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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: 2-165992194-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165992194&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165992194,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000674923.1",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5081A>T",
"hgvs_p": "p.Tyr1694Phe",
"transcript": "NM_001165963.4",
"protein_id": "NP_001159435.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2009,
"cds_start": 5081,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5559,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "ENST00000674923.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5081A>T",
"hgvs_p": "p.Tyr1694Phe",
"transcript": "ENST00000674923.1",
"protein_id": "ENSP00000501589.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2009,
"cds_start": 5081,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5559,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "NM_001165963.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5081A>T",
"hgvs_p": "p.Tyr1694Phe",
"transcript": "ENST00000303395.9",
"protein_id": "ENSP00000303540.4",
"transcript_support_level": 5,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2009,
"cds_start": 5081,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 5472,
"cdna_end": null,
"cdna_length": 11853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5048A>T",
"hgvs_p": "p.Tyr1683Phe",
"transcript": "ENST00000375405.7",
"protein_id": "ENSP00000364554.3",
"transcript_support_level": 5,
"aa_start": 1683,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5048,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 5066,
"cdna_end": null,
"cdna_length": 8097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4997A>T",
"hgvs_p": "p.Tyr1666Phe",
"transcript": "ENST00000409050.2",
"protein_id": "ENSP00000386312.1",
"transcript_support_level": 5,
"aa_start": 1666,
"aa_end": null,
"aa_length": 1981,
"cds_start": 4997,
"cds_end": null,
"cds_length": 5946,
"cdna_start": 5282,
"cdna_end": null,
"cdna_length": 7376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5081A>T",
"hgvs_p": "p.Tyr1694Phe",
"transcript": "NM_001202435.3",
"protein_id": "NP_001189364.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2009,
"cds_start": 5081,
"cds_end": null,
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"cdna_start": 5337,
"cdna_end": null,
"cdna_length": 12890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5081A>T",
"hgvs_p": "p.Tyr1694Phe",
"transcript": "NM_001353948.2",
"protein_id": "NP_001340877.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2009,
"cds_start": 5081,
"cds_end": null,
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"cdna_start": 5380,
"cdna_end": null,
"cdna_length": 12933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5048A>T",
"hgvs_p": "p.Tyr1683Phe",
"transcript": "NM_001353949.2",
"protein_id": "NP_001340878.1",
"transcript_support_level": null,
"aa_start": 1683,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5048,
"cds_end": null,
"cds_length": 5997,
"cdna_start": 5212,
"cdna_end": null,
"cdna_length": 12765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5048A>T",
"hgvs_p": "p.Tyr1683Phe",
"transcript": "NM_001353950.2",
"protein_id": "NP_001340879.1",
"transcript_support_level": null,
"aa_start": 1683,
"aa_end": null,
"aa_length": 1998,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
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"exon_count": 27,
"intron_rank": null,
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5048A>T",
"hgvs_p": "p.Tyr1683Phe",
"transcript": "NM_001353951.2",
"protein_id": "NP_001340880.1",
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"aa_start": 1683,
"aa_end": null,
"aa_length": 1998,
"cds_start": 5048,
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"cdna_start": 5347,
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
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"exon_count": 28,
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"gene_symbol": "SCN1A",
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"hgvs_c": "c.5048A>T",
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"transcript": "NM_001353952.2",
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},
{
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],
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"transcript": "NM_006920.6",
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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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],
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5048A>T",
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"transcript": "ENST00000640036.1",
"protein_id": "ENSP00000491573.1",
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},
{
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"gene_symbol": "SCN1A",
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.5045A>T",
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"intron_rank": null,
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"gene_symbol": "SCN1A",
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"hgvs_c": "c.5045A>T",
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"transcript": "ENST00000641575.1",
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"transcript": "NM_001353958.2",
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},
{
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],
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"intron_rank": null,
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.4994A>T",
"hgvs_p": "p.Tyr1665Phe",
"transcript": "NM_001353960.2",
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},
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],
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"transcript": "ENST00000658447.1",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
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"intron_variant"
],
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"exon_count": 3,
"intron_rank": 1,
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"gene_symbol": "SCN1A-AS1",
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"hgvs_c": "n.406-23419T>A",
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"transcript": "ENST00000671284.1",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
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"intron_variant"
],
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"exon_count": 4,
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"gene_symbol": "LOC102724058",
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"transcript": "NR_110598.1",
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"feature": null
}
],
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"dbsnp": "rs121918777",
"frequency_reference_population": 6.841143e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84114e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8876180052757263,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.9,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2632,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.867,
"phylop100way_prediction": "Pathogenic",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000674923.1",
"gene_symbol": "SCN1A",
"hgnc_id": 10585,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.5081A>T",
"hgvs_p": "p.Tyr1694Phe"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000597623.4",
"gene_symbol": "SCN1A-AS1",
"hgnc_id": 54069,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.202-23419T>A",
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},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NR_110598.1",
"gene_symbol": "LOC102724058",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.176-23419T>A",
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}
],
"clinvar_disease": "Seizure",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Seizure",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}