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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: 2-166204355-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=166204355&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 166204355,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_001365536.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "c.4503+5A>G",
"hgvs_p": null,
"transcript": "NM_001365536.1",
"protein_id": "NP_001352465.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1988,
"cds_start": -4,
"cds_end": null,
"cds_length": 5967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9752,
"mane_select": "ENST00000642356.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "c.4503+5A>G",
"hgvs_p": null,
"transcript": "ENST00000642356.2",
"protein_id": "ENSP00000495601.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1988,
"cds_start": -4,
"cds_end": null,
"cds_length": 5967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9752,
"mane_select": "NM_001365536.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "c.4503+5A>G",
"hgvs_p": null,
"transcript": "ENST00000303354.11",
"protein_id": "ENSP00000304748.7",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1988,
"cds_start": -4,
"cds_end": null,
"cds_length": 5967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "c.4470+5A>G",
"hgvs_p": null,
"transcript": "ENST00000409672.5",
"protein_id": "ENSP00000386306.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1977,
"cds_start": -4,
"cds_end": null,
"cds_length": 5934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "c.4470+5A>G",
"hgvs_p": null,
"transcript": "ENST00000645907.1",
"protein_id": "ENSP00000495983.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1977,
"cds_start": -4,
"cds_end": null,
"cds_length": 5934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SCN1A-AS1",
"gene_hgnc_id": 54069,
"hgvs_c": "n.611+4537T>C",
"hgvs_p": null,
"transcript": "ENST00000447809.2",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2305,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "c.4470+5A>G",
"hgvs_p": null,
"transcript": "NM_002977.4",
"protein_id": "NP_002968.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1977,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 9719,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCN1A-AS1",
"gene_hgnc_id": 54069,
"hgvs_c": "n.308+4537T>C",
"hgvs_p": null,
"transcript": "ENST00000630020.3",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"hgvs_c": "n.880+5A>G",
"hgvs_p": null,
"transcript": "ENST00000646694.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 15,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SCN1A-AS1",
"gene_hgnc_id": 54069,
"hgvs_c": "n.744+4537T>C",
"hgvs_p": null,
"transcript": "ENST00000651013.1",
"protein_id": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 19,
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"gene_symbol": "SCN1A-AS1",
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"hgvs_c": "n.1289+4537T>C",
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},
{
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],
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},
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],
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},
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],
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},
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],
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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-AS1",
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"hgvs_c": "n.513+4537T>C",
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],
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],
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},
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],
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},
{
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"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 25,
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"gene_symbol": "SCN9A",
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"hgvs_c": "c.4503+5A>G",
"hgvs_p": null,
"transcript": "XM_011511616.4",
"protein_id": "XP_011509918.1",
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"feature": null
},
{
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"strand": false,
"consequences": [
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"intron_variant"
],
"exon_rank": null,
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"intron_rank": 25,
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"gene_symbol": "SCN9A",
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"hgvs_c": "c.4503+5A>G",
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},
{
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"intron_variant"
],
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"protein_id": "XP_011509920.1",
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},
{
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],
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},
{
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"intron_variant"
],
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}
],
"gene_symbol": "SCN9A",
"gene_hgnc_id": 10597,
"dbsnp": "rs757433463",
"frequency_reference_population": 0.000008752528,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000829001,
"gnomad_genomes_af": 0.0000131569,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.47999998927116394,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.13199999928474426,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.21,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0010828018383641,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001365536.1",
"gene_symbol": "SCN9A",
"hgnc_id": 10597,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,SD,AR",
"hgvs_c": "c.4503+5A>G",
"hgvs_p": null
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000447809.2",
"gene_symbol": "SCN1A-AS1",
"hgnc_id": 54069,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.611+4537T>C",
"hgvs_p": null
}
],
"clinvar_disease": " hereditary sensory and autonomic, type 2A, type 7,Generalized epilepsy with febrile seizures plus,Neuropathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}