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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: 17-41725052-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=41725052&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 41725052,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000347901.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1509G>T",
"hgvs_p": "p.Thr503Thr",
"transcript": "NM_177977.3",
"protein_id": "NP_817084.2",
"transcript_support_level": null,
"aa_start": 503,
"aa_end": null,
"aa_length": 619,
"cds_start": 1509,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1518,
"cdna_end": null,
"cdna_length": 3930,
"mane_select": "ENST00000347901.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1509G>T",
"hgvs_p": "p.Thr503Thr",
"transcript": "ENST00000347901.9",
"protein_id": "ENSP00000334002.4",
"transcript_support_level": 1,
"aa_start": 503,
"aa_end": null,
"aa_length": 619,
"cds_start": 1509,
"cds_end": null,
"cds_length": 1860,
"cdna_start": 1518,
"cdna_end": null,
"cdna_length": 3930,
"mane_select": "NM_177977.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1665G>T",
"hgvs_p": "p.Thr555Thr",
"transcript": "ENST00000310778.5",
"protein_id": "ENSP00000309392.5",
"transcript_support_level": 1,
"aa_start": 555,
"aa_end": null,
"aa_length": 671,
"cds_start": 1665,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1675,
"cdna_end": null,
"cdna_length": 4087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1434G>T",
"hgvs_p": "p.Thr478Thr",
"transcript": "ENST00000393939.6",
"protein_id": "ENSP00000377513.2",
"transcript_support_level": 1,
"aa_start": 478,
"aa_end": null,
"aa_length": 594,
"cds_start": 1434,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 1444,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1605G>T",
"hgvs_p": "p.Thr535Thr",
"transcript": "NM_001367459.1",
"protein_id": "NP_001354388.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 636,
"cds_start": 1605,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1614,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1569G>T",
"hgvs_p": "p.Thr523Thr",
"transcript": "NM_001367460.1",
"protein_id": "NP_001354389.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 624,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1875,
"cdna_start": 1578,
"cdna_end": null,
"cdna_length": 2152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1458G>T",
"hgvs_p": "p.Thr486Thr",
"transcript": "NM_001079870.1",
"protein_id": "NP_001073339.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 602,
"cds_start": 1458,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 3883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1458G>T",
"hgvs_p": "p.Thr486Thr",
"transcript": "ENST00000341193.9",
"protein_id": "ENSP00000343170.5",
"transcript_support_level": 2,
"aa_start": 486,
"aa_end": null,
"aa_length": 602,
"cds_start": 1458,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 3880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1434G>T",
"hgvs_p": "p.Thr478Thr",
"transcript": "NM_001079871.1",
"protein_id": "NP_001073340.1",
"transcript_support_level": null,
"aa_start": 478,
"aa_end": null,
"aa_length": 594,
"cds_start": 1434,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 1446,
"cdna_end": null,
"cdna_length": 3859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1434G>T",
"hgvs_p": "p.Thr478Thr",
"transcript": "NM_001367461.1",
"protein_id": "NP_001354390.1",
"transcript_support_level": null,
"aa_start": 478,
"aa_end": null,
"aa_length": 579,
"cds_start": 1434,
"cds_end": null,
"cds_length": 1740,
"cdna_start": 1443,
"cdna_end": null,
"cdna_length": 2017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.30G>T",
"hgvs_p": "p.Thr10Thr",
"transcript": "ENST00000458656.5",
"protein_id": "ENSP00000404640.1",
"transcript_support_level": 2,
"aa_start": 10,
"aa_end": null,
"aa_length": 111,
"cds_start": 30,
"cds_end": null,
"cds_length": 336,
"cdna_start": 30,
"cdna_end": null,
"cdna_length": 601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.90G>T",
"hgvs_p": "p.Thr30Thr",
"transcript": "ENST00000442364.1",
"protein_id": "ENSP00000388981.1",
"transcript_support_level": 3,
"aa_start": 30,
"aa_end": null,
"aa_length": 73,
"cds_start": 90,
"cds_end": null,
"cds_length": 222,
"cdna_start": 90,
"cdna_end": null,
"cdna_length": 487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.1331+807G>T",
"hgvs_p": null,
"transcript": "NM_001367462.1",
"protein_id": "NP_001354391.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 470,
"cds_start": -4,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"hgvs_c": "c.38+807G>T",
"hgvs_p": null,
"transcript": "ENST00000455021.5",
"protein_id": "ENSP00000397242.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 39,
"cds_start": -4,
"cds_end": null,
"cds_length": 120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HAP1",
"gene_hgnc_id": 4812,
"dbsnp": "rs782272213",
"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": -0.6700000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.025,
"phylop100way_prediction": "Benign",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000347901.9",
"gene_symbol": "HAP1",
"hgnc_id": 4812,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1509G>T",
"hgvs_p": "p.Thr503Thr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}