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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: 9-136429731-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136429731&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 136429731,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000371712.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1879C>T",
"hgvs_p": "p.Gln627*",
"transcript": "NM_019892.6",
"protein_id": "NP_063945.2",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 644,
"cds_start": 1879,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 2305,
"cdna_end": null,
"cdna_length": 3417,
"mane_select": "ENST00000371712.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1879C>T",
"hgvs_p": "p.Gln627*",
"transcript": "ENST00000371712.4",
"protein_id": "ENSP00000360777.3",
"transcript_support_level": 1,
"aa_start": 627,
"aa_end": null,
"aa_length": 644,
"cds_start": 1879,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 2305,
"cdna_end": null,
"cdna_length": 3417,
"mane_select": "NM_019892.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1876C>T",
"hgvs_p": "p.Gln626*",
"transcript": "NM_001318502.2",
"protein_id": "NP_001305431.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 643,
"cds_start": 1876,
"cds_end": null,
"cds_length": 1932,
"cdna_start": 2302,
"cdna_end": null,
"cdna_length": 3414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.1777C>T",
"hgvs_p": "p.Gln593*",
"transcript": "ENST00000676019.1",
"protein_id": "ENSP00000501984.1",
"transcript_support_level": null,
"aa_start": 593,
"aa_end": null,
"aa_length": 610,
"cds_start": 1777,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 2203,
"cdna_end": null,
"cdna_length": 3315,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.*23C>T",
"hgvs_p": null,
"transcript": "XM_017014926.2",
"protein_id": "XP_016870415.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 602,
"cds_start": -4,
"cds_end": null,
"cds_length": 1809,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3370,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"hgvs_c": "c.*23C>T",
"hgvs_p": null,
"transcript": "XM_047423603.1",
"protein_id": "XP_047279559.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 601,
"cds_start": -4,
"cds_end": null,
"cds_length": 1806,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "INPP5E",
"gene_hgnc_id": 21474,
"dbsnp": "rs121918127",
"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": 0.6200000047683716,
"computational_prediction_selected": "Pathogenic",
"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": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.488,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371712.4",
"gene_symbol": "INPP5E",
"hgnc_id": 21474,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1879C>T",
"hgvs_p": "p.Gln627*"
}
],
"clinvar_disease": "Joubert syndrome 1,MORM syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "MORM syndrome|MORM syndrome;Joubert syndrome 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}