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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: 9-134765684-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=134765684&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 134765684,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000093.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A1",
"gene_hgnc_id": 2209,
"hgvs_c": "c.2038C>A",
"hgvs_p": "p.Pro680Thr",
"transcript": "NM_000093.5",
"protein_id": "NP_000084.3",
"transcript_support_level": null,
"aa_start": 680,
"aa_end": null,
"aa_length": 1838,
"cds_start": 2038,
"cds_end": null,
"cds_length": 5517,
"cdna_start": 2423,
"cdna_end": null,
"cdna_length": 8442,
"mane_select": "ENST00000371817.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A1",
"gene_hgnc_id": 2209,
"hgvs_c": "c.2038C>A",
"hgvs_p": "p.Pro680Thr",
"transcript": "ENST00000371817.8",
"protein_id": "ENSP00000360882.3",
"transcript_support_level": 1,
"aa_start": 680,
"aa_end": null,
"aa_length": 1838,
"cds_start": 2038,
"cds_end": null,
"cds_length": 5517,
"cdna_start": 2423,
"cdna_end": null,
"cdna_length": 8442,
"mane_select": "NM_000093.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A1",
"gene_hgnc_id": 2209,
"hgvs_c": "c.2038C>A",
"hgvs_p": "p.Pro680Thr",
"transcript": "NM_001278074.1",
"protein_id": "NP_001265003.1",
"transcript_support_level": null,
"aa_start": 680,
"aa_end": null,
"aa_length": 1838,
"cds_start": 2038,
"cds_end": null,
"cds_length": 5517,
"cdna_start": 2421,
"cdna_end": null,
"cdna_length": 8440,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A1",
"gene_hgnc_id": 2209,
"hgvs_c": "c.2038C>A",
"hgvs_p": "p.Pro680Thr",
"transcript": "ENST00000371820.4",
"protein_id": "ENSP00000360885.4",
"transcript_support_level": 2,
"aa_start": 680,
"aa_end": null,
"aa_length": 1838,
"cds_start": 2038,
"cds_end": null,
"cds_length": 5517,
"cdna_start": 2423,
"cdna_end": null,
"cdna_length": 8442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL5A1",
"gene_hgnc_id": 2209,
"hgvs_c": "c.2038C>A",
"hgvs_p": "p.Pro680Thr",
"transcript": "XM_017014266.3",
"protein_id": "XP_016869755.1",
"transcript_support_level": null,
"aa_start": 680,
"aa_end": null,
"aa_length": 1715,
"cds_start": 2038,
"cds_end": null,
"cds_length": 5148,
"cdna_start": 2423,
"cdna_end": null,
"cdna_length": 7727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL5A1",
"gene_hgnc_id": 2209,
"dbsnp": "rs376920171",
"frequency_reference_population": 0.000016735406,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.00001711,
"gnomad_genomes_af": 0.0000131397,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5760684013366699,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.741,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1638,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.705,
"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": "Benign",
"acmg_criteria": "BS1,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000093.5",
"gene_symbol": "COL5A1",
"hgnc_id": 2209,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2038C>A",
"hgvs_p": "p.Pro680Thr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}