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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: 14-20475153-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=20475153&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 20475153,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000361505.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.553C>T",
"hgvs_p": "p.Arg185Cys",
"transcript": "NM_000270.4",
"protein_id": "NP_000261.2",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 289,
"cds_start": 553,
"cds_end": null,
"cds_length": 870,
"cdna_start": 672,
"cdna_end": null,
"cdna_length": 1477,
"mane_select": "ENST00000361505.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.553C>T",
"hgvs_p": "p.Arg185Cys",
"transcript": "ENST00000361505.10",
"protein_id": "ENSP00000354532.6",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 289,
"cds_start": 553,
"cds_end": null,
"cds_length": 870,
"cdna_start": 672,
"cdna_end": null,
"cdna_length": 1477,
"mane_select": "NM_000270.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.2976C>T",
"hgvs_p": null,
"transcript": "ENST00000556293.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 3757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.982C>T",
"hgvs_p": null,
"transcript": "ENST00000557229.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 1764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.670C>T",
"hgvs_p": "p.Arg224Cys",
"transcript": "ENST00000553591.2",
"protein_id": "ENSP00000452421.2",
"transcript_support_level": 5,
"aa_start": 224,
"aa_end": null,
"aa_length": 328,
"cds_start": 670,
"cds_end": null,
"cds_length": 987,
"cdna_start": 777,
"cdna_end": null,
"cdna_length": 1582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.553C>T",
"hgvs_p": "p.Arg185Cys",
"transcript": "ENST00000697613.1",
"protein_id": "ENSP00000513359.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 289,
"cds_start": 553,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1209,
"cdna_end": null,
"cdna_length": 2014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Cys",
"transcript": "ENST00000697614.1",
"protein_id": "ENSP00000513360.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 210,
"cds_start": 316,
"cds_end": null,
"cds_length": 633,
"cdna_start": 641,
"cdna_end": null,
"cdna_length": 1446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.861C>T",
"hgvs_p": null,
"transcript": "ENST00000554056.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.3919C>T",
"hgvs_p": null,
"transcript": "ENST00000556754.2",
"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": 4729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.1381C>T",
"hgvs_p": null,
"transcript": "ENST00000697615.1",
"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": 2127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258908",
"gene_hgnc_id": null,
"hgvs_c": "n.187-59G>A",
"hgvs_p": null,
"transcript": "ENST00000554678.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.*245C>T",
"hgvs_p": null,
"transcript": "ENST00000554065.1",
"protein_id": "ENSP00000451108.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 60,
"cds_start": -4,
"cds_end": null,
"cds_length": 184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"dbsnp": "rs373569964",
"frequency_reference_population": 0.00002602124,
"hom_count_reference_population": 0,
"allele_count_reference_population": 42,
"gnomad_exomes_af": 0.0000273619,
"gnomad_genomes_af": 0.0000131423,
"gnomad_exomes_ac": 40,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5392279624938965,
"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": 0.521,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1913,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.11,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000361505.10",
"gene_symbol": "PNP",
"hgnc_id": 7892,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.553C>T",
"hgvs_p": "p.Arg185Cys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000554678.1",
"gene_symbol": "ENSG00000258908",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.187-59G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Purine-nucleoside phosphorylase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Purine-nucleoside phosphorylase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}