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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: 3-129437354-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129437354&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MBD4",
"hgnc_id": 6919,
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_003925.3",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "IFT122",
"hgnc_id": 13556,
"hgvs_c": "n.288+4122G>C",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000687461.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1,BS2",
"acmg_score": -12,
"allele_count_reference_population": 4467,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 574,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2394,
"cdna_start": null,
"cds_end": null,
"cds_length": 1725,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001276270.2",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000429544.7",
"protein_coding": true,
"protein_id": "NP_001263199.1",
"strand": false,
"transcript": "NM_001276270.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 574,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2394,
"cdna_start": null,
"cds_end": null,
"cds_length": 1725,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000429544.7",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001276270.2",
"protein_coding": true,
"protein_id": "ENSP00000394080.2",
"strand": false,
"transcript": "ENST00000429544.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 580,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2470,
"cdna_start": null,
"cds_end": null,
"cds_length": 1743,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000249910.5",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000249910.1",
"strand": false,
"transcript": "ENST00000249910.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 540,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2099,
"cdna_start": null,
"cds_end": null,
"cds_length": 1623,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000503197.5",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424873.1",
"strand": false,
"transcript": "ENST00000503197.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 262,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1684,
"cdna_start": null,
"cds_end": null,
"cds_length": 789,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000393278.6",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.247+454C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000376959.2",
"strand": false,
"transcript": "ENST00000393278.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
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"aa_length": 580,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2412,
"cdna_start": null,
"cds_end": null,
"cds_length": 1743,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_003925.3",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_003916.1",
"strand": false,
"transcript": "NM_003925.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 579,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2169,
"cdna_start": null,
"cds_end": null,
"cds_length": 1740,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000853350.1",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000523409.1",
"strand": false,
"transcript": "ENST00000853350.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 574,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2399,
"cdna_start": null,
"cds_end": null,
"cds_length": 1725,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000915033.1",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585092.1",
"strand": false,
"transcript": "ENST00000915033.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
"canonical": false,
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"cdna_start": null,
"cds_end": null,
"cds_length": 1722,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000853349.1",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000523408.1",
"strand": false,
"transcript": "ENST00000853349.1",
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},
{
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"biotype": "protein_coding",
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"cds_end": null,
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"consequences": [
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],
"exon_count": 7,
"exon_rank": null,
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"feature": "NM_001276271.2",
"gene_hgnc_id": 6919,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001263200.1",
"strand": false,
"transcript": "NM_001276271.2",
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},
{
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"consequences": [
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],
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"feature": "ENST00000507208.1",
"gene_hgnc_id": 6919,
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},
{
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],
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"feature": "ENST00000915034.1",
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},
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],
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"feature": "NM_001276272.2",
"gene_hgnc_id": 6919,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001263201.1",
"strand": false,
"transcript": "NM_001276272.2",
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},
{
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],
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"feature": "ENST00000853351.1",
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"hgvs_c": "c.336-157C>G",
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},
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],
"exon_count": 7,
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"feature": "NM_001276273.2",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.247+454C>G",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "NP_001263202.1",
"strand": false,
"transcript": "NM_001276273.2",
"transcript_support_level": null
},
{
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"consequences": [
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],
"exon_count": 7,
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"feature": "XM_024453810.2",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "c.336-46C>G",
"hgvs_p": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309578.1",
"strand": false,
"transcript": "XM_024453810.2",
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},
{
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],
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"feature": "XM_047449153.1",
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"protein_id": "XP_047305109.1",
"strand": false,
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},
{
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],
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"feature": "ENST00000505883.1",
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"strand": false,
"transcript": "ENST00000505883.1",
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},
{
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],
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"feature": "ENST00000509587.1",
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"transcript": "ENST00000509587.1",
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},
{
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"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": null,
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"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000509828.1",
"gene_hgnc_id": 6919,
"gene_symbol": "MBD4",
"hgvs_c": "n.104+2376C>G",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000422690.1",
"strand": false,
"transcript": "ENST00000509828.1",
"transcript_support_level": 2
},
{
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"aa_start": null,
"biotype": "pseudogene",
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"cdna_end": null,
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"cds_end": null,
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"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 31,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000687461.1",
"gene_hgnc_id": 13556,
"gene_symbol": "IFT122",
"hgvs_c": "n.288+4122G>C",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
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