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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: 7-142751940-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=142751940&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM1",
"PP3_Moderate",
"BS2_Supporting"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRSS1",
"hgnc_id": 9475,
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Val123Met",
"inheritance_mode": "AD",
"pathogenic_score": 4,
"score": 3,
"transcript": "NM_002769.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"intragenic_variant"
],
"gene_symbol": "TRB",
"hgnc_id": 12155,
"hgvs_c": "n.142751940G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP3_Moderate,BS2_Supporting",
"acmg_score": 3,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": 0.8929,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.29,
"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": "Pathogenic",
"computational_score_selected": 0.8417682647705078,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 247,
"aa_ref": "V",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 809,
"cdna_start": 380,
"cds_end": null,
"cds_length": 744,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002769.5",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Val123Met",
"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": "M",
"aa_end": null,
"aa_length": 247,
"aa_ref": "V",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 809,
"cdna_start": 380,
"cds_end": null,
"cds_length": 744,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000311737.12",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Val123Met",
"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": "M",
"aa_end": null,
"aa_length": 261,
"aa_ref": "V",
"aa_start": 137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 803,
"cdna_start": 426,
"cds_end": null,
"cds_length": 786,
"cds_start": 409,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000486171.5",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.409G>A",
"hgvs_p": "p.Val137Met",
"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": "M",
"aa_end": null,
"aa_length": 192,
"aa_ref": "V",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 789,
"cdna_start": 380,
"cds_end": null,
"cds_length": 579,
"cds_start": 367,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000492062.2",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Val123Met",
"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": 1,
"exon_rank_end": null,
"feature": "ENST00000463701.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.831G>A",
"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": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1433,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000485223.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.1365G>A",
"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": "ENST00000485223.1",
"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": 3,
"exon_rank_end": null,
"feature": "NR_172947.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.309G>A",
"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": 3,
"exon_rank_end": null,
"feature": "NR_172948.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.306G>A",
"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": 3,
"exon_rank_end": null,
"feature": "NR_172949.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.306G>A",
"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": 2,
"exon_rank_end": null,
"feature": "NR_172950.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.220G>A",
"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": 3,
"exon_rank_end": null,
"feature": "NR_172951.1",
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"hgvs_c": "n.154G>A",
"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.142751940G>A",
"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": "rs144403091",
"effect": "missense_variant",
"frequency_reference_population": 0.000019828361,
"gene_hgnc_id": 9475,
"gene_symbol": "PRSS1",
"gnomad_exomes_ac": 28,
"gnomad_exomes_af": 0.0000191534,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000263206,
"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": "Uncertain_significance",
"phylop100way_score": 5.601,
"pos": 142751940,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.648,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_002769.5"
}
]
}