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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: 2-165989552-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165989552&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165989552,
"ref": "T",
"alt": "C",
"effect": "3_prime_UTR_variant",
"transcript": "NM_001165963.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_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.*1693A>G",
"hgvs_p": null,
"transcript": "NM_001165963.4",
"protein_id": "NP_001159435.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2009,
"cds_start": -4,
"cds_end": null,
"cds_length": 6030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "ENST00000674923.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_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.*1693A>G",
"hgvs_p": null,
"transcript": "ENST00000674923.1",
"protein_id": "ENSP00000501589.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2009,
"cds_start": -4,
"cds_end": null,
"cds_length": 6030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11940,
"mane_select": "NM_001165963.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_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.*1693A>G",
"hgvs_p": null,
"transcript": "ENST00000303395.9",
"protein_id": "ENSP00000303540.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2009,
"cds_start": -4,
"cds_end": null,
"cds_length": 6030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_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.*1693A>G",
"hgvs_p": null,
"transcript": "ENST00000375405.7",
"protein_id": "ENSP00000364554.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1998,
"cds_start": -4,
"cds_end": null,
"cds_length": 5997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_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": "n.*5216A>G",
"hgvs_p": null,
"transcript": "ENST00000636194.1",
"protein_id": "ENSP00000490288.1",
"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": 8508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_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": "n.*3590A>G",
"hgvs_p": null,
"transcript": "ENST00000637038.2",
"protein_id": "ENSP00000490184.2",
"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,
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"cdna_length": 8426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_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": "n.*7277A>G",
"hgvs_p": null,
"transcript": "ENST00000641996.1",
"protein_id": "ENSP00000493054.1",
"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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"cdna_length": 12903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_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": "n.*5666A>G",
"hgvs_p": null,
"transcript": "ENST00000671940.1",
"protein_id": "ENSP00000500336.1",
"transcript_support_level": null,
"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": 8315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_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": "n.10196A>G",
"hgvs_p": null,
"transcript": "ENST00000673490.1",
"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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"cdna_length": 10569,
"mane_select": null,
"mane_plus": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "n.*5759A>G",
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"transcript": "ENST00000689288.1",
"protein_id": "ENSP00000509637.1",
"transcript_support_level": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
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"gene_symbol": "SCN1A",
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"hgvs_c": "n.8140A>G",
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"transcript": "NR_148667.2",
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},
{
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"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
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"exon_count": 28,
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"gene_symbol": "SCN1A",
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},
{
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"strand": false,
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],
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"exon_count": 27,
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"gene_symbol": "SCN1A",
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"hgvs_c": "c.*1693A>G",
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"transcript": "NM_001353948.2",
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},
{
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],
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"gene_symbol": "SCN1A",
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],
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"gene_symbol": "SCN1A",
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"transcript": "NM_001353950.2",
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},
{
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],
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"gene_symbol": "SCN1A",
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],
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"gene_symbol": "SCN1A",
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"transcript": "NM_001353952.2",
"protein_id": "NP_001340881.1",
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},
{
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],
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"intron_rank": null,
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"gene_symbol": "SCN1A",
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"hgvs_c": "c.*1693A>G",
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"transcript": "NM_006920.6",
"protein_id": "NP_008851.3",
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],
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"intron_rank": null,
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"gene_symbol": "SCN1A",
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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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],
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"exon_count": 28,
"intron_rank": null,
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"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.*1693A>G",
"hgvs_p": null,
"transcript": "NM_001353954.2",
"protein_id": "NP_001340883.1",
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"aa_length": 1997,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
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"consequences": [
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],
"exon_rank": 27,
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"exon_count": 27,
"intron_rank": null,
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"gene_symbol": "SCN1A",
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"hgvs_c": "c.*1693A>G",
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"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"hgvs_c": "c.*1693A>G",
"hgvs_p": null,
"transcript": "ENST00000713692.1",
"protein_id": "ENSP00000518996.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1927,
"cds_start": -4,
"cds_end": null,
"cds_length": 5784,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN1A",
"gene_hgnc_id": 10585,
"dbsnp": "rs7591522",
"frequency_reference_population": 0.03653538,
"hom_count_reference_population": 337,
"allele_count_reference_population": 5562,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.0365354,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 5562,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 337,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.255,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001165963.4",
"gene_symbol": "SCN1A",
"hgnc_id": 10585,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.*1693A>G",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000597623.4",
"gene_symbol": "SCN1A-AS1",
"hgnc_id": 54069,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.202-26061T>C",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_110598.1",
"gene_symbol": "LOC102724058",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.176-26061T>C",
"hgvs_p": null
}
],
"clinvar_disease": " 3, familial hemiplegic, type 2,Epilepsy,Generalized epilepsy with febrile seizures plus,Migraine,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:3",
"phenotype_combined": "Migraine, familial hemiplegic, 3|Epilepsy|Generalized epilepsy with febrile seizures plus, type 2|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}