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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: 3-193275056-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193275056&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193275056,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_198505.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A5",
"gene_hgnc_id": 31789,
"hgvs_c": "c.3643T>C",
"hgvs_p": "p.Trp1215Arg",
"transcript": "NM_198505.4",
"protein_id": "NP_940907.2",
"transcript_support_level": null,
"aa_start": 1215,
"aa_end": null,
"aa_length": 1218,
"cds_start": 3643,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000342358.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198505.4"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A5",
"gene_hgnc_id": 31789,
"hgvs_c": "c.3643T>C",
"hgvs_p": "p.Trp1215Arg",
"transcript": "ENST00000342358.9",
"protein_id": "ENSP00000341942.4",
"transcript_support_level": 1,
"aa_start": 1215,
"aa_end": null,
"aa_length": 1218,
"cds_start": 3643,
"cds_end": null,
"cds_length": 3657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_198505.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342358.9"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A5",
"gene_hgnc_id": 31789,
"hgvs_c": "c.2389T>C",
"hgvs_p": "p.Trp797Arg",
"transcript": "XM_047448075.1",
"protein_id": "XP_047304031.1",
"transcript_support_level": null,
"aa_start": 797,
"aa_end": null,
"aa_length": 800,
"cds_start": 2389,
"cds_end": null,
"cds_length": 2403,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448075.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A5",
"gene_hgnc_id": 31789,
"hgvs_c": "c.1966T>C",
"hgvs_p": "p.Trp656Arg",
"transcript": "XM_017006305.1",
"protein_id": "XP_016861794.1",
"transcript_support_level": null,
"aa_start": 656,
"aa_end": null,
"aa_length": 659,
"cds_start": 1966,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006305.1"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLAAT1",
"gene_hgnc_id": 14922,
"hgvs_c": "c.406-1909A>G",
"hgvs_p": null,
"transcript": "XM_011513034.2",
"protein_id": "XP_011511336.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 237,
"cds_start": null,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513034.2"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLAAT1",
"gene_hgnc_id": 14922,
"hgvs_c": "c.406-1909A>G",
"hgvs_p": null,
"transcript": "XM_011513035.3",
"protein_id": "XP_011511337.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": null,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513035.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A5",
"gene_hgnc_id": 31789,
"hgvs_c": "n.1465T>C",
"hgvs_p": null,
"transcript": "ENST00000495496.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000495496.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "PLAAT1",
"gene_hgnc_id": 14922,
"hgvs_c": "n.*60-2580A>G",
"hgvs_p": null,
"transcript": "ENST00000416012.1",
"protein_id": "ENSP00000414431.1",
"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": "ENST00000416012.1"
}
],
"gene_symbol": "ATP13A5",
"gene_hgnc_id": 31789,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.43553709983825684,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.571,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2134,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.562,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_198505.4",
"gene_symbol": "ATP13A5",
"hgnc_id": 31789,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3643T>C",
"hgvs_p": "p.Trp1215Arg"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XM_011513034.2",
"gene_symbol": "PLAAT1",
"hgnc_id": 14922,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.406-1909A>G",
"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
}