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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: 7-142749522-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=142749522&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 142749522,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000311737.12",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"transcript": "NM_002769.5",
"protein_id": "NP_002760.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 247,
"cds_start": 38,
"cds_end": null,
"cds_length": 744,
"cdna_start": 51,
"cdna_end": null,
"cdna_length": 809,
"mane_select": "ENST00000311737.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"transcript": "ENST00000311737.12",
"protein_id": "ENSP00000308720.7",
"transcript_support_level": 1,
"aa_start": 13,
"aa_end": null,
"aa_length": 247,
"cds_start": 38,
"cds_end": null,
"cds_length": 744,
"cdna_start": 51,
"cdna_end": null,
"cdna_length": 809,
"mane_select": "NM_002769.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"transcript": "ENST00000486171.5",
"protein_id": "ENSP00000417854.1",
"transcript_support_level": 5,
"aa_start": 13,
"aa_end": null,
"aa_length": 261,
"cds_start": 38,
"cds_end": null,
"cds_length": 786,
"cdna_start": 55,
"cdna_end": null,
"cdna_length": 803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"transcript": "ENST00000492062.2",
"protein_id": "ENSP00000419912.2",
"transcript_support_level": 2,
"aa_start": 13,
"aa_end": null,
"aa_length": 192,
"cds_start": 38,
"cds_end": null,
"cds_length": 579,
"cdna_start": 51,
"cdna_end": null,
"cdna_length": 789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "ENST00000485223.1",
"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": 1433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.42C>T",
"hgvs_p": null,
"transcript": "ENST00000497041.1",
"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": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "NR_172947.1",
"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": 738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "NR_172948.1",
"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": 735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "NR_172949.1",
"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": 735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "NR_172950.1",
"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": 649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"hgvs_c": "n.51C>T",
"hgvs_p": null,
"transcript": "NR_172951.1",
"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": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": null,
"strand": true,
"consequences": [
"intragenic_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": null,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRB",
"gene_hgnc_id": 12155,
"hgvs_c": "n.142749522C>T",
"hgvs_p": null,
"transcript": null,
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRSS1",
"gene_hgnc_id": 9475,
"dbsnp": "rs773357729",
"frequency_reference_population": 0.000008054343,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000820866,
"gnomad_genomes_af": 0.00000657177,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8353538513183594,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3840000033378601,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.683,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1618,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.097,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.747236930457113,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,BS2_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000311737.12",
"gene_symbol": "PRSS1",
"hgnc_id": 9475,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "",
"gene_symbol": "TRB",
"hgnc_id": 12155,
"effects": [
"intragenic_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142749522C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary pancreatitis,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "Hereditary pancreatitis|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}