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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: 11-108310139-TTA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=108310139&ref=TTA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 108310139,
"ref": "TTA",
"alt": "T",
"effect": "intron_variant",
"transcript": "NM_000051.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-17_5763-16delAT",
"hgvs_p": null,
"transcript": "NM_000051.4",
"protein_id": "NP_000042.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12915,
"mane_select": "ENST00000675843.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-20_5763-19delTA",
"hgvs_p": null,
"transcript": "ENST00000675843.1",
"protein_id": "ENSP00000501606.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12915,
"mane_select": "NM_000051.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": 39,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-20_5763-19delTA",
"hgvs_p": null,
"transcript": "ENST00000452508.7",
"protein_id": "ENSP00000388058.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "n.*827-20_*827-19delTA",
"hgvs_p": null,
"transcript": "ENST00000527805.6",
"protein_id": "ENSP00000435747.2",
"transcript_support_level": 1,
"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": 9287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": 39,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-17_5763-16delAT",
"hgvs_p": null,
"transcript": "NM_001351834.2",
"protein_id": "NP_001338763.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-20_5763-19delTA",
"hgvs_p": null,
"transcript": "ENST00000278616.10",
"protein_id": "ENSP00000278616.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": 39,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-20_5763-19delTA",
"hgvs_p": null,
"transcript": "ENST00000601453.3",
"protein_id": "ENSP00000469471.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 14216,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": 39,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "c.5763-20_5763-19delTA",
"hgvs_p": null,
"transcript": "ENST00000713844.1",
"protein_id": "ENSP00000519149.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3056,
"cds_start": -4,
"cds_end": null,
"cds_length": 9171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9550,
"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": "C11orf65",
"gene_hgnc_id": 28519,
"hgvs_c": "c.641-1070_641-1069delTA",
"hgvs_p": null,
"transcript": "NM_001330368.2",
"protein_id": "NP_001317297.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": -4,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"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": "C11orf65",
"gene_hgnc_id": 28519,
"hgvs_c": "c.641-1070_641-1069delTA",
"hgvs_p": null,
"transcript": "ENST00000525729.5",
"protein_id": "ENSP00000433395.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 246,
"cds_start": -4,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
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"cdna_length": 1263,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "C11orf65",
"gene_hgnc_id": 28519,
"hgvs_c": "c.*39-1070_*39-1069delTA",
"hgvs_p": null,
"transcript": "NM_001351110.2",
"protein_id": "NP_001338039.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 242,
"cds_start": -4,
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"feature": null
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 37,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATM",
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"hgvs_c": "n.1978-20_1978-19delTA",
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"transcript": "ENST00000524792.5",
"protein_id": null,
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 19,
"intron_rank": 1,
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"gene_symbol": "ATM",
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"hgvs_c": "n.182-20_182-19delTA",
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"transcript": "ENST00000525056.2",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 37,
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"gene_symbol": "ATM",
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"hgvs_c": "n.5675-20_5675-19delTA",
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"transcript": "ENST00000529588.6",
"protein_id": "ENSP00000435524.2",
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},
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],
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"hgvs_c": "n.80-20_80-19delTA",
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"transcript": "ENST00000532765.1",
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},
{
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"strand": true,
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],
"exon_rank": null,
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"intron_rank": 6,
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"gene_symbol": "ATM",
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"hgvs_c": "n.1167-20_1167-19delTA",
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],
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"gene_symbol": "ATM",
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"hgvs_c": "n.*827-20_*827-19delTA",
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"transcript": "ENST00000675595.1",
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},
{
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"strand": true,
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],
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"exon_count": 27,
"intron_rank": 2,
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"gene_symbol": "ATM",
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"hgvs_c": "n.520-20_520-19delTA",
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"transcript": "ENST00000682286.1",
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"strand": true,
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],
"exon_rank": null,
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"intron_rank": 1,
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"gene_symbol": "ATM",
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"hgvs_c": "n.181-20_181-19delTA",
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],
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},
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],
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},
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 6,
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"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "n.1477-20_1477-19delTA",
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"transcript": "ENST00000684152.1",
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"feature": null
},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"hgvs_c": "n.*5234-20_*5234-19delTA",
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"transcript": "ENST00000713593.1",
"protein_id": "ENSP00000518889.1",
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"cds_start": -4,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1501,
"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": "C11orf65",
"gene_hgnc_id": 28519,
"hgvs_c": "c.658-1070_658-1069delTA",
"hgvs_p": null,
"transcript": "XM_047426467.1",
"protein_id": "XP_047282423.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 293,
"cds_start": -4,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1278,
"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": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "C11orf65",
"gene_hgnc_id": 28519,
"hgvs_c": "c.695-1070_695-1069delTA",
"hgvs_p": null,
"transcript": "XM_047426473.1",
"protein_id": "XP_047282429.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 264,
"cds_start": -4,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATM",
"gene_hgnc_id": 795,
"dbsnp": "rs1064793040",
"frequency_reference_population": 0.0000034378863,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000343789,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.283,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 8,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6_Very_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_000051.4",
"gene_symbol": "ATM",
"hgnc_id": 795,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.5763-17_5763-16delAT",
"hgvs_p": null
},
{
"score": -6,
"benign_score": 8,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6_Very_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001330368.2",
"gene_symbol": "C11orf65",
"hgnc_id": 28519,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.641-1070_641-1069delTA",
"hgvs_p": null
}
],
"clinvar_disease": "Ataxia-telangiectasia syndrome,Familial cancer of breast,Hereditary cancer-predisposing syndrome,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "not specified|Hereditary cancer-predisposing syndrome|Ataxia-telangiectasia syndrome|Familial cancer of breast",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}