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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: 11-118137101-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=118137101&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SCN4B",
"hgnc_id": 10592,
"hgvs_c": "c.613T>C",
"hgvs_p": "p.Ser205Pro",
"inheritance_mode": "AD,Unknown",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_174934.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 41,
"alphamissense_prediction": null,
"alphamissense_score": 0.771,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.16,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Cardiovascular phenotype,Long QT syndrome 10",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5822206735610962,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 228,
"aa_ref": "S",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4487,
"cdna_start": 763,
"cds_end": null,
"cds_length": 687,
"cds_start": 613,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_174934.4",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "c.613T>C",
"hgvs_p": "p.Ser205Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000324727.9",
"protein_coding": true,
"protein_id": "NP_777594.1",
"strand": false,
"transcript": "NM_174934.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 228,
"aa_ref": "S",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4487,
"cdna_start": 763,
"cds_end": null,
"cds_length": 687,
"cds_start": 613,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000324727.9",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "c.613T>C",
"hgvs_p": "p.Ser205Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_174934.4",
"protein_coding": true,
"protein_id": "ENSP00000322460.4",
"strand": false,
"transcript": "ENST00000324727.9",
"transcript_support_level": 1
},
{
"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": 4480,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000415030.6",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "n.756T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000415030.6",
"transcript_support_level": 1
},
{
"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": 1206,
"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": "ENST00000531550.1",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "n.678T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000531550.1",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 118,
"aa_ref": "S",
"aa_start": 95,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4480,
"cdna_start": 756,
"cds_end": null,
"cds_length": 357,
"cds_start": 283,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001142349.2",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "c.283T>C",
"hgvs_p": "p.Ser95Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135821.1",
"strand": false,
"transcript": "NM_001142349.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 94,
"aa_ref": "S",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4085,
"cdna_start": 361,
"cds_end": null,
"cds_length": 285,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001142348.2",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "c.211T>C",
"hgvs_p": "p.Ser71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135820.1",
"strand": false,
"transcript": "NM_001142348.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 94,
"aa_ref": "S",
"aa_start": 71,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 566,
"cdna_start": 426,
"cds_end": null,
"cds_length": 285,
"cds_start": 211,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000529878.1",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "c.211T>C",
"hgvs_p": "p.Ser71Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000436343.1",
"strand": false,
"transcript": "ENST00000529878.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3969,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000423160.2",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "n.247T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000423160.2",
"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": 4326,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NR_024527.2",
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"hgvs_c": "n.602T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_024527.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs761183228",
"effect": "missense_variant",
"frequency_reference_population": 0.00002541044,
"gene_hgnc_id": 10592,
"gene_symbol": "SCN4B",
"gnomad_exomes_ac": 38,
"gnomad_exomes_af": 0.0000260018,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197272,
"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": "Long QT syndrome 10|Cardiovascular phenotype",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.144,
"pos": 118137101,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.682,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_174934.4"
}
]
}