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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: 3-38709595-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38709595&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38709595,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_006514.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4164G>A",
"hgvs_p": "p.Trp1388*",
"transcript": "NM_006514.4",
"protein_id": "NP_006505.4",
"transcript_support_level": null,
"aa_start": 1388,
"aa_end": null,
"aa_length": 1956,
"cds_start": 4164,
"cds_end": null,
"cds_length": 5871,
"cdna_start": 4377,
"cdna_end": null,
"cdna_length": 6626,
"mane_select": "ENST00000449082.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4164G>A",
"hgvs_p": "p.Trp1388*",
"transcript": "ENST00000449082.3",
"protein_id": "ENSP00000390600.2",
"transcript_support_level": 1,
"aa_start": 1388,
"aa_end": null,
"aa_length": 1956,
"cds_start": 4164,
"cds_end": null,
"cds_length": 5871,
"cdna_start": 4377,
"cdna_end": null,
"cdna_length": 6626,
"mane_select": "NM_006514.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4161G>A",
"hgvs_p": "p.Trp1387*",
"transcript": "ENST00000643924.1",
"protein_id": "ENSP00000495595.1",
"transcript_support_level": null,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1955,
"cds_start": 4161,
"cds_end": null,
"cds_length": 5868,
"cdna_start": 4193,
"cdna_end": null,
"cdna_length": 5903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4188G>A",
"hgvs_p": "p.Trp1396*",
"transcript": "ENST00000655275.1",
"protein_id": "ENSP00000499510.1",
"transcript_support_level": null,
"aa_start": 1396,
"aa_end": null,
"aa_length": 1964,
"cds_start": 4188,
"cds_end": null,
"cds_length": 5895,
"cdna_start": 4450,
"cdna_end": null,
"cdna_length": 6704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4161G>A",
"hgvs_p": "p.Trp1387*",
"transcript": "NM_001293306.2",
"protein_id": "NP_001280235.2",
"transcript_support_level": null,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1955,
"cds_start": 4161,
"cds_end": null,
"cds_length": 5868,
"cdna_start": 4161,
"cdna_end": null,
"cdna_length": 5871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3870G>A",
"hgvs_p": "p.Trp1290*",
"transcript": "NM_001293307.2",
"protein_id": "NP_001280236.2",
"transcript_support_level": null,
"aa_start": 1290,
"aa_end": null,
"aa_length": 1858,
"cds_start": 3870,
"cds_end": null,
"cds_length": 5577,
"cdna_start": 3870,
"cdna_end": null,
"cdna_length": 5580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4173G>A",
"hgvs_p": "p.Trp1391*",
"transcript": "XM_005265371.4",
"protein_id": "XP_005265428.1",
"transcript_support_level": null,
"aa_start": 1391,
"aa_end": null,
"aa_length": 1959,
"cds_start": 4173,
"cds_end": null,
"cds_length": 5880,
"cdna_start": 4173,
"cdna_end": null,
"cdna_length": 6422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.4170G>A",
"hgvs_p": "p.Trp1390*",
"transcript": "XM_011533993.3",
"protein_id": "XP_011532295.1",
"transcript_support_level": null,
"aa_start": 1390,
"aa_end": null,
"aa_length": 1958,
"cds_start": 4170,
"cds_end": null,
"cds_length": 5877,
"cdna_start": 4170,
"cdna_end": null,
"cdna_length": 6419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"hgvs_c": "c.3879G>A",
"hgvs_p": "p.Trp1293*",
"transcript": "XM_011533994.3",
"protein_id": "XP_011532296.1",
"transcript_support_level": null,
"aa_start": 1293,
"aa_end": null,
"aa_length": 1861,
"cds_start": 3879,
"cds_end": null,
"cds_length": 5586,
"cdna_start": 3879,
"cdna_end": null,
"cdna_length": 6128,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN10A",
"gene_hgnc_id": 10582,
"dbsnp": "rs756253735",
"frequency_reference_population": 0.000015566626,
"hom_count_reference_population": 1,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000144438,
"gnomad_genomes_af": 0.0000262999,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6299999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.812,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_006514.4",
"gene_symbol": "SCN10A",
"hgnc_id": 10582,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.4164G>A",
"hgvs_p": "p.Trp1388*"
}
],
"clinvar_disease": "Brugada syndrome,Cardiovascular phenotype,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Brugada syndrome|not provided|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}