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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: 1-103078887-CA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=103078887&ref=CA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "COL11A1",
"hgnc_id": 2186,
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -16,
"transcript": "NM_080629.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS1,BS2",
"acmg_score": -16,
"allele_count_reference_population": 335,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "1",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Connective tissue disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1806,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7311,
"cdna_start": null,
"cds_end": null,
"cds_length": 5421,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 67,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001854.4",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370096.9",
"protein_coding": true,
"protein_id": "NP_001845.3",
"strand": false,
"transcript": "NM_001854.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1806,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7311,
"cdna_start": null,
"cds_end": null,
"cds_length": 5421,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 67,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000370096.9",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001854.4",
"protein_coding": true,
"protein_id": "ENSP00000359114.3",
"strand": false,
"transcript": "ENST00000370096.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1690,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5442,
"cdna_start": null,
"cds_end": null,
"cds_length": 5073,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 65,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000512756.5",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426533.1",
"strand": false,
"transcript": "ENST00000512756.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1818,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7347,
"cdna_start": null,
"cds_end": null,
"cds_length": 5457,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 67,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_080629.3",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542196.2",
"strand": false,
"transcript": "NM_080629.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1818,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7327,
"cdna_start": null,
"cds_end": null,
"cds_length": 5457,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 67,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000358392.6",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000351163.2",
"strand": false,
"transcript": "ENST00000358392.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1788,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5817,
"cdna_start": null,
"cds_end": null,
"cds_length": 5367,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 66,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000862751.1",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532810.1",
"strand": false,
"transcript": "ENST00000862751.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1767,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7194,
"cdna_start": null,
"cds_end": null,
"cds_length": 5304,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 66,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001190709.2",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177638.1",
"strand": false,
"transcript": "NM_001190709.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1767,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7173,
"cdna_start": null,
"cds_end": null,
"cds_length": 5304,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 66,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000353414.8",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000302551.6",
"strand": false,
"transcript": "ENST00000353414.8",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1721,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7052,
"cdna_start": null,
"cds_end": null,
"cds_length": 5166,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 66,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000918009.1",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588068.1",
"strand": false,
"transcript": "ENST00000918009.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1690,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6963,
"cdna_start": null,
"cds_end": null,
"cds_length": 5073,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 65,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_080630.4",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542197.3",
"strand": false,
"transcript": "NM_080630.4",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
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"cdna_length": 2790,
"cdna_start": null,
"cds_end": null,
"cds_length": 2343,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000461720.6",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000494909.1",
"strand": false,
"transcript": "ENST00000461720.6",
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},
{
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"biotype": "protein_coding",
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"cdna_length": 2858,
"cdna_start": null,
"cds_end": null,
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"consequences": [
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],
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"feature": "ENST00000647280.1",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000494583.1",
"strand": false,
"transcript": "ENST00000647280.1",
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},
{
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"feature": "ENST00000644186.1",
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"protein_coding": true,
"protein_id": "ENSP00000493821.1",
"strand": false,
"transcript": "ENST00000644186.1",
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},
{
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"biotype": "protein_coding",
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"cds_start": null,
"consequences": [
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],
"exon_count": 26,
"exon_rank": null,
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"feature": "ENST00000645458.1",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 3,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000494179.1",
"strand": false,
"transcript": "ENST00000645458.1",
"transcript_support_level": null
},
{
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"consequences": [
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],
"exon_count": 15,
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"feature": "ENST00000427239.5",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000408640.1",
"strand": false,
"transcript": "ENST00000427239.5",
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},
{
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"cds_start": null,
"consequences": [
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],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000447608.1",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.56-17delT",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000410177.1",
"strand": false,
"transcript": "ENST00000447608.1",
"transcript_support_level": 5
},
{
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7464,
"cdna_start": null,
"cds_end": null,
"cds_length": 5574,
"cds_start": null,
"consequences": [
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],
"exon_count": 68,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017000334.2",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "c.275-17delT",
"hgvs_p": null,
"intron_rank": 2,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_016855823.1",
"strand": false,
"transcript": "XM_017000334.2",
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},
{
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],
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"feature": "XM_017000335.2",
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"strand": false,
"transcript": "XM_017000335.2",
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},
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"intron_variant"
],
"exon_count": 59,
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"feature": "XM_017000336.2",
"gene_hgnc_id": 2186,
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"hgvs_c": "c.275-17delT",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_016855825.1",
"strand": false,
"transcript": "XM_017000336.2",
"transcript_support_level": null
},
{
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"biotype": "pseudogene",
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"consequences": [
"intron_variant"
],
"exon_count": 68,
"exon_rank": null,
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"feature": "NR_134980.2",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "n.619-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_134980.2",
"transcript_support_level": null
},
{
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"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
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"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 40,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007085257.1",
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"hgvs_c": "n.619-17delT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007085257.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs3841819",
"effect": "intron_variant",
"frequency_reference_population": 0.00021456699,
"gene_hgnc_id": 2186,
"gene_symbol": "COL11A1",
"gnomad_exomes_ac": 317,
"gnomad_exomes_af": 0.000224952,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 18,
"gnomad_genomes_af": 0.000118346,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|Connective tissue disorder|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.378,
"pos": 103078887,
"ref": "CA",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_080629.3"
}
]
}