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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: 11-46859145-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=46859145&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 15,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "LRP4",
"hgnc_id": 6696,
"hgvs_c": "c.5556C>T",
"hgvs_p": "p.Ala1852Ala",
"inheritance_mode": "AR,SD",
"pathogenic_score": 0,
"score": -15,
"transcript": "NM_002334.4",
"verdict": "Benign"
},
{
"benign_score": 10,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LRP4-AS1",
"hgnc_id": 44128,
"hgvs_c": "n.196+12428G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -10,
"transcript": "ENST00000502049.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1",
"acmg_score": -15,
"allele_count_reference_population": 79,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "11",
"clinvar_classification": "Likely benign",
"clinvar_disease": "Cenani-Lenz syndactyly syndrome,Congenital myasthenic syndrome 17,Sclerosteosis 2,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.36000001430511475,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1905,
"aa_ref": "A",
"aa_start": 1852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8155,
"cdna_start": 5727,
"cds_end": null,
"cds_length": 5718,
"cds_start": 5556,
"consequences": [
"synonymous_variant"
],
"exon_count": 38,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "NM_002334.4",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "c.5556C>T",
"hgvs_p": "p.Ala1852Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000378623.6",
"protein_coding": true,
"protein_id": "NP_002325.2",
"strand": false,
"transcript": "NM_002334.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1905,
"aa_ref": "A",
"aa_start": 1852,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8155,
"cdna_start": 5727,
"cds_end": null,
"cds_length": 5718,
"cds_start": 5556,
"consequences": [
"synonymous_variant"
],
"exon_count": 38,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "ENST00000378623.6",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "c.5556C>T",
"hgvs_p": "p.Ala1852Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002334.4",
"protein_coding": true,
"protein_id": "ENSP00000367888.1",
"strand": false,
"transcript": "ENST00000378623.6",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1722,
"aa_ref": "A",
"aa_start": 1669,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7469,
"cdna_start": 5194,
"cds_end": null,
"cds_length": 5169,
"cds_start": 5007,
"consequences": [
"synonymous_variant"
],
"exon_count": 35,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000858258.1",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "c.5007C>T",
"hgvs_p": "p.Ala1669Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528317.1",
"strand": false,
"transcript": "ENST00000858258.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1637,
"aa_ref": "A",
"aa_start": 1584,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7297,
"cdna_start": 4869,
"cds_end": null,
"cds_length": 4914,
"cds_start": 4752,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "XM_011520103.3",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "c.4752C>T",
"hgvs_p": "p.Ala1584Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518405.1",
"strand": false,
"transcript": "XM_011520103.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1160,
"aa_ref": "A",
"aa_start": 1107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7706,
"cdna_start": 5278,
"cds_end": null,
"cds_length": 3483,
"cds_start": 3321,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011520104.3",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "c.3321C>T",
"hgvs_p": "p.Ala1107Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011518406.1",
"strand": false,
"transcript": "XM_011520104.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1809,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8217,
"cdna_start": null,
"cds_end": null,
"cds_length": 5430,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 39,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "XM_017017734.2",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "c.*188C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016873223.1",
"strand": false,
"transcript": "XM_017017734.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2774,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000529604.1",
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"hgvs_c": "n.499C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000529604.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1544,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000502049.4",
"gene_hgnc_id": 44128,
"gene_symbol": "LRP4-AS1",
"hgvs_c": "n.196+12428G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000502049.4",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 731,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000531719.5",
"gene_hgnc_id": 44128,
"gene_symbol": "LRP4-AS1",
"hgvs_c": "n.291+6199G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000531719.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1540,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_038909.1",
"gene_hgnc_id": 44128,
"gene_symbol": "LRP4-AS1",
"hgvs_c": "n.197+12428G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_038909.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200514161",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00004894168,
"gene_hgnc_id": 6696,
"gene_symbol": "LRP4",
"gnomad_exomes_ac": 69,
"gnomad_exomes_af": 0.0000471992,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.0000656694,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Sclerosteosis 2;Congenital myasthenic syndrome 17;Cenani-Lenz syndactyly syndrome|not provided|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.233,
"pos": 46859145,
"ref": "G",
"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_002334.4"
}
]
}