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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: 13-24680753-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=24680753&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 24680753,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_001676.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP12A",
"gene_hgnc_id": 13816,
"hgvs_c": "c.9+1G>A",
"hgvs_p": null,
"transcript": "NM_001676.7",
"protein_id": "NP_001667.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1039,
"cds_start": -4,
"cds_end": null,
"cds_length": 3120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4406,
"mane_select": "ENST00000381946.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP12A",
"gene_hgnc_id": 13816,
"hgvs_c": "c.9+1G>A",
"hgvs_p": null,
"transcript": "ENST00000381946.5",
"protein_id": "ENSP00000371372.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1039,
"cds_start": -4,
"cds_end": null,
"cds_length": 3120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4406,
"mane_select": "NM_001676.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP12A",
"gene_hgnc_id": 13816,
"hgvs_c": "c.9+1G>A",
"hgvs_p": null,
"transcript": "ENST00000218548.10",
"protein_id": "ENSP00000218548.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1045,
"cds_start": -4,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3732,
"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_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP12A",
"gene_hgnc_id": 13816,
"hgvs_c": "c.9+1G>A",
"hgvs_p": null,
"transcript": "NM_001185085.2",
"protein_id": "NP_001172014.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1045,
"cds_start": -4,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303666",
"gene_hgnc_id": null,
"hgvs_c": "n.72+3747C>T",
"hgvs_p": null,
"transcript": "ENST00000796402.1",
"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": 364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP12A",
"gene_hgnc_id": 13816,
"dbsnp": "rs762356809",
"frequency_reference_population": 0.0008934608,
"hom_count_reference_population": 2,
"allele_count_reference_population": 1340,
"gnomad_exomes_af": 0.00090319,
"gnomad_genomes_af": 0.000807404,
"gnomad_exomes_ac": 1217,
"gnomad_genomes_ac": 123,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17000000178813934,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9279999732971191,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.391,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999989917668626,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Strong,BS2",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PVS1_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001676.7",
"gene_symbol": "ATP12A",
"hgnc_id": 13816,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.9+1G>A",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000796402.1",
"gene_symbol": "ENSG00000303666",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.72+3747C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}