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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: 2-38350559-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=38350559&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 38350559,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000378954.9",
"consequences": [
{
"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": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.119-7047A>G",
"hgvs_p": null,
"transcript": "NM_001135673.4",
"protein_id": "NP_001129145.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 583,
"cds_start": -4,
"cds_end": null,
"cds_length": 1752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3805,
"mane_select": "ENST00000378954.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.119-7047A>G",
"hgvs_p": null,
"transcript": "ENST00000378954.9",
"protein_id": "ENSP00000368237.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 583,
"cds_start": -4,
"cds_end": null,
"cds_length": 1752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3805,
"mane_select": "NM_001135673.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "n.118+26584A>G",
"hgvs_p": null,
"transcript": "ENST00000405384.6",
"protein_id": "ENSP00000383944.2",
"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": 1905,
"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": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.119-7047A>G",
"hgvs_p": null,
"transcript": "NM_001330463.2",
"protein_id": "NP_001317392.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 584,
"cds_start": -4,
"cds_end": null,
"cds_length": 1755,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4297,
"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": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.104-7047A>G",
"hgvs_p": null,
"transcript": "NM_001330462.1",
"protein_id": "NP_001317391.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4726,
"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": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.119-7047A>G",
"hgvs_p": null,
"transcript": "NM_022374.5",
"protein_id": "NP_071769.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4282,
"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": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.119-7047A>G",
"hgvs_p": null,
"transcript": "ENST00000419554.6",
"protein_id": "ENSP00000415336.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 579,
"cds_start": -4,
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"cds_length": 1740,
"cdna_start": null,
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"cdna_length": 2335,
"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": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.65-7047A>G",
"hgvs_p": null,
"transcript": "NM_001330459.1",
"protein_id": "NP_001317388.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 566,
"cds_start": -4,
"cds_end": null,
"cds_length": 1701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4578,
"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": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.65-7047A>G",
"hgvs_p": null,
"transcript": "NM_001308076.1",
"protein_id": "NP_001295005.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 565,
"cds_start": -4,
"cds_end": null,
"cds_length": 1698,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4086,
"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,
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"intron_rank": 1,
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"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.65-7047A>G",
"hgvs_p": null,
"transcript": "ENST00000452935.6",
"protein_id": "ENSP00000390743.2",
"transcript_support_level": 2,
"aa_start": null,
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"aa_length": 565,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 13,
"intron_rank": 1,
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"gene_symbol": "ATL2",
"gene_hgnc_id": 24047,
"hgvs_c": "c.-151+25557A>G",
"hgvs_p": null,
"transcript": "NM_001330460.1",
"protein_id": "NP_001317389.1",
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"cds_start": -4,
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},
{
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],
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},
{
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],
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"gene_symbol": "ATL2",
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"hgvs_c": "c.-151+26584A>G",
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},
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],
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"gene_symbol": "ATL2",
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},
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],
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},
{
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],
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"gene_symbol": "ATL2",
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},
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],
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"gene_symbol": "ATL2",
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"transcript": "NM_001330464.2",
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},
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],
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"gene_symbol": "ATL2",
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"hgvs_c": "c.113-7047A>G",
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"transcript": "ENST00000443098.5",
"protein_id": "ENSP00000410592.1",
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},
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],
"exon_rank": null,
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"gene_symbol": "ATL2",
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"hgvs_c": "c.229+3508A>G",
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},
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},
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],
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},
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],
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"gene_symbol": "ATL2",
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"hgvs_c": "n.229+3508A>G",
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"transcript": "ENST00000456736.5",
"protein_id": "ENSP00000413216.1",
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},
{
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"consequences": [
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],
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"exon_count": 3,
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"gene_symbol": "ATL2",
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"hgvs_c": "n.132-7047A>G",
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},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
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"gene_symbol": "ATL2",
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"transcript": "ENST00000486927.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATL2",
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"dbsnp": "rs6737169",
"frequency_reference_population": 0.29150003,
"hom_count_reference_population": 6579,
"allele_count_reference_population": 44315,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.2915,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 44315,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 6579,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -1,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.447,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000378954.9",
"gene_symbol": "ATL2",
"hgnc_id": 24047,
"effects": [
"intron_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.119-7047A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}