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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: 3-38718784-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38718784&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCN10A",
"hgnc_id": 10582,
"hgvs_c": "c.3550G>A",
"hgvs_p": "p.Ala1184Thr",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_006514.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.0764,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.24,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.07474508881568909,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1956,
"aa_ref": "A",
"aa_start": 1184,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6626,
"cdna_start": 3763,
"cds_end": null,
"cds_length": 5871,
"cds_start": 3550,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "NM_006514.4",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3550G>A",
"hgvs_p": "p.Ala1184Thr",
"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": "T",
"aa_end": null,
"aa_length": 1956,
"aa_ref": "A",
"aa_start": 1184,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6626,
"cdna_start": 3763,
"cds_end": null,
"cds_length": 5871,
"cds_start": 3550,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000449082.3",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3550G>A",
"hgvs_p": "p.Ala1184Thr",
"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": "T",
"aa_end": null,
"aa_length": 1955,
"aa_ref": "A",
"aa_start": 1183,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5903,
"cdna_start": 3579,
"cds_end": null,
"cds_length": 5868,
"cds_start": 3547,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "ENST00000643924.1",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3547G>A",
"hgvs_p": "p.Ala1183Thr",
"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": "T",
"aa_end": null,
"aa_length": 1964,
"aa_ref": "A",
"aa_start": 1192,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6704,
"cdna_start": 3836,
"cds_end": null,
"cds_length": 5895,
"cds_start": 3574,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000655275.1",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3574G>A",
"hgvs_p": "p.Ala1192Thr",
"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": "T",
"aa_end": null,
"aa_length": 1955,
"aa_ref": "A",
"aa_start": 1183,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5871,
"cdna_start": 3547,
"cds_end": null,
"cds_length": 5868,
"cds_start": 3547,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "NM_001293306.2",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3547G>A",
"hgvs_p": "p.Ala1183Thr",
"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": "T",
"aa_end": null,
"aa_length": 1858,
"aa_ref": "A",
"aa_start": 1086,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5580,
"cdna_start": 3256,
"cds_end": null,
"cds_length": 5577,
"cds_start": 3256,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "NM_001293307.2",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3256G>A",
"hgvs_p": "p.Ala1086Thr",
"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": "T",
"aa_end": null,
"aa_length": 1959,
"aa_ref": "A",
"aa_start": 1187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6422,
"cdna_start": 3559,
"cds_end": null,
"cds_length": 5880,
"cds_start": 3559,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_005265371.4",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3559G>A",
"hgvs_p": "p.Ala1187Thr",
"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": "T",
"aa_end": null,
"aa_length": 1958,
"aa_ref": "A",
"aa_start": 1186,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6419,
"cdna_start": 3556,
"cds_end": null,
"cds_length": 5877,
"cds_start": 3556,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_011533993.3",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3556G>A",
"hgvs_p": "p.Ala1186Thr",
"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": "T",
"aa_end": null,
"aa_length": 1861,
"aa_ref": "A",
"aa_start": 1089,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6128,
"cdna_start": 3265,
"cds_end": null,
"cds_length": 5586,
"cds_start": 3265,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 19,
"exon_rank_end": null,
"feature": "XM_011533994.3",
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"hgvs_c": "c.3265G>A",
"hgvs_p": "p.Ala1089Thr",
"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": "rs759842238",
"effect": "missense_variant",
"frequency_reference_population": 6.840516e-7,
"gene_hgnc_id": 10582,
"gene_symbol": "SCN10A",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84052e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.968,
"pos": 38718784,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.324,
"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"
}
]
}