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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: 14-20476546-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=20476546&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 20476546,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000361505.10",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.815A>G",
"hgvs_p": "p.Glu272Gly",
"transcript": "NM_000270.4",
"protein_id": "NP_000261.2",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 289,
"cds_start": 815,
"cds_end": null,
"cds_length": 870,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 1477,
"mane_select": "ENST00000361505.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.815A>G",
"hgvs_p": "p.Glu272Gly",
"transcript": "ENST00000361505.10",
"protein_id": "ENSP00000354532.6",
"transcript_support_level": 1,
"aa_start": 272,
"aa_end": null,
"aa_length": 289,
"cds_start": 815,
"cds_end": null,
"cds_length": 870,
"cdna_start": 934,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.3238A>G",
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.1244A>G",
"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": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.932A>G",
"hgvs_p": "p.Glu311Gly",
"transcript": "ENST00000553591.2",
"protein_id": "ENSP00000452421.2",
"transcript_support_level": 5,
"aa_start": 311,
"aa_end": null,
"aa_length": 328,
"cds_start": 932,
"cds_end": null,
"cds_length": 987,
"cdna_start": 1039,
"cdna_end": null,
"cdna_length": 1582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.815A>G",
"hgvs_p": "p.Glu272Gly",
"transcript": "ENST00000697613.1",
"protein_id": "ENSP00000513359.1",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 289,
"cds_start": 815,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1471,
"cdna_end": null,
"cdna_length": 2014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "c.578A>G",
"hgvs_p": "p.Glu193Gly",
"transcript": "ENST00000697614.1",
"protein_id": "ENSP00000513360.1",
"transcript_support_level": null,
"aa_start": 193,
"aa_end": null,
"aa_length": 210,
"cds_start": 578,
"cds_end": null,
"cds_length": 633,
"cdna_start": 903,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.1123A>G",
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.4181A>G",
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"hgvs_c": "n.1643A>G",
"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.186+358T>C",
"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
}
],
"gene_symbol": "PNP",
"gene_hgnc_id": 7892,
"dbsnp": "rs773751064",
"frequency_reference_population": 0.000038412498,
"hom_count_reference_population": 0,
"allele_count_reference_population": 62,
"gnomad_exomes_af": 0.0000396747,
"gnomad_genomes_af": 0.0000262867,
"gnomad_exomes_ac": 58,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2943124771118164,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.465,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2156,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.122,
"phylop100way_prediction": "Pathogenic",
"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": "Likely_benign",
"acmg_criteria": "BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000361505.10",
"gene_symbol": "PNP",
"hgnc_id": 7892,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.815A>G",
"hgvs_p": "p.Glu272Gly"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000554678.1",
"gene_symbol": "ENSG00000258908",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.186+358T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Purine-nucleoside phosphorylase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Purine-nucleoside phosphorylase deficiency|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}