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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: 17-44352876-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=44352876&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 44352876,
"ref": "C",
"alt": "T",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000053867.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*78C>T",
"hgvs_p": null,
"transcript": "NM_002087.4",
"protein_id": "NP_002078.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": -4,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": "ENST00000053867.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*78C>T",
"hgvs_p": null,
"transcript": "ENST00000053867.8",
"protein_id": "ENSP00000053867.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": -4,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": "NM_002087.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*78C>T",
"hgvs_p": null,
"transcript": "ENST00000589265.5",
"protein_id": "ENSP00000467616.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 436,
"cds_start": -4,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*224C>T",
"hgvs_p": null,
"transcript": "ENST00000586443.1",
"protein_id": "ENSP00000465673.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 387,
"cds_start": -4,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*107C>T",
"hgvs_p": null,
"transcript": "ENST00000586242.1",
"protein_id": "ENSP00000467837.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 109,
"cds_start": -4,
"cds_end": null,
"cds_length": 330,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"dbsnp": "rs5848",
"frequency_reference_population": 0.31138813,
"hom_count_reference_population": 74437,
"allele_count_reference_population": 437273,
"gnomad_exomes_af": 0.300031,
"gnomad_genomes_af": 0.405009,
"gnomad_exomes_ac": 375744,
"gnomad_genomes_ac": 61529,
"gnomad_exomes_homalt": 59842,
"gnomad_genomes_homalt": 14595,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8100000023841858,
"computational_prediction_selected": "Benign",
"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": -0.81,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.491,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000053867.8",
"gene_symbol": "GRN",
"hgnc_id": 4601,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.*78C>T",
"hgvs_p": null
}
],
"clinvar_disease": " SUSCEPTIBILITY TO,FRONTOTEMPORAL LOBAR DEGENERATION WITH UBIQUITIN-POSITIVE INCLUSIONS,GRN-related frontotemporal lobar degeneration with Tdp43 inclusions,Ischemic stroke,Neuronal ceroid lipofuscinosis 11,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "FRONTOTEMPORAL LOBAR DEGENERATION WITH UBIQUITIN-POSITIVE INCLUSIONS, SUSCEPTIBILITY TO|GRN-related frontotemporal lobar degeneration with Tdp43 inclusions|Neuronal ceroid lipofuscinosis 11;GRN-related frontotemporal lobar degeneration with Tdp43 inclusions|Ischemic stroke|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}