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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: 6-45912748-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=45912748&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 45912748,
"ref": "A",
"alt": "G",
"effect": "intron_variant",
"transcript": "ENST00000339561.12",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.588+1480T>C",
"hgvs_p": null,
"transcript": "NM_016929.5",
"protein_id": "NP_058625.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": -4,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5706,
"mane_select": "ENST00000339561.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.588+1480T>C",
"hgvs_p": null,
"transcript": "ENST00000339561.12",
"protein_id": "ENSP00000344165.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": -4,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5706,
"mane_select": "NM_016929.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.1065+1480T>C",
"hgvs_p": null,
"transcript": "ENST00000185206.12",
"protein_id": "ENSP00000185206.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.1065+1480T>C",
"hgvs_p": null,
"transcript": "NM_001114086.2",
"protein_id": "NP_001107558.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.1065+1480T>C",
"hgvs_p": null,
"transcript": "NM_001370650.1",
"protein_id": "NP_001357579.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.623+1030T>C",
"hgvs_p": null,
"transcript": "ENST00000644324.1",
"protein_id": "ENSP00000495186.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 242,
"cds_start": -4,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.471+1480T>C",
"hgvs_p": null,
"transcript": "NM_001370649.1",
"protein_id": "NP_001357578.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 212,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.589-9T>C",
"hgvs_p": null,
"transcript": "NM_001256023.2",
"protein_id": "NP_001242952.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 205,
"cds_start": -4,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "c.589-9T>C",
"hgvs_p": null,
"transcript": "ENST00000544153.3",
"protein_id": "ENSP00000439195.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 205,
"cds_start": -4,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
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"cdna_length": 1991,
"mane_select": null,
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"feature": null
},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"gene_symbol": "CLIC5",
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"hgvs_c": "c.588+1480T>C",
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"transcript": "ENST00000644878.1",
"protein_id": "ENSP00000493894.1",
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},
{
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"consequences": [
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],
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"gene_symbol": "CLIC5",
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"hgvs_c": "n.536+1030T>C",
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"transcript": "ENST00000484572.2",
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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": "CLIC5",
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "n.906+1480T>C",
"hgvs_p": null,
"transcript": "XR_007059275.1",
"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": 4501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"hgvs_c": "n.1171+1480T>C",
"hgvs_p": null,
"transcript": "XR_926258.4",
"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": 4766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLIC5",
"gene_hgnc_id": 13517,
"dbsnp": "rs75878754",
"frequency_reference_population": 0.008585991,
"hom_count_reference_population": 417,
"allele_count_reference_population": 13038,
"gnomad_exomes_af": 0.0073749,
"gnomad_genomes_af": 0.0194531,
"gnomad_exomes_ac": 10076,
"gnomad_genomes_ac": 2962,
"gnomad_exomes_homalt": 336,
"gnomad_genomes_homalt": 81,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.493,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000569439264402225,
"dbscsnv_ada_prediction": "Benign",
"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": "ENST00000339561.12",
"gene_symbol": "CLIC5",
"hgnc_id": 13517,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.588+1480T>C",
"hgvs_p": null
}
],
"clinvar_disease": "CLIC5-related disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided|CLIC5-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}