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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: X-139551223-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=139551223&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 139551223,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000218099.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Val228Ile",
"transcript": "NM_000133.4",
"protein_id": "NP_000124.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 461,
"cds_start": 682,
"cds_end": null,
"cds_length": 1386,
"cdna_start": 708,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": "ENST00000218099.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Val228Ile",
"transcript": "ENST00000218099.7",
"protein_id": "ENSP00000218099.2",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 461,
"cds_start": 682,
"cds_end": null,
"cds_length": 1386,
"cdna_start": 708,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": "NM_000133.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"hgvs_c": "c.568G>A",
"hgvs_p": "p.Val190Ile",
"transcript": "ENST00000394090.2",
"protein_id": "ENSP00000377650.2",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 423,
"cds_start": 568,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 568,
"cdna_end": null,
"cdna_length": 1272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"hgvs_c": "c.568G>A",
"hgvs_p": "p.Val190Ile",
"transcript": "NM_001313913.2",
"protein_id": "NP_001300842.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 423,
"cds_start": 568,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 594,
"cdna_end": null,
"cdna_length": 2686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"transcript": "XM_005262397.5",
"protein_id": "XP_005262454.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 418,
"cds_start": 553,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 579,
"cdna_end": null,
"cdna_length": 2671,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"hgvs_c": "n.1349G>A",
"hgvs_p": null,
"transcript": "ENST00000643157.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "F9",
"gene_hgnc_id": 3551,
"dbsnp": "rs137852243",
"frequency_reference_population": 0.0000016533216,
"hom_count_reference_population": 1,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 9.10641e-7,
"gnomad_genomes_af": 0.00000896395,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8851318359375,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.596,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1256,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.361,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000218099.7",
"gene_symbol": "F9",
"hgnc_id": 3551,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.682G>A",
"hgvs_p": "p.Val228Ile"
}
],
"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
}