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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: 2-165294010-TAAAAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165294010&ref=TAAAAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165294010,
"ref": "TAAAAA",
"alt": "T",
"effect": "intron_variant",
"transcript": "NM_001040142.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1739_-51-1735delAAAAA",
"hgvs_p": null,
"transcript": "NM_001040142.2",
"protein_id": "NP_001035232.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": "ENST00000375437.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1739_-51-1735delAAAAA",
"hgvs_p": null,
"transcript": "NM_001371246.1",
"protein_id": "NP_001358175.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": "ENST00000631182.3",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1762_-51-1758delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000375437.7",
"protein_id": "ENSP00000364586.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": "NM_001040142.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1762_-51-1758delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000631182.3",
"protein_id": "ENSP00000486885.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8776,
"mane_select": null,
"mane_plus": "NM_001371246.1",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1762_-51-1758delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000424833.5",
"protein_id": "ENSP00000406454.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 504,
"cds_start": -4,
"cds_end": null,
"cds_length": 1517,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1739_-51-1735delAAAAA",
"hgvs_p": null,
"transcript": "NM_001040143.2",
"protein_id": "NP_001035233.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1739_-51-1735delAAAAA",
"hgvs_p": null,
"transcript": "NM_001371247.1",
"protein_id": "NP_001358176.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 8604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1762_-51-1758delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000636071.2",
"protein_id": "ENSP00000490107.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
"cds_end": null,
"cds_length": 6018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-51-1762_-51-1758delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000637266.2",
"protein_id": "ENSP00000490866.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2005,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-552-1869_-552-1865delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000636985.2",
"protein_id": "ENSP00000490849.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"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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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.313-1762_313-1758delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000635945.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
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"cds_start": -4,
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},
{
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"strand": true,
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"intron_variant"
],
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"gene_symbol": "SCN2A",
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"hgvs_c": "n.-51-1762_-51-1758delAAAAA",
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"transcript": "ENST00000636135.1",
"protein_id": "ENSP00000489821.1",
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"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
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"gene_symbol": "SCN2A",
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"hgvs_c": "n.-51-1762_-51-1758delAAAAA",
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"transcript": "ENST00000636384.2",
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},
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],
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"gene_symbol": "SCN2A",
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"hgvs_c": "n.-51-1762_-51-1758delAAAAA",
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"transcript": "ENST00000637367.1",
"protein_id": "ENSP00000490592.1",
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},
{
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"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.141-1869_141-1865delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000638151.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-176_-172delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000283256.10",
"protein_id": "ENSP00000283256.6",
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 25,
"intron_rank": null,
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"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.-33_-29delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000480032.4",
"protein_id": null,
"transcript_support_level": 1,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
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"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "c.-176_-172delAAAAA",
"hgvs_p": null,
"transcript": "NM_021007.3",
"protein_id": "NP_066287.2",
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"aa_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.-176_-172delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000636662.2",
"protein_id": "ENSP00000489873.1",
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},
{
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"strand": true,
"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"hgvs_c": "n.-176_-172delAAAAA",
"hgvs_p": null,
"transcript": "ENST00000636769.1",
"protein_id": "ENSP00000490800.1",
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}
],
"gene_symbol": "SCN2A",
"gene_hgnc_id": 10588,
"dbsnp": "rs67417831",
"frequency_reference_population": 0.003646586,
"hom_count_reference_population": 0,
"allele_count_reference_population": 550,
"gnomad_exomes_af": 0.00545815,
"gnomad_genomes_af": 0.000572226,
"gnomad_exomes_ac": 518,
"gnomad_genomes_ac": 32,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.328,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BS1,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001040142.2",
"gene_symbol": "SCN2A",
"hgnc_id": 10588,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-51-1739_-51-1735delAAAAA",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}