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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: 7-142752929-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=142752929&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRSS1",
"hgnc_id": 9475,
"hgvs_c": "c.653A>T",
"hgvs_p": "p.Asp218Val",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_002769.5",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intragenic_variant"
],
"gene_symbol": "TRB",
"hgnc_id": 12155,
"hgvs_c": "n.142752929A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 11,
"alphamissense_prediction": null,
"alphamissense_score": 0.194,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"chr": "7",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Hereditary pancreatitis",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.22918877005577087,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 247,
"aa_ref": "D",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 809,
"cdna_start": 666,
"cds_end": null,
"cds_length": 744,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_002769.5",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.653A>T",
"hgvs_p": "p.Asp218Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000311737.12",
"protein_coding": true,
"protein_id": "NP_002760.1",
"strand": true,
"transcript": "NM_002769.5",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 247,
"aa_ref": "D",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 809,
"cdna_start": 666,
"cds_end": null,
"cds_length": 744,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000311737.12",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.653A>T",
"hgvs_p": "p.Asp218Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002769.5",
"protein_coding": true,
"protein_id": "ENSP00000308720.7",
"strand": true,
"transcript": "ENST00000311737.12",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 261,
"aa_ref": "D",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 803,
"cdna_start": 712,
"cds_end": null,
"cds_length": 786,
"cds_start": 695,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000486171.5",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.695A>T",
"hgvs_p": "p.Asp232Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417854.1",
"strand": true,
"transcript": "ENST00000486171.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 192,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 789,
"cdna_start": null,
"cds_end": null,
"cds_length": 579,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000492062.2",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.*57A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419912.2",
"strand": true,
"transcript": "ENST00000492062.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1260,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000463701.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.1117A>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": "ENST00000463701.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 738,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_172947.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.595A>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": "NR_172947.1",
"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": 735,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_172948.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.592A>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": "NR_172948.1",
"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": 735,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_172949.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.592A>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": "NR_172949.1",
"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": 649,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NR_172950.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.506A>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": "NR_172950.1",
"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": 583,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_172951.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.440A>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": "NR_172951.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": null,
"canonical": null,
"cdna_end": null,
"cdna_length": null,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intragenic_variant"
],
"exon_count": null,
"exon_rank": null,
"exon_rank_end": null,
"feature": null,
"gene_hgnc_id": 12155,
"gene_symbol": "TRB",
"hgvs_c": "n.142752929A>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": null,
"protein_id": null,
"strand": true,
"transcript": null,
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199878511",
"effect": "missense_variant",
"frequency_reference_population": 0.000006815771,
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"gnomad_exomes_ac": 9,
"gnomad_exomes_af": 0.00000615682,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131484,
"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": "Uncertain significance",
"phenotype_combined": "Hereditary pancreatitis",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.924,
"pos": 142752929,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.224,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002769.5"
}
]
}