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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: 2-165994164-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165994164&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165994164,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001165963.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"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.4834G>T",
"hgvs_p": "p.Val1612Phe",
"transcript": "NM_001165963.4",
"protein_id": "NP_001159435.1",
"transcript_support_level": null,
"aa_start": 1612,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4834,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5312,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "ENST00000674923.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4834G>T",
"hgvs_p": "p.Val1612Phe",
"transcript": "ENST00000674923.1",
"protein_id": "ENSP00000501589.1",
"transcript_support_level": null,
"aa_start": 1612,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4834,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5312,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "NM_001165963.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4834G>T",
"hgvs_p": "p.Val1612Phe",
"transcript": "ENST00000303395.9",
"protein_id": "ENSP00000303540.4",
"transcript_support_level": 5,
"aa_start": 1612,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4834,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5225,
"cdna_end": null,
"cdna_length": 11853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4801G>T",
"hgvs_p": "p.Val1601Phe",
"transcript": "ENST00000375405.7",
"protein_id": "ENSP00000364554.3",
"transcript_support_level": 5,
"aa_start": 1601,
"aa_end": null,
"aa_length": 1998,
"cds_start": 4801,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 4819,
"cdna_end": null,
"cdna_length": 8097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4750G>T",
"hgvs_p": "p.Val1584Phe",
"transcript": "ENST00000409050.2",
"protein_id": "ENSP00000386312.1",
"transcript_support_level": 5,
"aa_start": 1584,
"aa_end": null,
"aa_length": 1981,
"cds_start": 4750,
"cds_end": null,
"cds_length": 5946,
"cdna_start": 5035,
"cdna_end": null,
"cdna_length": 7376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4834G>T",
"hgvs_p": "p.Val1612Phe",
"transcript": "NM_001202435.3",
"protein_id": "NP_001189364.1",
"transcript_support_level": null,
"aa_start": 1612,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4834,
"cds_end": null,
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"cdna_start": 5090,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4834G>T",
"hgvs_p": "p.Val1612Phe",
"transcript": "NM_001353948.2",
"protein_id": "NP_001340877.1",
"transcript_support_level": null,
"aa_start": 1612,
"aa_end": null,
"aa_length": 2009,
"cds_start": 4834,
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"cdna_start": 5133,
"cdna_end": null,
"cdna_length": 12933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4801G>T",
"hgvs_p": "p.Val1601Phe",
"transcript": "NM_001353949.2",
"protein_id": "NP_001340878.1",
"transcript_support_level": null,
"aa_start": 1601,
"aa_end": null,
"aa_length": 1998,
"cds_start": 4801,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 4965,
"cdna_end": null,
"cdna_length": 12765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"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.4801G>T",
"hgvs_p": "p.Val1601Phe",
"transcript": "NM_001353950.2",
"protein_id": "NP_001340879.1",
"transcript_support_level": null,
"aa_start": 1601,
"aa_end": null,
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},
{
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"strand": false,
"consequences": [
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],
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
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"hgvs_p": "p.Val1601Phe",
"transcript": "NM_001353951.2",
"protein_id": "NP_001340880.1",
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},
{
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"strand": false,
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],
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},
{
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},
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},
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"gene_symbol": "SCN1A",
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},
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],
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4747G>T",
"hgvs_p": "p.Val1583Phe",
"transcript": "NM_001353960.2",
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},
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},
{
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"canonical": false,
"protein_coding": false,
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],
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"exon_count": 3,
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},
{
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],
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"gene_symbol": "LOC102724058",
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},
{
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"consequences": [
"downstream_gene_variant"
],
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"gene_symbol": "SCN1A",
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}
],
"gene_symbol": "SCN1A",
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"dbsnp": "rs121918808",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
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"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9464231729507446,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.929,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.988,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.817,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001165963.4",
"gene_symbol": "SCN1A",
"hgnc_id": 10585,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.4834G>T",
"hgvs_p": "p.Val1612Phe"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000597623.4",
"gene_symbol": "SCN1A-AS1",
"hgnc_id": 54069,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.202-21449C>A",
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},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NR_110598.1",
"gene_symbol": "LOC102724058",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.176-21449C>A",
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}
],
"clinvar_disease": "Developmental and epileptic encephalopathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Developmental and epileptic encephalopathy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}