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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: 2-165994386-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165994386&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165994386,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000674923.1",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4612G>A",
"hgvs_p": "p.Val1538Ile",
"transcript": "NM_001165963.4",
"protein_id": "NP_001159435.1",
"transcript_support_level": null,
"aa_start": 1538,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4612,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5090,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "ENST00000674923.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4612G>A",
"hgvs_p": "p.Val1538Ile",
"transcript": "ENST00000674923.1",
"protein_id": "ENSP00000501589.1",
"transcript_support_level": null,
"aa_start": 1538,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4612,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5090,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "NM_001165963.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4612G>A",
"hgvs_p": "p.Val1538Ile",
"transcript": "ENST00000303395.9",
"protein_id": "ENSP00000303540.4",
"transcript_support_level": 5,
"aa_start": 1538,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4612,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5003,
"cdna_end": null,
"cdna_length": 11853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4579G>A",
"hgvs_p": "p.Val1527Ile",
"transcript": "ENST00000375405.7",
"protein_id": "ENSP00000364554.3",
"transcript_support_level": 5,
"aa_start": 1527,
"aa_end": null,
"aa_length": 1998,
"cds_start": 4579,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 4597,
"cdna_end": null,
"cdna_length": 8097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4528G>A",
"hgvs_p": "p.Val1510Ile",
"transcript": "ENST00000409050.2",
"protein_id": "ENSP00000386312.1",
"transcript_support_level": 5,
"aa_start": 1510,
"aa_end": null,
"aa_length": 1981,
"cds_start": 4528,
"cds_end": null,
"cds_length": 5946,
"cdna_start": 4813,
"cdna_end": null,
"cdna_length": 7376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4612G>A",
"hgvs_p": "p.Val1538Ile",
"transcript": "NM_001202435.3",
"protein_id": "NP_001189364.1",
"transcript_support_level": null,
"aa_start": 1538,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4612,
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"cdna_start": 4868,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4612G>A",
"hgvs_p": "p.Val1538Ile",
"transcript": "NM_001353948.2",
"protein_id": "NP_001340877.1",
"transcript_support_level": null,
"aa_start": 1538,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4612,
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"cdna_start": 4911,
"cdna_end": null,
"cdna_length": 12933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4579G>A",
"hgvs_p": "p.Val1527Ile",
"transcript": "NM_001353949.2",
"protein_id": "NP_001340878.1",
"transcript_support_level": null,
"aa_start": 1527,
"aa_end": null,
"aa_length": 1998,
"cds_start": 4579,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 4743,
"cdna_end": null,
"cdna_length": 12765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4579G>A",
"hgvs_p": "p.Val1527Ile",
"transcript": "NM_001353950.2",
"protein_id": "NP_001340879.1",
"transcript_support_level": null,
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"aa_end": null,
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},
{
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],
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
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"hgvs_p": "p.Val1527Ile",
"transcript": "NM_001353951.2",
"protein_id": "NP_001340880.1",
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"aa_end": null,
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},
{
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],
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},
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},
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},
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4525G>A",
"hgvs_p": "p.Val1509Ile",
"transcript": "NM_001353960.2",
"protein_id": "NP_001340889.1",
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{
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"protein_coding": false,
"strand": true,
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},
{
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"strand": true,
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],
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"exon_count": 3,
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"gene_symbol": "SCN1A-AS1",
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},
{
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"intron_variant"
],
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"gene_symbol": "LOC102724058",
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}
],
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"dbsnp": "rs780360360",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.00000958408,
"gnomad_genomes_af": 0.0000329216,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.48517709970474243,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.591,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1688,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.861,
"phylop100way_prediction": "Uncertain_significance",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,PP2,BS2",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 4,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP2",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000674923.1",
"gene_symbol": "SCN1A",
"hgnc_id": 10585,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.4612G>A",
"hgvs_p": "p.Val1538Ile"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000597623.4",
"gene_symbol": "SCN1A-AS1",
"hgnc_id": 54069,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.202-21227C>T",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NR_110598.1",
"gene_symbol": "LOC102724058",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.176-21227C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 3, familial hemiplegic, type 2,Developmental and epileptic encephalopathy,Generalized epilepsy with febrile seizures plus,Inborn genetic diseases,Migraine,Severe myoclonic epilepsy in infancy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:6",
"phenotype_combined": "not provided|Migraine, familial hemiplegic, 3;Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy|Generalized epilepsy with febrile seizures plus, type 2|Developmental and epileptic encephalopathy|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}