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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: 10-97600168-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=97600168&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 97600168,
"ref": "G",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000370646.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.700+5G>T",
"hgvs_p": null,
"transcript": "NM_138413.4",
"protein_id": "NP_612422.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 327,
"cds_start": -4,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2442,
"mane_select": "ENST00000370646.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.700+5G>T",
"hgvs_p": null,
"transcript": "ENST00000370646.9",
"protein_id": "ENSP00000359680.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 327,
"cds_start": -4,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2442,
"mane_select": "NM_138413.4",
"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": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000249967",
"gene_hgnc_id": null,
"hgvs_c": "c.212-1689G>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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.212-1689G>T",
"hgvs_p": null,
"transcript": "ENST00000370647.8",
"protein_id": "ENSP00000359681.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1999,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "n.1801G>T",
"hgvs_p": null,
"transcript": "ENST00000465608.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.212-1689G>T",
"hgvs_p": null,
"transcript": "NM_001134670.2",
"protein_id": "NP_001128142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": -4,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1953,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"hgvs_c": "c.109+5G>T",
"hgvs_p": null,
"transcript": "ENST00000370642.4",
"protein_id": "ENSP00000359676.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 84,
"cds_start": -4,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HOGA1",
"gene_hgnc_id": 25155,
"dbsnp": "rs185803104",
"frequency_reference_population": 0.0022654484,
"hom_count_reference_population": 4,
"allele_count_reference_population": 3650,
"gnomad_exomes_af": 0.0023442,
"gnomad_genomes_af": 0.00151079,
"gnomad_exomes_ac": 3420,
"gnomad_genomes_ac": 230,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3499999940395355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9739999771118164,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.625,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.64,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999984993662291,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Very_Strong,BS2_Supporting",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 1,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong",
"BS2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "ENST00000370646.9",
"gene_symbol": "HOGA1",
"hgnc_id": 25155,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.700+5G>T",
"hgvs_p": null
},
{
"score": 8,
"benign_score": 4,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong",
"BS2"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000370649.3",
"gene_symbol": "ENSG00000249967",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.212-1689G>T",
"hgvs_p": null
}
],
"clinvar_disease": "HOGA1-related disorder,Primary hyperoxaluria type 3,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:13 O:1",
"phenotype_combined": "Primary hyperoxaluria type 3|not provided|HOGA1-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}