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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: 15-86674322-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=86674322&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 86674322,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001386094.1",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.3044G>C",
"hgvs_p": "p.Cys1015Ser",
"transcript": "NM_001386094.1",
"protein_id": "NP_001373023.1",
"transcript_support_level": null,
"aa_start": 1015,
"aa_end": null,
"aa_length": 1121,
"cds_start": 3044,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000614907.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001386094.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.3044G>C",
"hgvs_p": "p.Cys1015Ser",
"transcript": "ENST00000614907.3",
"protein_id": "ENSP00000490608.2",
"transcript_support_level": 5,
"aa_start": 1015,
"aa_end": null,
"aa_length": 1121,
"cds_start": 3044,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001386094.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614907.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.3107G>C",
"hgvs_p": "p.Cys1036Ser",
"transcript": "NM_152336.4",
"protein_id": "NP_689549.3",
"transcript_support_level": null,
"aa_start": 1036,
"aa_end": null,
"aa_length": 1112,
"cds_start": 3107,
"cds_end": null,
"cds_length": 3339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152336.4"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.3107G>C",
"hgvs_p": "p.Cys1036Ser",
"transcript": "ENST00000441037.7",
"protein_id": "ENSP00000413001.3",
"transcript_support_level": 5,
"aa_start": 1036,
"aa_end": null,
"aa_length": 1112,
"cds_start": 3107,
"cds_end": null,
"cds_length": 3339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441037.7"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.3011G>C",
"hgvs_p": "p.Cys1004Ser",
"transcript": "XM_017021918.3",
"protein_id": "XP_016877407.1",
"transcript_support_level": null,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1110,
"cds_start": 3011,
"cds_end": null,
"cds_length": 3333,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017021918.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.2960G>C",
"hgvs_p": "p.Cys987Ser",
"transcript": "XM_017021919.3",
"protein_id": "XP_016877408.1",
"transcript_support_level": null,
"aa_start": 987,
"aa_end": null,
"aa_length": 1093,
"cds_start": 2960,
"cds_end": null,
"cds_length": 3282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017021919.3"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "c.3044G>C",
"hgvs_p": "p.Cys1015Ser",
"transcript": "XM_011521227.4",
"protein_id": "XP_011519529.1",
"transcript_support_level": null,
"aa_start": 1015,
"aa_end": null,
"aa_length": 1057,
"cds_start": 3044,
"cds_end": null,
"cds_length": 3174,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521227.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"hgvs_c": "n.203G>C",
"hgvs_p": null,
"transcript": "ENST00000681381.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000681381.1"
}
],
"gene_symbol": "AGBL1",
"gene_hgnc_id": 26504,
"dbsnp": "rs181958589",
"frequency_reference_population": 0.0019521097,
"hom_count_reference_population": 6,
"allele_count_reference_population": 3147,
"gnomad_exomes_af": 0.00202017,
"gnomad_genomes_af": 0.00129988,
"gnomad_exomes_ac": 2949,
"gnomad_genomes_ac": 198,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.020041704177856445,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.296,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7889,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.909,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001386094.1",
"gene_symbol": "AGBL1",
"hgnc_id": 26504,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3044G>C",
"hgvs_p": "p.Cys1015Ser"
}
],
"clinvar_disease": " 8, Fuchs endothelial,Corneal dystrophy,Fuchs' endothelial dystrophy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"phenotype_combined": "Corneal dystrophy, Fuchs endothelial, 8|Fuchs' endothelial dystrophy|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}