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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: 20-4699448-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=4699448&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 4699448,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000379440.9",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "NM_000311.5",
"protein_id": "NP_000302.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 295,
"cdna_end": null,
"cdna_length": 2435,
"mane_select": "ENST00000379440.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "ENST00000379440.9",
"protein_id": "ENSP00000368752.4",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 295,
"cdna_end": null,
"cdna_length": 2435,
"mane_select": "NM_000311.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "ENST00000424424.2",
"protein_id": "ENSP00000411599.2",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 287,
"cdna_end": null,
"cdna_length": 2429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "ENST00000430350.2",
"protein_id": "ENSP00000399376.2",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 397,
"cdna_end": null,
"cdna_length": 2539,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "ENST00000457586.2",
"protein_id": "ENSP00000415284.2",
"transcript_support_level": 1,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 432,
"cdna_end": null,
"cdna_length": 2574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Pro47Ser",
"transcript": "NM_001271561.3",
"protein_id": "NP_001258490.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 73,
"cds_start": 139,
"cds_end": null,
"cds_length": 222,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 2431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "NM_001080121.3",
"protein_id": "NP_001073590.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 2430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "NM_001080122.3",
"protein_id": "NP_001073591.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 286,
"cdna_end": null,
"cdna_length": 2426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "NM_001080123.3",
"protein_id": "NP_001073592.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 2659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro",
"transcript": "NM_183079.4",
"protein_id": "NP_898902.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 253,
"cds_start": 228,
"cds_end": null,
"cds_length": 762,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 2431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRNP",
"gene_hgnc_id": 9449,
"dbsnp": "rs112637437",
"frequency_reference_population": 0.00012181631,
"hom_count_reference_population": 2,
"allele_count_reference_population": 196,
"gnomad_exomes_af": 0.000128195,
"gnomad_genomes_af": 0.0000598962,
"gnomad_exomes_ac": 187,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7200000286102295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.147,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000379440.9",
"gene_symbol": "PRNP",
"hgnc_id": 9449,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.228C>T",
"hgvs_p": "p.Pro76Pro"
}
],
"clinvar_disease": "Huntington disease-like 1,Inherited prion disease,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "not specified|Inherited prion disease|Huntington disease-like 1|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}