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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: 1-28592578-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=28592578&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 28592578,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001193532.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB42",
"gene_hgnc_id": 28702,
"hgvs_c": "c.67A>C",
"hgvs_p": "p.Thr23Pro",
"transcript": "NM_001193532.3",
"protein_id": "NP_001180461.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 218,
"cds_start": 67,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000465518.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193532.3"
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB42",
"gene_hgnc_id": 28702,
"hgvs_c": "c.67A>C",
"hgvs_p": "p.Thr23Pro",
"transcript": "ENST00000465518.3",
"protein_id": "ENSP00000491546.1",
"transcript_support_level": 2,
"aa_start": 23,
"aa_end": null,
"aa_length": 218,
"cds_start": 67,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001193532.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000465518.3"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RAB42",
"gene_hgnc_id": 28702,
"hgvs_c": "c.-107+179A>C",
"hgvs_p": null,
"transcript": "ENST00000373826.3",
"protein_id": "ENSP00000362932.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 105,
"cds_start": null,
"cds_end": null,
"cds_length": 318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373826.3"
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAB42",
"gene_hgnc_id": 28702,
"hgvs_c": "c.67A>C",
"hgvs_p": "p.Thr23Pro",
"transcript": "NM_001385188.1",
"protein_id": "NP_001372117.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 106,
"cds_start": 67,
"cds_end": null,
"cds_length": 321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001385188.1"
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "TAF12",
"gene_hgnc_id": 11545,
"hgvs_c": "c.451-2192T>G",
"hgvs_p": null,
"transcript": "ENST00000688108.1",
"protein_id": "ENSP00000510282.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": null,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000688108.1"
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "TAF12",
"gene_hgnc_id": 11545,
"hgvs_c": "c.451-2192T>G",
"hgvs_p": null,
"transcript": "ENST00000471683.6",
"protein_id": "ENSP00000508634.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 194,
"cds_start": null,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000471683.6"
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "TAF12",
"gene_hgnc_id": 11545,
"hgvs_c": "c.451-2192T>G",
"hgvs_p": null,
"transcript": "ENST00000693642.1",
"protein_id": "ENSP00000509910.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 189,
"cds_start": null,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000693642.1"
},
{
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TAF12",
"gene_hgnc_id": 11545,
"hgvs_c": "c.373-2192T>G",
"hgvs_p": null,
"transcript": "ENST00000691563.1",
"protein_id": "ENSP00000508797.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000691563.1"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TAF12",
"gene_hgnc_id": 11545,
"hgvs_c": "c.205-2192T>G",
"hgvs_p": null,
"transcript": "ENST00000685589.1",
"protein_id": "ENSP00000509854.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 112,
"cds_start": null,
"cds_end": null,
"cds_length": 339,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685589.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RAB42",
"gene_hgnc_id": 28702,
"hgvs_c": "c.-107+179A>C",
"hgvs_p": null,
"transcript": "NM_152304.3",
"protein_id": "NP_689517.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 105,
"cds_start": null,
"cds_end": null,
"cds_length": 318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152304.3"
},
{
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "TAF12",
"gene_hgnc_id": 11545,
"hgvs_c": "n.*428-2192T>G",
"hgvs_p": null,
"transcript": "ENST00000692098.1",
"protein_id": "ENSP00000509051.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000692098.1"
}
],
"gene_symbol": "RAB42",
"gene_hgnc_id": 28702,
"dbsnp": "rs1666338613",
"frequency_reference_population": 0.0000032814428,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000187396,
"gnomad_genomes_af": 0.0000131825,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4036760628223419,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.7986,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.543,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001193532.3",
"gene_symbol": "RAB42",
"hgnc_id": 28702,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.67A>C",
"hgvs_p": "p.Thr23Pro"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000471683.6",
"gene_symbol": "TAF12",
"hgnc_id": 11545,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.451-2192T>G",
"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
}