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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: 17-65197160-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=65197160&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 65197160,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000262406.10",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.895T>C",
"hgvs_p": "p.Trp299Arg",
"transcript": "NM_003835.4",
"protein_id": "NP_003826.2",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 674,
"cds_start": 895,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 1066,
"cdna_end": null,
"cdna_length": 2492,
"mane_select": "ENST00000262406.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.895T>C",
"hgvs_p": "p.Trp299Arg",
"transcript": "ENST00000262406.10",
"protein_id": "ENSP00000262406.9",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 674,
"cds_start": 895,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 1066,
"cdna_end": null,
"cdna_length": 2492,
"mane_select": "NM_003835.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.886T>C",
"hgvs_p": "p.Trp296Arg",
"transcript": "ENST00000449996.7",
"protein_id": "ENSP00000396329.3",
"transcript_support_level": 1,
"aa_start": 296,
"aa_end": null,
"aa_length": 671,
"cds_start": 886,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 958,
"cdna_end": null,
"cdna_length": 2384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.886T>C",
"hgvs_p": "p.Trp296Arg",
"transcript": "ENST00000443584.7",
"protein_id": "ENSP00000405814.3",
"transcript_support_level": 1,
"aa_start": 296,
"aa_end": null,
"aa_length": 628,
"cds_start": 886,
"cds_end": null,
"cds_length": 1887,
"cdna_start": 979,
"cdna_end": null,
"cdna_length": 2078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.895T>C",
"hgvs_p": "p.Trp299Arg",
"transcript": "ENST00000635833.1",
"protein_id": "ENSP00000490658.1",
"transcript_support_level": 5,
"aa_start": 299,
"aa_end": null,
"aa_length": 674,
"cds_start": 895,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 895,
"cdna_end": null,
"cdna_length": 2308,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.886T>C",
"hgvs_p": "p.Trp296Arg",
"transcript": "NM_001081955.3",
"protein_id": "NP_001075424.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 671,
"cds_start": 886,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1057,
"cdna_end": null,
"cdna_length": 2483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "c.886T>C",
"hgvs_p": "p.Trp296Arg",
"transcript": "NM_001165933.2",
"protein_id": "NP_001159405.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 484,
"cds_start": 886,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1057,
"cdna_end": null,
"cdna_length": 4226,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "n.823T>C",
"hgvs_p": null,
"transcript": "ENST00000577595.1",
"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": 2238,
"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": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "n.903T>C",
"hgvs_p": null,
"transcript": "ENST00000581175.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1472,
"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": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"hgvs_c": "n.895T>C",
"hgvs_p": null,
"transcript": "ENST00000584234.5",
"protein_id": "ENSP00000463410.1",
"transcript_support_level": 5,
"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": 2387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RGS9",
"gene_hgnc_id": 10004,
"dbsnp": "rs121908449",
"frequency_reference_population": 0.00026707118,
"hom_count_reference_population": 0,
"allele_count_reference_population": 431,
"gnomad_exomes_af": 0.000275725,
"gnomad_genomes_af": 0.000183968,
"gnomad_exomes_ac": 403,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9744853973388672,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.733,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9999,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.81,
"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": "PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000262406.10",
"gene_symbol": "RGS9",
"hgnc_id": 10004,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.895T>C",
"hgvs_p": "p.Trp299Arg"
}
],
"clinvar_disease": "Bradyopsia,Leber congenital amaurosis,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Bradyopsia|Leber congenital amaurosis|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}