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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: 2-177663913-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=177663913&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 177663913,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_016953.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.2599C>T",
"hgvs_p": "p.Arg867Trp",
"transcript": "NM_016953.4",
"protein_id": "NP_058649.3",
"transcript_support_level": null,
"aa_start": 867,
"aa_end": null,
"aa_length": 933,
"cds_start": 2599,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2939,
"cdna_end": null,
"cdna_length": 9305,
"mane_select": "ENST00000286063.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.2599C>T",
"hgvs_p": "p.Arg867Trp",
"transcript": "ENST00000286063.11",
"protein_id": "ENSP00000286063.5",
"transcript_support_level": 1,
"aa_start": 867,
"aa_end": null,
"aa_length": 933,
"cds_start": 2599,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2939,
"cdna_end": null,
"cdna_length": 9305,
"mane_select": "NM_016953.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1849C>T",
"hgvs_p": "p.Arg617Trp",
"transcript": "ENST00000358450.8",
"protein_id": "ENSP00000351232.4",
"transcript_support_level": 1,
"aa_start": 617,
"aa_end": null,
"aa_length": 683,
"cds_start": 1849,
"cds_end": null,
"cds_length": 2052,
"cdna_start": 1948,
"cdna_end": null,
"cdna_length": 3489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1525C>T",
"hgvs_p": "p.Arg509Trp",
"transcript": "ENST00000409504.5",
"protein_id": "ENSP00000386539.1",
"transcript_support_level": 1,
"aa_start": 509,
"aa_end": null,
"aa_length": 575,
"cds_start": 1525,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1616,
"cdna_end": null,
"cdna_length": 2102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1267C>T",
"hgvs_p": "p.Arg423Trp",
"transcript": "ENST00000389683.7",
"protein_id": "ENSP00000374333.3",
"transcript_support_level": 1,
"aa_start": 423,
"aa_end": null,
"aa_length": 489,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 1417,
"cdna_end": null,
"cdna_length": 1781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1849C>T",
"hgvs_p": "p.Arg617Trp",
"transcript": "NM_001077197.2",
"protein_id": "NP_001070665.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 683,
"cds_start": 1849,
"cds_end": null,
"cds_length": 2052,
"cdna_start": 1948,
"cdna_end": null,
"cdna_length": 8314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1525C>T",
"hgvs_p": "p.Arg509Trp",
"transcript": "NM_001077358.2",
"protein_id": "NP_001070826.1",
"transcript_support_level": null,
"aa_start": 509,
"aa_end": null,
"aa_length": 575,
"cds_start": 1525,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1658,
"cdna_end": null,
"cdna_length": 8024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1267C>T",
"hgvs_p": "p.Arg423Trp",
"transcript": "NM_001077196.2",
"protein_id": "NP_001070664.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 489,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 7801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.205C>T",
"hgvs_p": "p.Arg69Trp",
"transcript": "ENST00000436700.5",
"protein_id": "ENSP00000406922.1",
"transcript_support_level": 2,
"aa_start": 69,
"aa_end": null,
"aa_length": 135,
"cds_start": 205,
"cds_end": null,
"cds_length": 408,
"cdna_start": 206,
"cdna_end": null,
"cdna_length": 1204,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "n.135C>T",
"hgvs_p": null,
"transcript": "ENST00000478646.5",
"protein_id": null,
"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": 570,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "n.353C>T",
"hgvs_p": null,
"transcript": "ENST00000488399.5",
"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": 540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PDE11A-AS1",
"gene_hgnc_id": 40433,
"hgvs_c": "n.365+10130G>A",
"hgvs_p": null,
"transcript": "ENST00000653062.1",
"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": 1506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDE11A-AS1",
"gene_hgnc_id": 40433,
"hgvs_c": "n.162+10365G>A",
"hgvs_p": null,
"transcript": "ENST00000815670.1",
"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": 773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"dbsnp": "rs61306957",
"frequency_reference_population": 0.00016868133,
"hom_count_reference_population": 1,
"allele_count_reference_population": 272,
"gnomad_exomes_af": 0.0001712,
"gnomad_genomes_af": 0.000144524,
"gnomad_exomes_ac": 250,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38362184166908264,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.11999999731779099,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.51,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2512,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.385,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.12,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_016953.4",
"gene_symbol": "PDE11A",
"hgnc_id": 8773,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2599C>T",
"hgvs_p": "p.Arg867Trp"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000653062.1",
"gene_symbol": "PDE11A-AS1",
"hgnc_id": 40433,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.365+10130G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}