": null,
"cds_length": 1521,
"cdna_start": 1296,
"cdna_end": null,
"cdna_length": 4334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.895G>A",
"hgvs_p": "p.Val299Ile",
"transcript": "ENST00000419395.6",
"protein_id": "ENSP00000415309.2",
"transcript_support_level": 2,
"aa_start": 299,
"aa_end": null,
"aa_length": 506,
"cds_start": 895,
"cds_end": null,
"cds_length": 1521,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 2816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Ile",
"transcript": "NM_001346102.2",
"protein_id": "NP_001333031.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 401,
"cds_start": 580,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 1183,
"cdna_end": null,
"cdna_length": 4221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Val106Ile",
"transcript": "NM_001346103.2",
"protein_id": "NP_001333032.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 313,
"cds_start": 316,
"cds_end": null,
"cds_length": 942,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 3999,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.676G>A",
"hgvs_p": "p.Val226Ile",
"transcript": "XM_047449604.1",
"protein_id": "XP_047305560.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 433,
"cds_start": 676,
"cds_end": null,
"cds_length": 1302,
"cdna_start": 778,
"cdna_end": null,
"cdna_length": 3816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.631G>A",
"hgvs_p": "p.Val211Ile",
"transcript": "XM_017007731.3",
"protein_id": "XP_016863220.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 418,
"cds_start": 631,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 764,
"cdna_end": null,
"cdna_length": 3802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Val201Ile",
"transcript": "XM_047449605.1",
"protein_id": "XP_047305561.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 408,
"cds_start": 601,
"cds_end": null,
"cds_length": 1227,
"cdna_start": 684,
"cdna_end": null,
"cdna_length": 3722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.991G>A",
"hgvs_p": "p.Val331Ile",
"transcript": "XM_005265717.3",
"protein_id": "XP_005265774.1",
"transcript_support_level": null,
"aa_start": 331,
"aa_end": null,
"aa_length": 357,
"cds_start": 991,
"cds_end": null,
"cds_length": 1074,
"cdna_start": 1392,
"cdna_end": null,
"cdna_length": 3887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.340G>A",
"hgvs_p": "p.Val114Ile",
"transcript": "XM_047449606.1",
"protein_id": "XP_047305562.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 321,
"cds_start": 340,
"cds_end": null,
"cds_length": 966,
"cdna_start": 442,
"cdna_end": null,
"cdna_length": 3480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Val106Ile",
"transcript": "XM_011534372.2",
"protein_id": "XP_011532674.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 313,
"cds_start": 316,
"cds_end": null,
"cds_length": 942,
"cdna_start": 1057,
"cdna_end": null,
"cdna_length": 4095,
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.991G>A",
"hgvs_p": null,
"transcript": "ENST00000505320.5",
"protein_id": "ENSP00000421204.1",
"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": 1911,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.1277G>A",
"hgvs_p": null,
"transcript": "ENST00000511028.1",
"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": 1919,
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.1392G>A",
"hgvs_p": null,
"transcript": "NR_123728.2",
"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": 4480,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.961G>A",
"hgvs_p": null,
"transcript": "NR_144359.2",
"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": 4049,
"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": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.1296G>A",
"hgvs_p": null,
"transcript": "XR_007096360.1",
"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": 1964,
"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": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.1392G>A",
"hgvs_p": null,
"transcript": "XR_941044.2",
"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": 1594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"hgvs_c": "n.*65G>A",
"hgvs_p": null,
"transcript": "ENST00000514670.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPATA18",
"gene_hgnc_id": 29579,
"dbsnp": "rs193921037",
"frequency_reference_population": 0.0000013727854,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137279,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4761471748352051,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.213,
"revel_prediction": "Benign",
"alphamissense_score": 0.2308,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.474,
"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": "ENST00000295213.9",
"gene_symbol": "SPATA18",
"hgnc_id": 29579,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.991G>A",
"hgvs_p": "p.Val331Ile"
}
],
"clinvar_disease": "Prostate cancer",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Prostate cancer",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}