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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: 3-38750082-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38750082&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Moderate",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCN10A",
"hgnc_id": 10582,
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Val620Ile",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_006514.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS2",
"acmg_score": -7,
"allele_count_reference_population": 119,
"alphamissense_prediction": null,
"alphamissense_score": 0.0863,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"chr": "3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 2, familial,Brugada syndrome,Cardiovascular phenotype,Episodic pain syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1269209086894989,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1956,
"aa_ref": "V",
"aa_start": 620,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6626,
"cdna_start": 2071,
"cds_end": null,
"cds_length": 5871,
"cds_start": 1858,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_006514.4",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Val620Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000449082.3",
"protein_coding": true,
"protein_id": "NP_006505.4",
"strand": false,
"transcript": "NM_006514.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1956,
"aa_ref": "V",
"aa_start": 620,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6626,
"cdna_start": 2071,
"cds_end": null,
"cds_length": 5871,
"cds_start": 1858,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000449082.3",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Val620Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006514.4",
"protein_coding": true,
"protein_id": "ENSP00000390600.2",
"strand": false,
"transcript": "ENST00000449082.3",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1955,
"aa_ref": "V",
"aa_start": 620,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5903,
"cdna_start": 1890,
"cds_end": null,
"cds_length": 5868,
"cds_start": 1858,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000643924.1",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Val620Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495595.1",
"strand": false,
"transcript": "ENST00000643924.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1964,
"aa_ref": "V",
"aa_start": 629,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6704,
"cdna_start": 2147,
"cds_end": null,
"cds_length": 5895,
"cds_start": 1885,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000655275.1",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1885G>A",
"hgvs_p": "p.Val629Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499510.1",
"strand": false,
"transcript": "ENST00000655275.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1955,
"aa_ref": "V",
"aa_start": 620,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5871,
"cdna_start": 1858,
"cds_end": null,
"cds_length": 5868,
"cds_start": 1858,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001293306.2",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1858G>A",
"hgvs_p": "p.Val620Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001280235.2",
"strand": false,
"transcript": "NM_001293306.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1858,
"aa_ref": "V",
"aa_start": 522,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5580,
"cdna_start": 1564,
"cds_end": null,
"cds_length": 5577,
"cds_start": 1564,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001293307.2",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1564G>A",
"hgvs_p": "p.Val522Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001280236.2",
"strand": false,
"transcript": "NM_001293307.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1959,
"aa_ref": "V",
"aa_start": 623,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6422,
"cdna_start": 1867,
"cds_end": null,
"cds_length": 5880,
"cds_start": 1867,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_005265371.4",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1867G>A",
"hgvs_p": "p.Val623Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005265428.1",
"strand": false,
"transcript": "XM_005265371.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1958,
"aa_ref": "V",
"aa_start": 623,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6419,
"cdna_start": 1867,
"cds_end": null,
"cds_length": 5877,
"cds_start": 1867,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011533993.3",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1867G>A",
"hgvs_p": "p.Val623Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532295.1",
"strand": false,
"transcript": "XM_011533993.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1861,
"aa_ref": "V",
"aa_start": 525,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6128,
"cdna_start": 1573,
"cds_end": null,
"cds_length": 5586,
"cds_start": 1573,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011533994.3",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.1573G>A",
"hgvs_p": "p.Val525Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532296.1",
"strand": false,
"transcript": "XM_011533994.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs151303346",
"effect": "missense_variant",
"frequency_reference_population": 0.00007472574,
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"gnomad_exomes_ac": 76,
"gnomad_exomes_af": 0.0000527713,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 43,
"gnomad_genomes_af": 0.000282315,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Brugada syndrome|not provided|Cardiovascular phenotype|Episodic pain syndrome, familial, 2|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.404,
"pos": 38750082,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.406,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006514.4"
}
]
}