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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: 5-38925240-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=38925240&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 38925240,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000274276.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln",
"transcript": "NM_003999.3",
"protein_id": "NP_003990.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 979,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2470,
"cdna_end": null,
"cdna_length": 5526,
"mane_select": "ENST00000274276.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln",
"transcript": "ENST00000274276.8",
"protein_id": "ENSP00000274276.3",
"transcript_support_level": 1,
"aa_start": 694,
"aa_end": null,
"aa_length": 979,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2470,
"cdna_end": null,
"cdna_length": 5526,
"mane_select": "NM_003999.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2084C>A",
"hgvs_p": "p.Pro695Gln",
"transcript": "NM_001323506.2",
"protein_id": "NP_001310435.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 980,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2212,
"cdna_end": null,
"cdna_length": 5268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln",
"transcript": "NM_001323505.2",
"protein_id": "NP_001310434.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 979,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2209,
"cdna_end": null,
"cdna_length": 5265,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2084C>A",
"hgvs_p": "p.Pro695Gln",
"transcript": "XM_005248384.1",
"protein_id": "XP_005248441.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 980,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2473,
"cdna_end": null,
"cdna_length": 5529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2084C>A",
"hgvs_p": "p.Pro695Gln",
"transcript": "XM_047417870.1",
"protein_id": "XP_047273826.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 980,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2322,
"cdna_end": null,
"cdna_length": 5378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln",
"transcript": "XM_047417871.1",
"protein_id": "XP_047273827.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 979,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2305,
"cdna_end": null,
"cdna_length": 5361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2084C>A",
"hgvs_p": "p.Pro695Gln",
"transcript": "XM_011514161.3",
"protein_id": "XP_011512463.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 800,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2403,
"cdna_start": 2473,
"cdna_end": null,
"cdna_length": 4138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln",
"transcript": "XM_017010019.2",
"protein_id": "XP_016865508.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 799,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 2470,
"cdna_end": null,
"cdna_length": 4135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln",
"transcript": "XM_047417872.1",
"protein_id": "XP_047273828.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 799,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 2209,
"cdna_end": null,
"cdna_length": 3874,
"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": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "n.2470C>A",
"hgvs_p": null,
"transcript": "XR_007058659.1",
"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": 3237,
"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": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "n.2209C>A",
"hgvs_p": null,
"transcript": "XR_007058660.1",
"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": 2976,
"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": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"hgvs_c": "n.2473C>A",
"hgvs_p": null,
"transcript": "XR_925661.1",
"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": 3240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OSMR",
"gene_hgnc_id": 8507,
"dbsnp": "rs387906822",
"frequency_reference_population": 6.8409094e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84091e-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": 0.6264637112617493,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.254,
"revel_prediction": "Benign",
"alphamissense_score": 0.2401,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.969,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": "PM1,PM2,PM5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PM5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000274276.8",
"gene_symbol": "OSMR",
"hgnc_id": 8507,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,SD",
"hgvs_c": "c.2081C>A",
"hgvs_p": "p.Pro694Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}