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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: 16-2784799-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2784799&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2784799,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_152891.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "NM_152891.3",
"protein_id": "NP_690851.2",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 1619,
"mane_select": "ENST00000682474.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "ENST00000682474.1",
"protein_id": "ENSP00000507560.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 1619,
"mane_select": "NM_152891.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "ENST00000293851.9",
"protein_id": "ENSP00000293851.5",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 848,
"cdna_end": null,
"cdna_length": 1694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "ENST00000570702.5",
"protein_id": "ENSP00000458369.1",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 830,
"cdna_end": null,
"cdna_length": 1676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.*267G>A",
"hgvs_p": null,
"transcript": "ENST00000576886.5",
"protein_id": "ENSP00000459051.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 115,
"cds_start": -4,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "NM_001385462.1",
"protein_id": "NP_001372391.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 831,
"cdna_end": null,
"cdna_length": 1677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "NM_001385463.1",
"protein_id": "NP_001372392.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 819,
"cdna_end": null,
"cdna_length": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn",
"transcript": "NM_001385464.1",
"protein_id": "NP_001372393.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 280,
"cds_start": 688,
"cds_end": null,
"cds_length": 843,
"cdna_start": 797,
"cdna_end": null,
"cdna_length": 1643,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "n.501G>A",
"hgvs_p": null,
"transcript": "NR_169625.1",
"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": 1347,
"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": "PRSS33",
"gene_hgnc_id": 30405,
"hgvs_c": "c.*145G>A",
"hgvs_p": null,
"transcript": "ENST00000571674.1",
"protein_id": "ENSP00000460368.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 235,
"cds_start": -4,
"cds_end": null,
"cds_length": 709,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRSS33",
"gene_hgnc_id": 30405,
"dbsnp": "rs1425565547",
"frequency_reference_population": 0.000004359491,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000275201,
"gnomad_genomes_af": 0.0000197099,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9766326546669006,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.897,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8509,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.644,
"phylop100way_prediction": "Uncertain_significance",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_152891.3",
"gene_symbol": "PRSS33",
"hgnc_id": 30405,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Asp230Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}