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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: 9-9939880-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=9939880&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PTPRD",
"hgnc_id": 9668,
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_002839.4",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000300622",
"hgnc_id": null,
"hgvs_c": "n.350+334C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000773010.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 5737,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.88,
"chr": "9",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8799999952316284,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1912,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10389,
"cdna_start": null,
"cds_end": null,
"cds_length": 5739,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 46,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002839.4",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000381196.9",
"protein_coding": true,
"protein_id": "NP_002830.1",
"strand": false,
"transcript": "NM_002839.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1912,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10389,
"cdna_start": null,
"cds_end": null,
"cds_length": 5739,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 46,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000381196.9",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002839.4",
"protein_coding": true,
"protein_id": "ENSP00000370593.3",
"strand": false,
"transcript": "ENST00000381196.9",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 202,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1697,
"cdna_start": null,
"cds_end": null,
"cds_length": 609,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000463477.5",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-543-1270G>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000417661.1",
"strand": false,
"transcript": "ENST00000463477.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1912,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10550,
"cdna_start": null,
"cds_end": null,
"cds_length": 5739,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 48,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000850942.1",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521027.1",
"strand": false,
"transcript": "ENST00000850942.1",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10134,
"cdna_start": null,
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"cds_length": 5799,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 47,
"exon_rank": null,
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"feature": "XM_017014958.3",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870447.1",
"strand": false,
"transcript": "XM_017014958.3",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10079,
"cdna_start": null,
"cds_end": null,
"cds_length": 5799,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 46,
"exon_rank": null,
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"feature": "XM_017014961.3",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016870450.1",
"strand": false,
"transcript": "XM_017014961.3",
"transcript_support_level": null
},
{
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"aa_end": null,
"aa_length": 1932,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10269,
"cdna_start": null,
"cds_end": null,
"cds_length": 5799,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 48,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047423641.1",
"gene_hgnc_id": 9668,
"gene_symbol": "PTPRD",
"hgvs_c": "c.-471-1270G>C",
"hgvs_p": null,
"intron_rank": 4,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047279597.1",
"strand": false,
"transcript": "XM_047423641.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"consequences": [
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],
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"feature": "XM_017014963.3",
"gene_hgnc_id": 9668,
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"protein_id": "XP_016870452.1",
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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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],
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"feature": "XM_017014974.3",
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"transcript": "NM_002839.4"
}
]
}