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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: 19-13963655-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=13963655&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 13963655,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002918.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2453T>A",
"hgvs_p": "p.Leu818Gln",
"transcript": "NM_002918.5",
"protein_id": "NP_002909.4",
"transcript_support_level": null,
"aa_start": 818,
"aa_end": null,
"aa_length": 979,
"cds_start": 2453,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2723,
"cdna_end": null,
"cdna_length": 4375,
"mane_select": "ENST00000254325.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2453T>A",
"hgvs_p": "p.Leu818Gln",
"transcript": "ENST00000254325.9",
"protein_id": "ENSP00000254325.3",
"transcript_support_level": 1,
"aa_start": 818,
"aa_end": null,
"aa_length": 979,
"cds_start": 2453,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2723,
"cdna_end": null,
"cdna_length": 4375,
"mane_select": "NM_002918.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2783T>A",
"hgvs_p": "p.Leu928Gln",
"transcript": "XM_011528166.3",
"protein_id": "XP_011526468.1",
"transcript_support_level": null,
"aa_start": 928,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2783,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 3102,
"cdna_end": null,
"cdna_length": 4754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2783T>A",
"hgvs_p": "p.Leu928Gln",
"transcript": "XM_011528167.3",
"protein_id": "XP_011526469.1",
"transcript_support_level": null,
"aa_start": 928,
"aa_end": null,
"aa_length": 1089,
"cds_start": 2783,
"cds_end": null,
"cds_length": 3270,
"cdna_start": 2902,
"cdna_end": null,
"cdna_length": 4554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2489T>A",
"hgvs_p": "p.Leu830Gln",
"transcript": "XM_047439192.1",
"protein_id": "XP_047295148.1",
"transcript_support_level": null,
"aa_start": 830,
"aa_end": null,
"aa_length": 991,
"cds_start": 2489,
"cds_end": null,
"cds_length": 2976,
"cdna_start": 2808,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2456T>A",
"hgvs_p": "p.Leu819Gln",
"transcript": "XM_011528169.3",
"protein_id": "XP_011526471.1",
"transcript_support_level": null,
"aa_start": 819,
"aa_end": null,
"aa_length": 980,
"cds_start": 2456,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2682,
"cdna_end": null,
"cdna_length": 4334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2456T>A",
"hgvs_p": "p.Leu819Gln",
"transcript": "XM_011528170.3",
"protein_id": "XP_011526472.1",
"transcript_support_level": null,
"aa_start": 819,
"aa_end": null,
"aa_length": 980,
"cds_start": 2456,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2531,
"cdna_end": null,
"cdna_length": 4183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2453T>A",
"hgvs_p": "p.Leu818Gln",
"transcript": "XM_047439193.1",
"protein_id": "XP_047295149.1",
"transcript_support_level": null,
"aa_start": 818,
"aa_end": null,
"aa_length": 979,
"cds_start": 2453,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2772,
"cdna_end": null,
"cdna_length": 4424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2453T>A",
"hgvs_p": "p.Leu818Gln",
"transcript": "XM_047439194.1",
"protein_id": "XP_047295150.1",
"transcript_support_level": null,
"aa_start": 818,
"aa_end": null,
"aa_length": 979,
"cds_start": 2453,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 2572,
"cdna_end": null,
"cdna_length": 4224,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "c.2159T>A",
"hgvs_p": "p.Leu720Gln",
"transcript": "XM_047439195.1",
"protein_id": "XP_047295151.1",
"transcript_support_level": null,
"aa_start": 720,
"aa_end": null,
"aa_length": 881,
"cds_start": 2159,
"cds_end": null,
"cds_length": 2646,
"cdna_start": 2478,
"cdna_end": null,
"cdna_length": 4130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"hgvs_c": "n.*49T>A",
"hgvs_p": null,
"transcript": "ENST00000588520.1",
"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": 241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RFX1",
"gene_hgnc_id": 9982,
"dbsnp": "rs1473347782",
"frequency_reference_population": 0.0000020678217,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000206782,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8742288947105408,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.403,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9998,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.268,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002918.5",
"gene_symbol": "RFX1",
"hgnc_id": 9982,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2453T>A",
"hgvs_p": "p.Leu818Gln"
}
],
"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
}