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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: 3-193407378-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193407378&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193407378,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_032279.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.3313G>A",
"hgvs_p": "p.Val1105Ile",
"transcript": "NM_032279.4",
"protein_id": "NP_115655.2",
"transcript_support_level": null,
"aa_start": 1105,
"aa_end": null,
"aa_length": 1196,
"cds_start": 3313,
"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": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.3313G>A",
"hgvs_p": "p.Val1105Ile",
"transcript": "ENST00000342695.9",
"protein_id": "ENSP00000339182.4",
"transcript_support_level": 1,
"aa_start": 1105,
"aa_end": null,
"aa_length": 1196,
"cds_start": 3313,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Val121Ile",
"transcript": "ENST00000400270.6",
"protein_id": "ENSP00000383129.2",
"transcript_support_level": 1,
"aa_start": 121,
"aa_end": null,
"aa_length": 212,
"cds_start": 361,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000400270.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.3256G>A",
"hgvs_p": "p.Val1086Ile",
"transcript": "ENST00000392443.7",
"protein_id": "ENSP00000376238.3",
"transcript_support_level": 5,
"aa_start": 1086,
"aa_end": null,
"aa_length": 1177,
"cds_start": 3256,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.3190G>A",
"hgvs_p": "p.Val1064Ile",
"transcript": "ENST00000901816.1",
"protein_id": "ENSP00000571875.1",
"transcript_support_level": null,
"aa_start": 1064,
"aa_end": null,
"aa_length": 1155,
"cds_start": 3190,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "c.3442G>A",
"hgvs_p": "p.Val1148Ile",
"transcript": "XM_047449063.1",
"protein_id": "XP_047305019.1",
"transcript_support_level": null,
"aa_start": 1148,
"aa_end": null,
"aa_length": 1239,
"cds_start": 3442,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.*474G>A",
"hgvs_p": null,
"transcript": "ENST00000428352.5",
"protein_id": "ENSP00000395367.1",
"transcript_support_level": 2,
"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": "ENST00000428352.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.*2756G>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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.299G>A",
"hgvs_p": null,
"transcript": "ENST00000482964.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000482964.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.*474G>A",
"hgvs_p": null,
"transcript": "ENST00000428352.5",
"protein_id": "ENSP00000395367.1",
"transcript_support_level": 2,
"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": "ENST00000428352.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"hgvs_c": "n.*2756G>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"
}
],
"gene_symbol": "ATP13A4",
"gene_hgnc_id": 25422,
"dbsnp": "rs763326526",
"frequency_reference_population": 0.000016118613,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000157433,
"gnomad_genomes_af": 0.0000197231,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07927379012107849,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.146,
"revel_prediction": "Benign",
"alphamissense_score": 0.064,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.428,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_032279.4",
"gene_symbol": "ATP13A4",
"hgnc_id": 25422,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3313G>A",
"hgvs_p": "p.Val1105Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}