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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: 15-101068737-AGAGTGGT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=101068737&ref=AGAGTGGT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 101068737,
"ref": "AGAGTGGT",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000388948.8",
"consequences": [
{
"aa_ref": "EWC",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "c.5939_5945delAGTGGTG",
"hgvs_p": "p.Glu1980fs",
"transcript": "NM_024652.6",
"protein_id": "NP_078928.3",
"transcript_support_level": null,
"aa_start": 1980,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5939,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 6156,
"cdna_end": null,
"cdna_length": 15674,
"mane_select": "ENST00000388948.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EWC",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "c.5939_5945delAGTGGTG",
"hgvs_p": "p.Glu1980fs",
"transcript": "ENST00000388948.8",
"protein_id": "ENSP00000373600.3",
"transcript_support_level": 5,
"aa_start": 1980,
"aa_end": null,
"aa_length": 2015,
"cds_start": 5939,
"cds_end": null,
"cds_length": 6048,
"cdna_start": 6156,
"cdna_end": null,
"cdna_length": 15674,
"mane_select": "NM_024652.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.*4065_*4071delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000525284.5",
"protein_id": "ENSP00000433069.1",
"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": 6494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.*135_*141delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000526457.3",
"protein_id": "ENSP00000436672.2",
"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": 11632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.*3703_*3709delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000531270.5",
"protein_id": "ENSP00000431668.1",
"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": 6015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.*4065_*4071delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000525284.5",
"protein_id": "ENSP00000433069.1",
"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": 6494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.*135_*141delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000526457.3",
"protein_id": "ENSP00000436672.2",
"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": 11632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.*3703_*3709delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000531270.5",
"protein_id": "ENSP00000431668.1",
"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": 6015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"hgvs_c": "n.1426_1432delAGTGGTG",
"hgvs_p": null,
"transcript": "ENST00000532145.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2790,
"mane_select": null,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259755",
"gene_hgnc_id": 58299,
"hgvs_c": "n.442-3080_442-3074delACCACTC",
"hgvs_p": null,
"transcript": "ENST00000559857.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 1392,
"mane_select": null,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259755",
"gene_hgnc_id": 58299,
"hgvs_c": "n.556-3080_556-3074delACCACTC",
"hgvs_p": null,
"transcript": "ENST00000715977.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2298,
"mane_select": null,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259755",
"gene_hgnc_id": 58299,
"hgvs_c": "n.117+17568_117+17574delACCACTC",
"hgvs_p": null,
"transcript": "ENST00000724428.1",
"protein_id": null,
"transcript_support_level": null,
"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": 834,
"mane_select": null,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259755",
"gene_hgnc_id": 58299,
"hgvs_c": "n.56+17696_56+17702delACCACTC",
"hgvs_p": null,
"transcript": "ENST00000724429.1",
"protein_id": null,
"transcript_support_level": null,
"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": 697,
"mane_select": null,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259755",
"gene_hgnc_id": 58299,
"hgvs_c": "n.558+16955_558+16961delACCACTC",
"hgvs_p": null,
"transcript": "ENST00000724430.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1276,
"mane_select": null,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000259755",
"gene_hgnc_id": 58299,
"hgvs_c": "n.119+17296_119+17302delACCACTC",
"hgvs_p": null,
"transcript": "ENST00000724431.1",
"protein_id": null,
"transcript_support_level": null,
"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": 760,
"mane_select": null,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRK1-AS1",
"gene_hgnc_id": 58299,
"hgvs_c": "n.1051-17965_1051-17959delACCACTC",
"hgvs_p": null,
"transcript": "XR_001751721.2",
"protein_id": null,
"transcript_support_level": null,
"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": 1768,
"mane_select": null,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRRK1-AS1",
"gene_hgnc_id": 58299,
"hgvs_c": "n.3216-17965_3216-17959delACCACTC",
"hgvs_p": null,
"transcript": "XR_001751723.2",
"protein_id": null,
"transcript_support_level": null,
"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": 3933,
"mane_select": null,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRK1-AS1",
"gene_hgnc_id": 58299,
"hgvs_c": "n.121-17965_121-17959delACCACTC",
"hgvs_p": null,
"transcript": "XR_001751724.2",
"protein_id": null,
"transcript_support_level": null,
"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": 838,
"mane_select": null,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRK1-AS1",
"gene_hgnc_id": 58299,
"hgvs_c": "n.1051-17965_1051-17959delACCACTC",
"hgvs_p": null,
"transcript": "XR_001751725.2",
"protein_id": null,
"transcript_support_level": null,
"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": 3377,
"mane_select": null,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRK1-AS1",
"gene_hgnc_id": 58299,
"hgvs_c": "n.1051-17965_1051-17959delACCACTC",
"hgvs_p": null,
"transcript": "XR_001751726.2",
"protein_id": null,
"transcript_support_level": null,
"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": 3371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRRK1",
"gene_hgnc_id": 18608,
"dbsnp": "rs886038213",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.987,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000388948.8",
"gene_symbol": "LRRK1",
"hgnc_id": 18608,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5939_5945delAGTGGTG",
"hgvs_p": "p.Glu1980fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000559857.2",
"gene_symbol": "ENSG00000259755",
"hgnc_id": 58299,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.442-3080_442-3074delACCACTC",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "XR_001751721.2",
"gene_symbol": "LRRK1-AS1",
"hgnc_id": 58299,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1051-17965_1051-17959delACCACTC",
"hgvs_p": null
}
],
"clinvar_disease": "Osteosclerotic metaphyseal dysplasia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Osteosclerotic metaphyseal dysplasia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}