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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: 21-43169126-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=43169126&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CRYAA",
"hgnc_id": 2388,
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Trp9Cys",
"inheritance_mode": "AD,AR",
"pathogenic_score": 9,
"score": 9,
"transcript": "NM_000394.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC107987300",
"hgnc_id": null,
"hgvs_c": "n.546+1911C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "XR_007067885.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong",
"acmg_score": 9,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9238,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"chr": "21",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9736024141311646,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 173,
"aa_ref": "W",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1139,
"cdna_start": 119,
"cds_end": null,
"cds_length": 522,
"cds_start": 27,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_000394.4",
"gene_hgnc_id": 2388,
"gene_symbol": "CRYAA",
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Trp9Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000291554.6",
"protein_coding": true,
"protein_id": "NP_000385.1",
"strand": true,
"transcript": "NM_000394.4",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 173,
"aa_ref": "W",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1139,
"cdna_start": 119,
"cds_end": null,
"cds_length": 522,
"cds_start": 27,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000291554.6",
"gene_hgnc_id": 2388,
"gene_symbol": "CRYAA",
"hgvs_c": "c.27G>C",
"hgvs_p": "p.Trp9Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000394.4",
"protein_coding": true,
"protein_id": "ENSP00000291554.2",
"strand": true,
"transcript": "ENST00000291554.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1128,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000482775.1",
"gene_hgnc_id": 2388,
"gene_symbol": "CRYAA",
"hgvs_c": "n.40G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000482775.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4695,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007067885.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC107987300",
"hgvs_c": "n.546+1911C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007067885.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs74315440",
"effect": "missense_variant",
"frequency_reference_population": 0.0000010420835,
"gene_hgnc_id": 2388,
"gene_symbol": "CRYAA",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 0.00000104208,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.11,
"pos": 43169126,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.914,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000394.4"
}
]
}