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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: 3-194406320-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=194406320&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 14,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ATP13A3",
"hgnc_id": 24113,
"hgvs_c": "c.3574-204G>A",
"hgvs_p": null,
"inheritance_mode": "SD",
"pathogenic_score": 0,
"score": -14,
"transcript": "NM_001367549.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_score": -14,
"allele_count_reference_population": 56066,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -1.01,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -1.0099999904632568,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1256,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7538,
"cdna_start": null,
"cds_end": null,
"cds_length": 3771,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 34,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001367549.1",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3574-204G>A",
"hgvs_p": null,
"intron_rank": 33,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000645319.2",
"protein_coding": true,
"protein_id": "NP_001354478.1",
"strand": false,
"transcript": "NM_001367549.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1256,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7538,
"cdna_start": null,
"cds_end": null,
"cds_length": 3771,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 34,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000645319.2",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3574-204G>A",
"hgvs_p": null,
"intron_rank": 33,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001367549.1",
"protein_coding": true,
"protein_id": "ENSP00000494937.2",
"strand": false,
"transcript": "ENST00000645319.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4819,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000429136.7",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "n.1420-204G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000429136.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3651,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000461660.2",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "n.678-204G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000461660.2",
"transcript_support_level": 1
},
{
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"aa_end": null,
"aa_length": 1295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7676,
"cdna_start": null,
"cds_end": null,
"cds_length": 3888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 35,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000963858.1",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3691-204G>A",
"hgvs_p": null,
"intron_rank": 34,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633917.1",
"strand": false,
"transcript": "ENST00000963858.1",
"transcript_support_level": null
},
{
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"aa_length": 1295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7446,
"cdna_start": null,
"cds_end": null,
"cds_length": 3888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 34,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000963862.1",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3691-204G>A",
"hgvs_p": null,
"intron_rank": 33,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633921.1",
"strand": false,
"transcript": "ENST00000963862.1",
"transcript_support_level": null
},
{
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"aa_end": null,
"aa_length": 1256,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7366,
"cdna_start": null,
"cds_end": null,
"cds_length": 3771,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 33,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000856972.1",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3574-204G>A",
"hgvs_p": null,
"intron_rank": 32,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527031.1",
"strand": false,
"transcript": "ENST00000856972.1",
"transcript_support_level": null
},
{
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"aa_length": 1256,
"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7237,
"cdna_start": null,
"cds_end": null,
"cds_length": 3771,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 34,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000856973.1",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3574-204G>A",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000527032.1",
"strand": false,
"transcript": "ENST00000856973.1",
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},
{
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"cdna_start": null,
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"cds_start": null,
"consequences": [
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],
"exon_count": 34,
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"feature": "ENST00000856974.1",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3574-204G>A",
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"intron_rank": 33,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000527033.1",
"strand": false,
"transcript": "ENST00000856974.1",
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},
{
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"consequences": [
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],
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"feature": "ENST00000856975.1",
"gene_hgnc_id": 24113,
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},
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],
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"feature": "ENST00000920215.1",
"gene_hgnc_id": 24113,
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},
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"feature": "ENST00000920218.1",
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},
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"consequences": [
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],
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"feature": "ENST00000963860.1",
"gene_hgnc_id": 24113,
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},
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"feature": "NM_001374836.1",
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"mane_plus": null,
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"protein_id": "NP_001361765.1",
"strand": false,
"transcript": "NM_001374836.1",
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},
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],
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"feature": "ENST00000920212.1",
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"mane_plus": null,
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"protein_coding": true,
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"strand": false,
"transcript": "ENST00000920212.1",
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},
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],
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"feature": "ENST00000963864.1",
"gene_hgnc_id": 24113,
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},
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"feature": "NM_024524.4",
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},
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"consequences": [
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],
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"feature": "ENST00000439040.6",
"gene_hgnc_id": 24113,
"gene_symbol": "ATP13A3",
"hgvs_c": "c.3484-204G>A",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000416508.1",
"strand": false,
"transcript": "ENST00000439040.6",
"transcript_support_level": 5
},
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"consequences": [
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],
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"feature": "ENST00000645538.1",
"gene_hgnc_id": 24113,
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"hgvs_c": "c.3484-204G>A",
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"mane_plus": null,
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"protein_coding": true,
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"transcript": "ENST00000645538.1",
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},
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