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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: 3-81578051-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=81578051&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 81578051,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000429644.7",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.1492G>T",
"hgvs_p": "p.Glu498*",
"transcript": "NM_000158.4",
"protein_id": "NP_000149.4",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 702,
"cds_start": 1492,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1620,
"cdna_end": null,
"cdna_length": 2941,
"mane_select": "ENST00000429644.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.1492G>T",
"hgvs_p": "p.Glu498*",
"transcript": "ENST00000429644.7",
"protein_id": "ENSP00000410833.2",
"transcript_support_level": 1,
"aa_start": 498,
"aa_end": null,
"aa_length": 702,
"cds_start": 1492,
"cds_end": null,
"cds_length": 2109,
"cdna_start": 1620,
"cdna_end": null,
"cdna_length": 2941,
"mane_select": "NM_000158.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.1369G>T",
"hgvs_p": "p.Glu457*",
"transcript": "ENST00000489715.1",
"protein_id": "ENSP00000419638.1",
"transcript_support_level": 2,
"aa_start": 457,
"aa_end": null,
"aa_length": 661,
"cds_start": 1369,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 2513,
"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": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "n.1620G>T",
"hgvs_p": null,
"transcript": "XR_007095662.1",
"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": 8416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "n.-108G>T",
"hgvs_p": null,
"transcript": "ENST00000484687.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 863,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"dbsnp": "rs201758548",
"frequency_reference_population": 0.0000013736056,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137361,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.552,
"phylop100way_prediction": "Pathogenic",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "ENST00000429644.7",
"gene_symbol": "GBE1",
"hgnc_id": 4180,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1492G>T",
"hgvs_p": "p.Glu498*"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}