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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: 9-37919929-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=37919929&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SHB",
"hgnc_id": 10838,
"hgvs_c": "c.1422G>A",
"hgvs_p": "p.Pro474Pro",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_003028.3",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000255872",
"hgnc_id": null,
"hgvs_c": "n.*560-19979G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000540557.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_score": -13,
"allele_count_reference_population": 910,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.61,
"chr": "9",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6100000143051147,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 509,
"aa_ref": "P",
"aa_start": 474,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6035,
"cdna_start": 2004,
"cds_end": null,
"cds_length": 1530,
"cds_start": 1422,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_003028.3",
"gene_hgnc_id": 10838,
"gene_symbol": "SHB",
"hgvs_c": "c.1422G>A",
"hgvs_p": "p.Pro474Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000377707.4",
"protein_coding": true,
"protein_id": "NP_003019.2",
"strand": false,
"transcript": "NM_003028.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 509,
"aa_ref": "P",
"aa_start": 474,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6035,
"cdna_start": 2004,
"cds_end": null,
"cds_length": 1530,
"cds_start": 1422,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000377707.4",
"gene_hgnc_id": 10838,
"gene_symbol": "SHB",
"hgvs_c": "c.1422G>A",
"hgvs_p": "p.Pro474Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003028.3",
"protein_coding": true,
"protein_id": "ENSP00000366936.3",
"strand": false,
"transcript": "ENST00000377707.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 2591,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000540557.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255872",
"hgvs_c": "n.*560-19979G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000457548.1",
"strand": false,
"transcript": "ENST00000540557.1",
"transcript_support_level": 5
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 508,
"aa_ref": "P",
"aa_start": 473,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2775,
"cdna_start": 1989,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1419,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000920838.1",
"gene_hgnc_id": 10838,
"gene_symbol": "SHB",
"hgvs_c": "c.1419G>A",
"hgvs_p": "p.Pro473Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000590897.1",
"strand": false,
"transcript": "ENST00000920838.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 437,
"aa_ref": "P",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1655,
"cdna_start": 1276,
"cds_end": null,
"cds_length": 1314,
"cds_start": 1206,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000854896.1",
"gene_hgnc_id": 10838,
"gene_symbol": "SHB",
"hgvs_c": "c.1206G>A",
"hgvs_p": "p.Pro402Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524955.1",
"strand": false,
"transcript": "ENST00000854896.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs184250370",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00056378514,
"gene_hgnc_id": 10838,
"gene_symbol": "SHB",
"gnomad_exomes_ac": 489,
"gnomad_exomes_af": 0.000334523,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 421,
"gnomad_genomes_af": 0.00276417,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -4.413,
"pos": 37919929,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003028.3"
}
]
}