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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: 11-47980997-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=47980997&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 47980997,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002843.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys",
"transcript": "NM_002843.4",
"protein_id": "NP_002834.3",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 1337,
"cds_start": 85,
"cds_end": null,
"cds_length": 4014,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 7845,
"mane_select": "ENST00000418331.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys",
"transcript": "ENST00000418331.7",
"protein_id": "ENSP00000400010.2",
"transcript_support_level": 1,
"aa_start": 29,
"aa_end": null,
"aa_length": 1337,
"cds_start": 85,
"cds_end": null,
"cds_length": 4014,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 7845,
"mane_select": "NM_002843.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys",
"transcript": "ENST00000440289.6",
"protein_id": "ENSP00000409733.2",
"transcript_support_level": 1,
"aa_start": 29,
"aa_end": null,
"aa_length": 539,
"cds_start": 85,
"cds_end": null,
"cds_length": 1620,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 3158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.427C>T",
"hgvs_p": "p.Arg143Cys",
"transcript": "ENST00000698881.1",
"protein_id": "ENSP00000514003.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 1451,
"cds_start": 427,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 573,
"cdna_end": null,
"cdna_length": 7979,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys",
"transcript": "NM_001098503.2",
"protein_id": "NP_001091973.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 539,
"cds_start": 85,
"cds_end": null,
"cds_length": 1620,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 3179,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys",
"transcript": "ENST00000527952.1",
"protein_id": "ENSP00000435618.1",
"transcript_support_level": 5,
"aa_start": 29,
"aa_end": null,
"aa_length": 145,
"cds_start": 85,
"cds_end": null,
"cds_length": 440,
"cdna_start": 271,
"cdna_end": null,
"cdna_length": 626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys",
"transcript": "ENST00000534219.5",
"protein_id": "ENSP00000432686.1",
"transcript_support_level": 3,
"aa_start": 29,
"aa_end": null,
"aa_length": 119,
"cds_start": 85,
"cds_end": null,
"cds_length": 360,
"cdna_start": 271,
"cdna_end": null,
"cdna_length": 546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.427C>T",
"hgvs_p": "p.Arg143Cys",
"transcript": "XM_047427374.1",
"protein_id": "XP_047283330.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 1104,
"cds_start": 427,
"cds_end": null,
"cds_length": 3315,
"cdna_start": 439,
"cdna_end": null,
"cdna_length": 3404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"hgvs_c": "c.48+379C>T",
"hgvs_p": null,
"transcript": "XM_017018085.2",
"protein_id": "XP_016873574.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1321,
"cds_start": -4,
"cds_end": null,
"cds_length": 3966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPRJ",
"gene_hgnc_id": 9673,
"dbsnp": "rs1853887524",
"frequency_reference_population": 0.0000033369483,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000190332,
"gnomad_genomes_af": 0.0000135225,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.18078798055648804,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.113,
"revel_prediction": "Benign",
"alphamissense_score": 0.6114,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.476,
"phylop100way_prediction": "Benign",
"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": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002843.4",
"gene_symbol": "PTPRJ",
"hgnc_id": 9673,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.85C>T",
"hgvs_p": "p.Arg29Cys"
}
],
"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
}