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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: 2-178451558-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=178451558&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "PJVK",
"hgnc_id": 29502,
"hgvs_c": "c.-234C>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_001042702.5",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "PRKRA",
"hgnc_id": 9438,
"hgvs_c": "n.-46G>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000470200.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.76,
"chr": "2",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7599999904632568,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 352,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": null,
"cds_end": null,
"cds_length": 1059,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001042702.5",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-234C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000644580.2",
"protein_coding": true,
"protein_id": "NP_001036167.1",
"strand": true,
"transcript": "NM_001042702.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 352,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": null,
"cds_end": null,
"cds_length": 1059,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000644580.2",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-234C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001042702.5",
"protein_coding": true,
"protein_id": "ENSP00000495855.2",
"strand": true,
"transcript": "ENST00000644580.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 352,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1602,
"cdna_start": null,
"cds_end": null,
"cds_length": 1059,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000970493.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-346C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640552.1",
"strand": true,
"transcript": "ENST00000970493.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 193,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1542,
"cdna_start": null,
"cds_end": null,
"cds_length": 582,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001353777.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-546C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001340706.1",
"strand": true,
"transcript": "NM_001353777.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 193,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1581,
"cdna_start": null,
"cds_end": null,
"cds_length": 582,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000642492.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-769C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496267.1",
"strand": true,
"transcript": "ENST00000642492.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 193,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1268,
"cdna_start": null,
"cds_end": null,
"cds_length": 582,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000645817.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-546C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495731.1",
"strand": true,
"transcript": "ENST00000645817.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 28,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 869,
"cdna_start": null,
"cds_end": null,
"cds_length": 89,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000643738.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-658C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493684.1",
"strand": true,
"transcript": "ENST00000643738.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 355,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2134,
"cdna_start": null,
"cds_end": null,
"cds_length": 1068,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001353775.2",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-283C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001340704.1",
"strand": true,
"transcript": "NM_001353775.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 193,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1289,
"cdna_start": null,
"cds_end": null,
"cds_length": 582,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000647226.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-769C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496024.1",
"strand": true,
"transcript": "ENST00000647226.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 3,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 647,
"cdna_start": null,
"cds_end": null,
"cds_length": 13,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000644554.1",
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"hgvs_c": "c.-780C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495037.1",
"strand": true,
"transcript": "ENST00000644554.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 550,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000470200.5",
"gene_hgnc_id": 9438,
"gene_symbol": "PRKRA",
"hgvs_c": "n.-46G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000470200.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs555344314",
"effect": "5_prime_UTR_variant",
"frequency_reference_population": 0.000013146824,
"gene_hgnc_id": 29502,
"gene_symbol": "PJVK",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131468,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.016,
"pos": 178451558,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001042702.5"
}
]
}