← Back to variant description
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: 3-193491389-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193491389&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193491389,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000342695.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.543A>G",
"hgvs_p": "p.Ile181Met",
"transcript": "NM_032279.4",
"protein_id": "NP_115655.2",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 1196,
"cds_start": 543,
"cds_end": null,
"cds_length": 3591,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 7372,
"mane_select": "ENST00000342695.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.543A>G",
"hgvs_p": "p.Ile181Met",
"transcript": "ENST00000342695.9",
"protein_id": "ENSP00000339182.4",
"transcript_support_level": 1,
"aa_start": 181,
"aa_end": null,
"aa_length": 1196,
"cds_start": 543,
"cds_end": null,
"cds_length": 3591,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 7372,
"mane_select": "NM_032279.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.651A>G",
"hgvs_p": null,
"transcript": "ENST00000490925.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.543A>G",
"hgvs_p": "p.Ile181Met",
"transcript": "ENST00000392443.7",
"protein_id": "ENSP00000376238.3",
"transcript_support_level": 5,
"aa_start": 181,
"aa_end": null,
"aa_length": 1177,
"cds_start": 543,
"cds_end": null,
"cds_length": 3534,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 4016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.543A>G",
"hgvs_p": "p.Ile181Met",
"transcript": "ENST00000295548.3",
"protein_id": "ENSP00000295548.3",
"transcript_support_level": 5,
"aa_start": 181,
"aa_end": null,
"aa_length": 576,
"cds_start": 543,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 543,
"cdna_end": null,
"cdna_length": 2157,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.672A>G",
"hgvs_p": "p.Ile224Met",
"transcript": "XM_047449063.1",
"protein_id": "XP_047305019.1",
"transcript_support_level": null,
"aa_start": 224,
"aa_end": null,
"aa_length": 1239,
"cds_start": 672,
"cds_end": null,
"cds_length": 3720,
"cdna_start": 936,
"cdna_end": null,
"cdna_length": 7669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.672A>G",
"hgvs_p": "p.Ile224Met",
"transcript": "XM_017007319.2",
"protein_id": "XP_016862808.2",
"transcript_support_level": null,
"aa_start": 224,
"aa_end": null,
"aa_length": 967,
"cds_start": 672,
"cds_end": null,
"cds_length": 2904,
"cdna_start": 936,
"cdna_end": null,
"cdna_length": 3260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.936A>G",
"hgvs_p": null,
"transcript": "XR_007095757.1",
"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": 3125,
"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": 28,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.*181+1528A>G",
"hgvs_p": null,
"transcript": "ENST00000450950.6",
"protein_id": "ENSP00000402023.2",
"transcript_support_level": 5,
"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": 3658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"dbsnp": "rs6788448",
"frequency_reference_population": 0.41088083,
"hom_count_reference_population": 135312,
"allele_count_reference_population": 649776,
"gnomad_exomes_af": 0.407834,
"gnomad_genomes_af": 0.439532,
"gnomad_exomes_ac": 582961,
"gnomad_genomes_ac": 66815,
"gnomad_exomes_homalt": 120481,
"gnomad_genomes_homalt": 14831,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0009139776229858398,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.405,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2139,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.414,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000342695.9",
"gene_symbol": "ATP13A4",
"hgnc_id": 25422,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.543A>G",
"hgvs_p": "p.Ile181Met"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}