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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: 12-106654280-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=106654280&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 106654280,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001206691.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Leu82Phe",
"transcript": "NM_213594.3",
"protein_id": "NP_998759.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 735,
"cds_start": 244,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000392842.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_213594.3"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Leu82Phe",
"transcript": "ENST00000392842.6",
"protein_id": "ENSP00000376585.1",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 735,
"cds_start": 244,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_213594.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392842.6"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Leu91Phe",
"transcript": "ENST00000357881.8",
"protein_id": "ENSP00000350552.4",
"transcript_support_level": 1,
"aa_start": 91,
"aa_end": null,
"aa_length": 744,
"cds_start": 271,
"cds_end": null,
"cds_length": 2235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357881.8"
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.376C>T",
"hgvs_p": null,
"transcript": "ENST00000536688.5",
"protein_id": null,
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000536688.5"
},
{
"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": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.114C>T",
"hgvs_p": null,
"transcript": "ENST00000552773.1",
"protein_id": null,
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000552773.1"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Leu91Phe",
"transcript": "NM_001206691.2",
"protein_id": "NP_001193620.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 744,
"cds_start": 271,
"cds_end": null,
"cds_length": 2235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206691.2"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Leu82Phe",
"transcript": "ENST00000959768.1",
"protein_id": "ENSP00000629827.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 734,
"cds_start": 244,
"cds_end": null,
"cds_length": 2205,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959768.1"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Leu53Phe",
"transcript": "ENST00000959769.1",
"protein_id": "ENSP00000629828.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 705,
"cds_start": 157,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959769.1"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.79C>T",
"hgvs_p": "p.Leu27Phe",
"transcript": "ENST00000551640.5",
"protein_id": "ENSP00000448694.1",
"transcript_support_level": 5,
"aa_start": 27,
"aa_end": null,
"aa_length": 255,
"cds_start": 79,
"cds_end": null,
"cds_length": 769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551640.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.-167C>T",
"hgvs_p": null,
"transcript": "ENST00000539967.6",
"protein_id": "ENSP00000473326.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": null,
"cds_end": null,
"cds_length": 436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539967.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "c.-6C>T",
"hgvs_p": null,
"transcript": "ENST00000549040.5",
"protein_id": "ENSP00000447735.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": null,
"cds_end": null,
"cds_length": 177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549040.5"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.271C>T",
"hgvs_p": null,
"transcript": "ENST00000536722.5",
"protein_id": "ENSP00000444163.1",
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000536722.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"hgvs_c": "n.157C>T",
"hgvs_p": null,
"transcript": "ENST00000546882.5",
"protein_id": "ENSP00000447423.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000546882.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.142+120410G>A",
"hgvs_p": null,
"transcript": "ENST00000549203.2",
"protein_id": null,
"transcript_support_level": 4,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000549203.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257545",
"gene_hgnc_id": null,
"hgvs_c": "n.229+120410G>A",
"hgvs_p": null,
"transcript": "ENST00000551505.4",
"protein_id": null,
"transcript_support_level": 4,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000551505.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC100287944",
"gene_hgnc_id": null,
"hgvs_c": "n.142+120410G>A",
"hgvs_p": null,
"transcript": "NR_040246.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_040246.1"
}
],
"gene_symbol": "RFX4",
"gene_hgnc_id": 9985,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7821263074874878,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.756,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.998,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.121,
"phylop100way_prediction": "Uncertain_significance",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001206691.2",
"gene_symbol": "RFX4",
"hgnc_id": 9985,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Leu91Phe"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000549203.2",
"gene_symbol": "ENSG00000257545",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+120410G>A",
"hgvs_p": null
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NR_040246.1",
"gene_symbol": "LOC100287944",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.142+120410G>A",
"hgvs_p": null
}
],
"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
}