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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: 3-183152460-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=183152460&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 183152460,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014398.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Met",
"transcript": "NM_014398.4",
"protein_id": "NP_055213.2",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 416,
"cds_start": 803,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 3196,
"mane_select": "ENST00000265598.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Met",
"transcript": "ENST00000265598.8",
"protein_id": "ENSP00000265598.3",
"transcript_support_level": 1,
"aa_start": 268,
"aa_end": null,
"aa_length": 416,
"cds_start": 803,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 3196,
"mane_select": "NM_014398.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"hgvs_c": "c.731C>T",
"hgvs_p": "p.Thr244Met",
"transcript": "ENST00000466939.1",
"protein_id": "ENSP00000418912.1",
"transcript_support_level": 2,
"aa_start": 244,
"aa_end": null,
"aa_length": 392,
"cds_start": 731,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 849,
"cdna_end": null,
"cdna_length": 1453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Met",
"transcript": "XM_005247360.6",
"protein_id": "XP_005247417.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 418,
"cds_start": 803,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1072,
"cdna_end": null,
"cdna_length": 7559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Met",
"transcript": "XM_047447967.1",
"protein_id": "XP_047303923.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 376,
"cds_start": 803,
"cds_end": null,
"cds_length": 1131,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Met",
"transcript": "XM_011512688.3",
"protein_id": "XP_011510990.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 354,
"cds_start": 803,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 1159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LAMP3",
"gene_hgnc_id": 14582,
"dbsnp": "rs151059567",
"frequency_reference_population": 0.000060756654,
"hom_count_reference_population": 0,
"allele_count_reference_population": 98,
"gnomad_exomes_af": 0.0000362833,
"gnomad_genomes_af": 0.000295535,
"gnomad_exomes_ac": 53,
"gnomad_genomes_ac": 45,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4477531611919403,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.301,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3198,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.276,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_014398.4",
"gene_symbol": "LAMP3",
"hgnc_id": 14582,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.803C>T",
"hgvs_p": "p.Thr268Met"
}
],
"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
}