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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: 5-132369842-ACCCTCCGCGGACGGTCTTGGGTCGCCTG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=132369842&ref=ACCCTCCGCGGACGGTCTTGGGTCGCCTG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 132369842,
"ref": "ACCCTCCGCGGACGGTCTTGGGTCGCCTG",
"alt": "A",
"effect": "5_prime_UTR_variant",
"transcript": "NM_003060.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "n.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000448810.6",
"protein_id": "ENSP00000401860.2",
"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": 2656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "NM_003060.4",
"protein_id": "NP_003051.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 557,
"cds_start": -4,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3277,
"mane_select": "ENST00000245407.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000245407.8",
"protein_id": "ENSP00000245407.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 557,
"cds_start": -4,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3277,
"mane_select": "NM_003060.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000435065.7",
"protein_id": "ENSP00000402760.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 581,
"cds_start": -4,
"cds_end": null,
"cds_length": 1746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "n.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000448810.6",
"protein_id": "ENSP00000401860.2",
"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": 2656,
"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_donor_variant",
"splice_region_variant",
"intron_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR3936HG",
"gene_hgnc_id": 40538,
"hgvs_c": "n.47_73+1delCAGGCGACCCAAGACCGTCCGCGGAGGG",
"hgvs_p": null,
"transcript": "ENST00000621103.4",
"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": 1793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "n.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000686757.1",
"protein_id": "ENSP00000510721.1",
"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": 3117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "n.6_33delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000687740.1",
"protein_id": null,
"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": 5649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "n.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000690900.1",
"protein_id": "ENSP00000510703.1",
"transcript_support_level": null,
"aa_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"hgvs_c": "n.6_33delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "ENST00000693763.1",
"protein_id": null,
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"aa_start": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
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"intron_rank": null,
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"gene_symbol": "SLC22A5",
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"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "NM_001308122.2",
"protein_id": "NP_001295051.1",
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},
{
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],
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"gene_symbol": "SLC22A5",
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"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
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"transcript": "ENST00000693308.1",
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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": "SLC22A5",
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"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
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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": "SLC22A5",
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"hgvs_c": "c.-553_-526delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
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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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"intron_rank": null,
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"gene_symbol": "SLC22A5",
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"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null,
"transcript": "XM_047417598.1",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"splice_region_variant",
"intron_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
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"gene_symbol": "MIR3936HG",
"gene_hgnc_id": 40538,
"hgvs_c": "n.301_327+1delCAGGCGACCCAAGACCGTCCGCGGAGGG",
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{
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"splice_region_variant",
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},
{
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},
{
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],
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"gene_symbol": "MIR3936HG",
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"hgvs_c": "n.-222_-195delCAGGCGACCCAAGACCGTCCGCGGAGGG",
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"feature": null
},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 5,
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"gene_symbol": "MIR3936HG",
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"feature": null
},
{
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"strand": true,
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"upstream_gene_variant"
],
"exon_rank": null,
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"gene_symbol": "MIR3936HG",
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},
{
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"upstream_gene_variant"
],
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},
{
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"upstream_gene_variant"
],
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"exon_count": 3,
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"gene_symbol": "MIR3936HG",
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"feature": null
}
],
"gene_symbol": "SLC22A5",
"gene_hgnc_id": 10969,
"dbsnp": "rs1279199437",
"frequency_reference_population": 0.00001316309,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131631,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"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": 1.878,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_003060.4",
"gene_symbol": "SLC22A5",
"hgnc_id": 10969,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-129_-102delCCTCCGCGGACGGTCTTGGGTCGCCTGC",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000621103.4",
"gene_symbol": "MIR3936HG",
"hgnc_id": 40538,
"effects": [
"splice_donor_variant",
"splice_region_variant",
"intron_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.47_73+1delCAGGCGACCCAAGACCGTCCGCGGAGGG",
"hgvs_p": null
}
],
"clinvar_disease": "Renal carnitine transport defect",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Renal carnitine transport defect",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}