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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: 2-177629520-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=177629520&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 177629520,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_016953.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.2689T>G",
"hgvs_p": "p.Ser897Ala",
"transcript": "NM_016953.4",
"protein_id": "NP_058649.3",
"transcript_support_level": null,
"aa_start": 897,
"aa_end": null,
"aa_length": 933,
"cds_start": 2689,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000286063.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016953.4"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.2689T>G",
"hgvs_p": "p.Ser897Ala",
"transcript": "ENST00000286063.11",
"protein_id": "ENSP00000286063.5",
"transcript_support_level": 1,
"aa_start": 897,
"aa_end": null,
"aa_length": 933,
"cds_start": 2689,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016953.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000286063.11"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1939T>G",
"hgvs_p": "p.Ser647Ala",
"transcript": "ENST00000358450.8",
"protein_id": "ENSP00000351232.4",
"transcript_support_level": 1,
"aa_start": 647,
"aa_end": null,
"aa_length": 683,
"cds_start": 1939,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358450.8"
},
{
"aa_ref": "S",
"aa_alt": "A",
"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.1615T>G",
"hgvs_p": "p.Ser539Ala",
"transcript": "ENST00000409504.5",
"protein_id": "ENSP00000386539.1",
"transcript_support_level": 1,
"aa_start": 539,
"aa_end": null,
"aa_length": 575,
"cds_start": 1615,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409504.5"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1357T>G",
"hgvs_p": "p.Ser453Ala",
"transcript": "ENST00000389683.7",
"protein_id": "ENSP00000374333.3",
"transcript_support_level": 1,
"aa_start": 453,
"aa_end": null,
"aa_length": 489,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389683.7"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1939T>G",
"hgvs_p": "p.Ser647Ala",
"transcript": "NM_001077197.2",
"protein_id": "NP_001070665.1",
"transcript_support_level": null,
"aa_start": 647,
"aa_end": null,
"aa_length": 683,
"cds_start": 1939,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001077197.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1615T>G",
"hgvs_p": "p.Ser539Ala",
"transcript": "NM_001077358.2",
"protein_id": "NP_001070826.1",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 575,
"cds_start": 1615,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001077358.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.1357T>G",
"hgvs_p": "p.Ser453Ala",
"transcript": "NM_001077196.2",
"protein_id": "NP_001070664.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 489,
"cds_start": 1357,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001077196.2"
},
{
"aa_ref": "S",
"aa_alt": "A",
"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": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "c.295T>G",
"hgvs_p": "p.Ser99Ala",
"transcript": "ENST00000436700.5",
"protein_id": "ENSP00000406922.1",
"transcript_support_level": 2,
"aa_start": 99,
"aa_end": null,
"aa_length": 135,
"cds_start": 295,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436700.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "n.225T>G",
"hgvs_p": null,
"transcript": "ENST00000478646.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000478646.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"hgvs_c": "n.443T>G",
"hgvs_p": null,
"transcript": "ENST00000488399.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000488399.5"
}
],
"gene_symbol": "PDE11A",
"gene_hgnc_id": 8773,
"dbsnp": "rs1356323763",
"frequency_reference_population": 6.840825e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84082e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3467038571834564,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.17000000178813934,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.305,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0706,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.292,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.17,
"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": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016953.4",
"gene_symbol": "PDE11A",
"hgnc_id": 8773,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2689T>G",
"hgvs_p": "p.Ser897Ala"
}
],
"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
}