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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: 11-46859188-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=46859188&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 46859188,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000378623.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.5513G>A",
"hgvs_p": "p.Arg1838Gln",
"transcript": "NM_002334.4",
"protein_id": "NP_002325.2",
"transcript_support_level": null,
"aa_start": 1838,
"aa_end": null,
"aa_length": 1905,
"cds_start": 5513,
"cds_end": null,
"cds_length": 5718,
"cdna_start": 5684,
"cdna_end": null,
"cdna_length": 8155,
"mane_select": "ENST00000378623.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.5513G>A",
"hgvs_p": "p.Arg1838Gln",
"transcript": "ENST00000378623.6",
"protein_id": "ENSP00000367888.1",
"transcript_support_level": 1,
"aa_start": 1838,
"aa_end": null,
"aa_length": 1905,
"cds_start": 5513,
"cds_end": null,
"cds_length": 5718,
"cdna_start": 5684,
"cdna_end": null,
"cdna_length": 8155,
"mane_select": "NM_002334.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.4709G>A",
"hgvs_p": "p.Arg1570Gln",
"transcript": "XM_011520103.3",
"protein_id": "XP_011518405.1",
"transcript_support_level": null,
"aa_start": 1570,
"aa_end": null,
"aa_length": 1637,
"cds_start": 4709,
"cds_end": null,
"cds_length": 4914,
"cdna_start": 4826,
"cdna_end": null,
"cdna_length": 7297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.3278G>A",
"hgvs_p": "p.Arg1093Gln",
"transcript": "XM_011520104.3",
"protein_id": "XP_011518406.1",
"transcript_support_level": null,
"aa_start": 1093,
"aa_end": null,
"aa_length": 1160,
"cds_start": 3278,
"cds_end": null,
"cds_length": 3483,
"cdna_start": 5235,
"cdna_end": null,
"cdna_length": 7706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "n.456G>A",
"hgvs_p": null,
"transcript": "ENST00000529604.1",
"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": 2774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"hgvs_c": "c.*145G>A",
"hgvs_p": null,
"transcript": "XM_017017734.2",
"protein_id": "XP_016873223.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1809,
"cds_start": -4,
"cds_end": null,
"cds_length": 5430,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8217,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRP4-AS1",
"gene_hgnc_id": 44128,
"hgvs_c": "n.196+12471C>T",
"hgvs_p": null,
"transcript": "ENST00000502049.4",
"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": 1544,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LRP4-AS1",
"gene_hgnc_id": 44128,
"hgvs_c": "n.291+6242C>T",
"hgvs_p": null,
"transcript": "ENST00000531719.5",
"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,
"cdna_end": null,
"cdna_length": 731,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LRP4-AS1",
"gene_hgnc_id": 44128,
"hgvs_c": "n.197+12471C>T",
"hgvs_p": null,
"transcript": "NR_038909.1",
"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": 1540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRP4",
"gene_hgnc_id": 6696,
"dbsnp": "rs770309253",
"frequency_reference_population": 0.000075587566,
"hom_count_reference_population": 1,
"allele_count_reference_population": 122,
"gnomad_exomes_af": 0.0000718251,
"gnomad_genomes_af": 0.000111741,
"gnomad_exomes_ac": 105,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10411128401756287,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.495,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0901,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.085,
"phylop100way_prediction": "Uncertain_significance",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000378623.6",
"gene_symbol": "LRP4",
"hgnc_id": 6696,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,SD",
"hgvs_c": "c.5513G>A",
"hgvs_p": "p.Arg1838Gln"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000502049.4",
"gene_symbol": "LRP4-AS1",
"hgnc_id": 44128,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.196+12471C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cenani-Lenz syndactyly syndrome,Congenital myasthenic syndrome 17,Inborn genetic diseases,Sclerosteosis 2,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "not provided|Cenani-Lenz syndactyly syndrome;Sclerosteosis 2;Congenital myasthenic syndrome 17|Cenani-Lenz syndactyly syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}