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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: 1-151343055-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=151343055&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 151343055,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000452671.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001025603.2",
"protein_id": "NP_001020774.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1155,
"cdna_end": null,
"cdna_length": 3570,
"mane_select": "ENST00000452671.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "ENST00000452671.7",
"protein_id": "ENSP00000389130.2",
"transcript_support_level": 1,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1155,
"cdna_end": null,
"cdna_length": 3570,
"mane_select": "NM_001025603.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "ENST00000290524.8",
"protein_id": "ENSP00000290524.4",
"transcript_support_level": 1,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1161,
"cdna_end": null,
"cdna_length": 3576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_000449.4",
"protein_id": "NP_000440.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1162,
"cdna_end": null,
"cdna_length": 3577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379412.1",
"protein_id": "NP_001366341.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379413.1",
"protein_id": "NP_001366342.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1222,
"cdna_end": null,
"cdna_length": 3637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379414.1",
"protein_id": "NP_001366343.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1222,
"cdna_end": null,
"cdna_length": 3637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379415.1",
"protein_id": "NP_001366344.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1222,
"cdna_end": null,
"cdna_length": 3637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379416.1",
"protein_id": "NP_001366345.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 3697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379417.1",
"protein_id": "NP_001366346.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 3630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "NM_001379418.1",
"protein_id": "NP_001366347.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1173,
"cdna_end": null,
"cdna_length": 3588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "ENST00000368870.6",
"protein_id": "ENSP00000357864.2",
"transcript_support_level": 5,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 2459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "ENST00000392746.7",
"protein_id": "ENSP00000376502.3",
"transcript_support_level": 5,
"aa_start": 328,
"aa_end": null,
"aa_length": 595,
"cds_start": 982,
"cds_end": null,
"cds_length": 1790,
"cdna_start": 1248,
"cdna_end": null,
"cdna_length": 2056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.862C>A",
"hgvs_p": "p.Arg288Arg",
"transcript": "NM_001379419.1",
"protein_id": "NP_001366348.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 576,
"cds_start": 862,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 1035,
"cdna_end": null,
"cdna_length": 3450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.862C>A",
"hgvs_p": "p.Arg288Arg",
"transcript": "NM_001379420.1",
"protein_id": "NP_001366349.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 576,
"cds_start": 862,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 1095,
"cdna_end": null,
"cdna_length": 3510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg",
"transcript": "XM_047426951.1",
"protein_id": "XP_047282907.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 616,
"cds_start": 982,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 3697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.469C>A",
"hgvs_p": "p.Arg157Arg",
"transcript": "XM_024448791.2",
"protein_id": "XP_024304559.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 445,
"cds_start": 469,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 810,
"cdna_end": null,
"cdna_length": 3225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"hgvs_c": "c.639+19C>A",
"hgvs_p": null,
"transcript": "ENST00000436637.5",
"protein_id": "ENSP00000390769.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 235,
"cds_start": -4,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RFX5-AS1",
"gene_hgnc_id": 40503,
"hgvs_c": "n.530-4577G>T",
"hgvs_p": null,
"transcript": "ENST00000811547.1",
"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": 789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RFX5",
"gene_hgnc_id": 9986,
"dbsnp": "rs78854744",
"frequency_reference_population": 0.00047906375,
"hom_count_reference_population": 7,
"allele_count_reference_population": 773,
"gnomad_exomes_af": 0.000473574,
"gnomad_genomes_af": 0.000531726,
"gnomad_exomes_ac": 692,
"gnomad_genomes_ac": 81,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.44999998807907104,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.103,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000452671.7",
"gene_symbol": "RFX5",
"hgnc_id": 9986,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.982C>A",
"hgvs_p": "p.Arg328Arg"
},
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000811547.1",
"gene_symbol": "RFX5-AS1",
"hgnc_id": 40503,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.530-4577G>T",
"hgvs_p": null
}
],
"clinvar_disease": "MHC class II deficiency",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "MHC class II deficiency",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}