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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: 10-13132107-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=13132107&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 13132107,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000378747.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "NM_001008212.2",
"protein_id": "NP_001008213.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3479,
"mane_select": "ENST00000378747.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "ENST00000378747.8",
"protein_id": "ENSP00000368021.3",
"transcript_support_level": 1,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3479,
"mane_select": "NM_001008212.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "ENST00000378748.7",
"protein_id": "ENSP00000368022.3",
"transcript_support_level": 1,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1804,
"cdna_end": null,
"cdna_length": 3521,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "ENST00000378757.6",
"protein_id": "ENSP00000368032.2",
"transcript_support_level": 1,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1587,
"cdna_end": null,
"cdna_length": 3321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1424C>T",
"hgvs_p": "p.Ala475Val",
"transcript": "ENST00000378752.7",
"protein_id": "ENSP00000368027.3",
"transcript_support_level": 1,
"aa_start": 475,
"aa_end": null,
"aa_length": 571,
"cds_start": 1424,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1771,
"cdna_end": null,
"cdna_length": 3488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "NM_001008211.1",
"protein_id": "NP_001008212.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1895,
"cdna_end": null,
"cdna_length": 3597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "NM_001008213.1",
"protein_id": "NP_001008214.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1880,
"cdna_end": null,
"cdna_length": 3582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "NM_021980.4",
"protein_id": "NP_068815.2",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 1674,
"cdna_end": null,
"cdna_length": 3376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val",
"transcript": "ENST00000263036.9",
"protein_id": "ENSP00000263036.3",
"transcript_support_level": 2,
"aa_start": 481,
"aa_end": null,
"aa_length": 577,
"cds_start": 1442,
"cds_end": null,
"cds_length": 1734,
"cdna_start": 2115,
"cdna_end": null,
"cdna_length": 2464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "c.1424C>T",
"hgvs_p": "p.Ala475Val",
"transcript": "ENST00000378764.6",
"protein_id": "ENSP00000368040.1",
"transcript_support_level": 5,
"aa_start": 475,
"aa_end": null,
"aa_length": 571,
"cds_start": 1424,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1943,
"cdna_end": null,
"cdna_length": 2498,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"hgvs_c": "n.298C>T",
"hgvs_p": null,
"transcript": "ENST00000469025.1",
"protein_id": null,
"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": 642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OPTN",
"gene_hgnc_id": 17142,
"dbsnp": "rs377219791",
"frequency_reference_population": 0.00005455328,
"hom_count_reference_population": 0,
"allele_count_reference_population": 88,
"gnomad_exomes_af": 0.0000568057,
"gnomad_genomes_af": 0.0000328991,
"gnomad_exomes_ac": 83,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8163797855377197,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.61,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.894,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.056,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000378747.8",
"gene_symbol": "OPTN",
"hgnc_id": 17142,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.1442C>T",
"hgvs_p": "p.Ala481Val"
}
],
"clinvar_disease": " E, open angle,Amyotrophic lateral sclerosis type 12,Glaucoma 1,Inborn genetic diseases,OPTN-related disorder,Primary open angle glaucoma,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "not specified|Amyotrophic lateral sclerosis type 12|Primary open angle glaucoma|Primary open angle glaucoma;Glaucoma 1, open angle, E;Amyotrophic lateral sclerosis type 12|Inborn genetic diseases|OPTN-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}