← 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: 3-193514861-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193514861&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193514861,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_032279.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Gly24Asp",
"transcript": "NM_032279.4",
"protein_id": "NP_115655.2",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 1196,
"cds_start": 71,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000342695.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032279.4"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Gly24Asp",
"transcript": "ENST00000342695.9",
"protein_id": "ENSP00000339182.4",
"transcript_support_level": 1,
"aa_start": 24,
"aa_end": null,
"aa_length": 1196,
"cds_start": 71,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032279.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342695.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.179G>A",
"hgvs_p": null,
"transcript": "ENST00000490925.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000490925.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Gly24Asp",
"transcript": "ENST00000392443.7",
"protein_id": "ENSP00000376238.3",
"transcript_support_level": 5,
"aa_start": 24,
"aa_end": null,
"aa_length": 1177,
"cds_start": 71,
"cds_end": null,
"cds_length": 3534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392443.7"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Gly24Asp",
"transcript": "ENST00000901816.1",
"protein_id": "ENSP00000571875.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 1155,
"cds_start": 71,
"cds_end": null,
"cds_length": 3468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000901816.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Gly24Asp",
"transcript": "ENST00000295548.3",
"protein_id": "ENSP00000295548.3",
"transcript_support_level": 5,
"aa_start": 24,
"aa_end": null,
"aa_length": 576,
"cds_start": 71,
"cds_end": null,
"cds_length": 1731,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295548.3"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Gly67Asp",
"transcript": "XM_047449063.1",
"protein_id": "XP_047305019.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1239,
"cds_start": 200,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449063.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Gly67Asp",
"transcript": "XM_017007319.2",
"protein_id": "XP_016862808.2",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 967,
"cds_start": 200,
"cds_end": null,
"cds_length": 2904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007319.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.71G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000450950.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.302G>A",
"hgvs_p": null,
"transcript": "ENST00000489140.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000489140.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.464G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007095757.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP13A4-AS1",
"gene_hgnc_id": 41095,
"hgvs_c": "n.99+7983C>T",
"hgvs_p": null,
"transcript": "ENST00000817206.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000817206.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP13A4-AS1",
"gene_hgnc_id": 41095,
"hgvs_c": "n.63+8019C>T",
"hgvs_p": null,
"transcript": "ENST00000817207.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000817207.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP13A4-AS1",
"gene_hgnc_id": 41095,
"hgvs_c": "n.96+7983C>T",
"hgvs_p": null,
"transcript": "ENST00000817208.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000817208.1"
}
],
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"dbsnp": "rs368997183",
"frequency_reference_population": 0.000023545741,
"hom_count_reference_population": 0,
"allele_count_reference_population": 38,
"gnomad_exomes_af": 0.0000232593,
"gnomad_genomes_af": 0.0000262985,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8492000102996826,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.609,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9814,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.764,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.1,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032279.4",
"gene_symbol": "ATP13A4",
"hgnc_id": 25422,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Gly24Asp"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000817206.1",
"gene_symbol": "ATP13A4-AS1",
"hgnc_id": 41095,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.99+7983C>T",
"hgvs_p": null
}
],
"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
}