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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: 13-41466897-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=41466897&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 41466897,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_014059.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Ala104Thr",
"transcript": "NM_014059.3",
"protein_id": "NP_054778.2",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 137,
"cds_start": 310,
"cds_end": null,
"cds_length": 414,
"cdna_start": 468,
"cdna_end": null,
"cdna_length": 958,
"mane_select": "ENST00000379359.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014059.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Ala104Thr",
"transcript": "ENST00000379359.4",
"protein_id": "ENSP00000368664.3",
"transcript_support_level": 1,
"aa_start": 104,
"aa_end": null,
"aa_length": 137,
"cds_start": 310,
"cds_end": null,
"cds_length": 414,
"cdna_start": 468,
"cdna_end": null,
"cdna_length": 958,
"mane_select": "NM_014059.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379359.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Ala121Thr",
"transcript": "ENST00000888696.1",
"protein_id": "ENSP00000558755.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 154,
"cds_start": 361,
"cds_end": null,
"cds_length": 465,
"cdna_start": 519,
"cdna_end": null,
"cdna_length": 1012,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888696.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "c.304G>A",
"hgvs_p": "p.Ala102Thr",
"transcript": "ENST00000888694.1",
"protein_id": "ENSP00000558753.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 135,
"cds_start": 304,
"cds_end": null,
"cds_length": 408,
"cdna_start": 480,
"cdna_end": null,
"cdna_length": 976,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888694.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Ala104Thr",
"transcript": "ENST00000888695.1",
"protein_id": "ENSP00000558754.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 134,
"cds_start": 310,
"cds_end": null,
"cds_length": 405,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 955,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888695.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "c.236-3581G>A",
"hgvs_p": null,
"transcript": "ENST00000888697.1",
"protein_id": "ENSP00000558756.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": null,
"cds_end": null,
"cds_length": 243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 787,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888697.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "n.141G>A",
"hgvs_p": null,
"transcript": "ENST00000487837.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 243,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000487837.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"hgvs_c": "n.736G>A",
"hgvs_p": null,
"transcript": "XR_941565.2",
"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": 749,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_941565.2"
}
],
"gene_symbol": "RGCC",
"gene_hgnc_id": 20369,
"dbsnp": "rs189261970",
"frequency_reference_population": 0.00003098262,
"hom_count_reference_population": 0,
"allele_count_reference_population": 50,
"gnomad_exomes_af": 0.0000143687,
"gnomad_genomes_af": 0.000190421,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 29,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.013755202293395996,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.042,
"revel_prediction": "Benign",
"alphamissense_score": 0.0642,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.595,
"phylop100way_prediction": "Benign",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_014059.3",
"gene_symbol": "RGCC",
"hgnc_id": 20369,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.310G>A",
"hgvs_p": "p.Ala104Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}