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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: 13-45194300-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=45194300&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 45194300,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_198404.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCTD4",
"gene_hgnc_id": 23227,
"hgvs_c": "c.268C>G",
"hgvs_p": "p.Leu90Val",
"transcript": "NM_198404.3",
"protein_id": "NP_940686.2",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 259,
"cds_start": 268,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379108.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198404.3"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCTD4",
"gene_hgnc_id": 23227,
"hgvs_c": "c.268C>G",
"hgvs_p": "p.Leu90Val",
"transcript": "ENST00000379108.2",
"protein_id": "ENSP00000368402.1",
"transcript_support_level": 6,
"aa_start": 90,
"aa_end": null,
"aa_length": 259,
"cds_start": 268,
"cds_end": null,
"cds_length": 780,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_198404.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379108.2"
},
{
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.305-13124G>C",
"hgvs_p": null,
"transcript": "NM_004128.3",
"protein_id": "NP_004119.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": null,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000340473.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004128.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.305-13124G>C",
"hgvs_p": null,
"transcript": "ENST00000340473.8",
"protein_id": "ENSP00000340823.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": null,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004128.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000340473.8"
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.382+10822G>C",
"hgvs_p": null,
"transcript": "ENST00000883031.1",
"protein_id": "ENSP00000553090.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 275,
"cds_start": null,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883031.1"
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.382+10182G>C",
"hgvs_p": null,
"transcript": "ENST00000912524.1",
"protein_id": "ENSP00000582583.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 275,
"cds_start": null,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912524.1"
},
{
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.305-13124G>C",
"hgvs_p": null,
"transcript": "ENST00000912523.1",
"protein_id": "ENSP00000582582.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": null,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912523.1"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.140+57494G>C",
"hgvs_p": null,
"transcript": "ENST00000883032.1",
"protein_id": "ENSP00000553091.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": null,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883032.1"
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "c.382+10822G>C",
"hgvs_p": null,
"transcript": "XM_011535052.4",
"protein_id": "XP_011533354.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 275,
"cds_start": null,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011535052.4"
},
{
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTF2F2",
"gene_hgnc_id": 4653,
"hgvs_c": "n.134-13124G>C",
"hgvs_p": null,
"transcript": "ENST00000706694.1",
"protein_id": "ENSP00000516507.1",
"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": "ENST00000706694.1"
}
],
"gene_symbol": "KCTD4",
"gene_hgnc_id": 23227,
"dbsnp": "rs1872777609",
"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": 0.9380059838294983,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.831,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6776,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.822,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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_198404.3",
"gene_symbol": "KCTD4",
"hgnc_id": 23227,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.268C>G",
"hgvs_p": "p.Leu90Val"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004128.3",
"gene_symbol": "GTF2F2",
"hgnc_id": 4653,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.305-13124G>C",
"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
}