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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: 2-74534149-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=74534149&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 74534149,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000264094.8",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr",
"transcript": "NM_032603.5",
"protein_id": "NP_115992.1",
"transcript_support_level": null,
"aa_start": 676,
"aa_end": null,
"aa_length": 753,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2106,
"cdna_end": null,
"cdna_length": 3689,
"mane_select": "ENST00000264094.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr",
"transcript": "ENST00000264094.8",
"protein_id": "ENSP00000264094.3",
"transcript_support_level": 1,
"aa_start": 676,
"aa_end": null,
"aa_length": 753,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2106,
"cdna_end": null,
"cdna_length": 3689,
"mane_select": "NM_032603.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.1859G>A",
"hgvs_p": "p.Cys620Tyr",
"transcript": "ENST00000409549.5",
"protein_id": "ENSP00000386696.1",
"transcript_support_level": 2,
"aa_start": 620,
"aa_end": null,
"aa_length": 697,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 2309,
"cdna_end": null,
"cdna_length": 2897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Cys531Tyr",
"transcript": "NM_001289164.3",
"protein_id": "NP_001276093.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 608,
"cds_start": 1592,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1671,
"cdna_end": null,
"cdna_length": 3254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Cys531Tyr",
"transcript": "ENST00000393937.6",
"protein_id": "ENSP00000377512.2",
"transcript_support_level": 5,
"aa_start": 531,
"aa_end": null,
"aa_length": 608,
"cds_start": 1592,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1687,
"cdna_end": null,
"cdna_length": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Cys531Tyr",
"transcript": "ENST00000409986.5",
"protein_id": "ENSP00000386545.1",
"transcript_support_level": 2,
"aa_start": 531,
"aa_end": null,
"aa_length": 586,
"cds_start": 1592,
"cds_end": null,
"cds_length": 1761,
"cdna_start": 1690,
"cdna_end": null,
"cdna_length": 2005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.1181G>A",
"hgvs_p": "p.Cys394Tyr",
"transcript": "ENST00000409249.5",
"protein_id": "ENSP00000387103.1",
"transcript_support_level": 5,
"aa_start": 394,
"aa_end": null,
"aa_length": 471,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 2431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.944G>A",
"hgvs_p": "p.Cys315Tyr",
"transcript": "NM_001289165.2",
"protein_id": "NP_001276094.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 392,
"cds_start": 944,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 1273,
"cdna_end": null,
"cdna_length": 2856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr",
"transcript": "XM_011533134.3",
"protein_id": "XP_011531436.1",
"transcript_support_level": null,
"aa_start": 676,
"aa_end": null,
"aa_length": 753,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2081,
"cdna_end": null,
"cdna_length": 3664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr",
"transcript": "XM_024453176.2",
"protein_id": "XP_024308944.1",
"transcript_support_level": null,
"aa_start": 676,
"aa_end": null,
"aa_length": 753,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2144,
"cdna_end": null,
"cdna_length": 3727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr",
"transcript": "XM_024453177.2",
"protein_id": "XP_024308945.1",
"transcript_support_level": null,
"aa_start": 676,
"aa_end": null,
"aa_length": 753,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2298,
"cdna_end": null,
"cdna_length": 3881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr",
"transcript": "XM_024453178.2",
"protein_id": "XP_024308946.1",
"transcript_support_level": null,
"aa_start": 676,
"aa_end": null,
"aa_length": 753,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 3373,
"cdna_end": null,
"cdna_length": 4956,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "n.1410G>A",
"hgvs_p": null,
"transcript": "ENST00000470907.6",
"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": 2837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"dbsnp": "rs786204838",
"frequency_reference_population": 6.8404694e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84047e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9815008640289307,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.701,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9997,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.879,
"phylop100way_prediction": "Pathogenic",
"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_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000264094.8",
"gene_symbol": "LOXL3",
"hgnc_id": 13869,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2027G>A",
"hgvs_p": "p.Cys676Tyr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}