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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: 3-142712158-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=142712158&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 142712158,
"ref": "G",
"alt": "C",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000457734.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "NM_001145319.2",
"protein_id": "NP_001138791.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3700,
"mane_select": "ENST00000457734.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "ENST00000457734.7",
"protein_id": "ENSP00000387890.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3700,
"mane_select": "NM_001145319.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "ENST00000337777.7",
"protein_id": "ENSP00000336831.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "NM_001172312.2",
"protein_id": "NP_001165783.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "NM_002670.3",
"protein_id": "NP_002661.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "XM_006713660.4",
"protein_id": "XP_006713723.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "XM_011512900.3",
"protein_id": "XP_011511202.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 4129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "XM_011512901.2",
"protein_id": "XP_011511203.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
"hgvs_p": null,
"transcript": "XM_011512903.3",
"protein_id": "XP_011511205.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 629,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 3812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
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"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
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"transcript": "XM_017006627.2",
"protein_id": "XP_016862116.1",
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"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
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"gene_symbol": "PLS1",
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"hgvs_c": "c.*151G>C",
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"transcript": "XM_047448321.1",
"protein_id": "XP_047304277.1",
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},
{
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],
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},
{
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],
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"gene_symbol": "PLS1",
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},
{
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],
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"gene_symbol": "PLS1",
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},
{
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],
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},
{
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],
"exon_rank": 20,
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"exon_count": 20,
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},
{
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],
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},
{
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],
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"gene_symbol": "PLS1",
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"hgvs_c": "c.*151G>C",
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"transcript": "XM_047448328.1",
"protein_id": "XP_047304284.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 2,
"intron_rank": 1,
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"gene_symbol": "ENSG00000287045",
"gene_hgnc_id": null,
"hgvs_c": "n.52+11672C>G",
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"transcript": "ENST00000664914.1",
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},
{
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],
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},
{
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],
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},
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"strand": false,
"consequences": [
"intron_variant"
],
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"exon_count": 2,
"intron_rank": 1,
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"gene_symbol": "ENSG00000287045",
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"hgvs_c": "n.138+11672C>G",
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"transcript": "ENST00000735308.1",
"protein_id": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"hgvs_c": "c.*151G>C",
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"transcript": "ENST00000497002.1",
"protein_id": "ENSP00000418700.1",
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}
],
"gene_symbol": "PLS1",
"gene_hgnc_id": 9090,
"dbsnp": "rs3773506",
"frequency_reference_population": 0.05793312,
"hom_count_reference_population": 1616,
"allele_count_reference_population": 37178,
"gnomad_exomes_af": 0.0519287,
"gnomad_genomes_af": 0.0772547,
"gnomad_exomes_ac": 25424,
"gnomad_genomes_ac": 11754,
"gnomad_exomes_homalt": 929,
"gnomad_genomes_homalt": 687,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"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": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.842,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000457734.7",
"gene_symbol": "PLS1",
"hgnc_id": 9090,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.*151G>C",
"hgvs_p": null
},
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000664914.1",
"gene_symbol": "ENSG00000287045",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.52+11672C>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}