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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: 10-97611535-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=97611535&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 97611535,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000370646.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.860G>T",
"hgvs_p": "p.Gly287Val",
"transcript": "NM_138413.4",
"protein_id": "NP_612422.2",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 327,
"cds_start": 860,
"cds_end": null,
"cds_length": 984,
"cdna_start": 1175,
"cdna_end": null,
"cdna_length": 2442,
"mane_select": "ENST00000370646.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.860G>T",
"hgvs_p": "p.Gly287Val",
"transcript": "ENST00000370646.9",
"protein_id": "ENSP00000359680.4",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 327,
"cds_start": 860,
"cds_end": null,
"cds_length": 984,
"cdna_start": 1175,
"cdna_end": null,
"cdna_length": 2442,
"mane_select": "NM_138413.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.371G>T",
"hgvs_p": "p.Gly124Val",
"transcript": "ENST00000370647.8",
"protein_id": "ENSP00000359681.4",
"transcript_support_level": 1,
"aa_start": 124,
"aa_end": null,
"aa_length": 164,
"cds_start": 371,
"cds_end": null,
"cds_length": 495,
"cdna_start": 732,
"cdna_end": null,
"cdna_length": 1999,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000249967",
"gene_hgnc_id": null,
"hgvs_c": "c.345+9545G>T",
"hgvs_p": null,
"transcript": "ENST00000370649.3",
"protein_id": "ENSP00000359683.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 449,
"cds_start": -4,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.371G>T",
"hgvs_p": "p.Gly124Val",
"transcript": "NM_001134670.2",
"protein_id": "NP_001128142.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 164,
"cds_start": 371,
"cds_end": null,
"cds_length": 495,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 1953,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"dbsnp": "rs138207257",
"frequency_reference_population": 0.000059475722,
"hom_count_reference_population": 0,
"allele_count_reference_population": 96,
"gnomad_exomes_af": 0.0000574599,
"gnomad_genomes_af": 0.0000788353,
"gnomad_exomes_ac": 84,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7520843148231506,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.25999999046325684,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.884,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8728,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.656,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.26,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000370646.9",
"gene_symbol": "HOGA1",
"hgnc_id": 25155,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.860G>T",
"hgvs_p": "p.Gly287Val"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000370649.3",
"gene_symbol": "ENSG00000249967",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.345+9545G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Primary hyperoxaluria type 3,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7",
"phenotype_combined": "Primary hyperoxaluria type 3|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}