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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: 14-56801931-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=56801931&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 56801931,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000672264.2",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.698A>G",
"hgvs_p": "p.Asn233Ser",
"transcript": "NM_021728.4",
"protein_id": "NP_068374.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 297,
"cds_start": 698,
"cds_end": null,
"cds_length": 894,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 3011,
"mane_select": "ENST00000672264.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.698A>G",
"hgvs_p": "p.Asn233Ser",
"transcript": "ENST00000672264.2",
"protein_id": "ENSP00000500115.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 297,
"cds_start": 698,
"cds_end": null,
"cds_length": 894,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 3011,
"mane_select": "NM_021728.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.698A>G",
"hgvs_p": "p.Asn233Ser",
"transcript": "ENST00000554845.2",
"protein_id": "ENSP00000451357.2",
"transcript_support_level": 1,
"aa_start": 233,
"aa_end": null,
"aa_length": 297,
"cds_start": 698,
"cds_end": null,
"cds_length": 894,
"cdna_start": 890,
"cdna_end": null,
"cdna_length": 1086,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "ENST00000339475.10",
"protein_id": "ENSP00000343819.5",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 930,
"cdna_end": null,
"cdna_length": 2956,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "ENST00000408990.8",
"protein_id": "ENSP00000386185.3",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 885,
"cdna_end": null,
"cdna_length": 2109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "ENST00000555006.5",
"protein_id": "ENSP00000452336.1",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1083,
"cdna_end": null,
"cdna_length": 1279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.*414A>G",
"hgvs_p": null,
"transcript": "ENST00000554788.5",
"protein_id": "ENSP00000474486.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 35,
"cds_start": -4,
"cds_end": null,
"cds_length": 108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.698A>G",
"hgvs_p": "p.Asn233Ser",
"transcript": "NM_001270525.2",
"protein_id": "NP_001257454.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 297,
"cds_start": 698,
"cds_end": null,
"cds_length": 894,
"cdna_start": 909,
"cdna_end": null,
"cdna_length": 2935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.698A>G",
"hgvs_p": "p.Asn233Ser",
"transcript": "ENST00000673481.1",
"protein_id": "ENSP00000500595.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 297,
"cds_start": 698,
"cds_end": null,
"cds_length": 894,
"cdna_start": 1048,
"cdna_end": null,
"cdna_length": 2240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "NM_001270523.2",
"protein_id": "NP_001257452.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "NM_001270524.2",
"protein_id": "NP_001257453.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1114,
"cdna_end": null,
"cdna_length": 3140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "NM_172337.3",
"protein_id": "NP_758840.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 885,
"cdna_end": null,
"cdna_length": 2911,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "ENST00000555804.2",
"protein_id": "ENSP00000451272.2",
"transcript_support_level": 4,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 981,
"cdna_end": null,
"cdna_length": 1177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "ENST00000673035.1",
"protein_id": "ENSP00000500061.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 964,
"cdna_end": null,
"cdna_length": 2154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.674A>G",
"hgvs_p": "p.Asn225Ser",
"transcript": "ENST00000685244.1",
"protein_id": "ENSP00000508798.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 289,
"cds_start": 674,
"cds_end": null,
"cds_length": 870,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 2089,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "n.809A>G",
"hgvs_p": null,
"transcript": "NR_073034.2",
"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": 2835,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "n.733A>G",
"hgvs_p": null,
"transcript": "NR_073036.2",
"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": 2759,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.361-50A>G",
"hgvs_p": null,
"transcript": "ENST00000672125.1",
"protein_id": "ENSP00000500744.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"hgvs_c": "c.*414A>G",
"hgvs_p": null,
"transcript": "ENST00000554559.5",
"protein_id": "ENSP00000450468.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 35,
"cds_start": -4,
"cds_end": null,
"cds_length": 108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OTX2",
"gene_hgnc_id": 8522,
"dbsnp": "rs370761964",
"frequency_reference_population": 0.000004956071,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000205215,
"gnomad_genomes_af": 0.0000328295,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12152034044265747,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.328,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0511,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.838,
"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": "PP2,PP5,BP4,BS2_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP5",
"BP4",
"BS2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000672264.2",
"gene_symbol": "OTX2",
"hgnc_id": 8522,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.698A>G",
"hgvs_p": "p.Asn233Ser"
}
],
"clinvar_disease": " 6, combined,Pituitary hormone deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Pituitary hormone deficiency, combined, 6",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}