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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: 20-3822265-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=3822265&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 3822265,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018347.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "NM_018347.3",
"protein_id": "NP_060817.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000615891.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018347.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000615891.2",
"protein_id": "ENSP00000481750.1",
"transcript_support_level": 1,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018347.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000615891.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000379573.6",
"protein_id": "ENSP00000368892.2",
"transcript_support_level": 1,
"aa_start": 50,
"aa_end": null,
"aa_length": 59,
"cds_start": 148,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379573.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "NM_001204446.2",
"protein_id": "NP_001191375.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204446.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "NM_001204447.2",
"protein_id": "NP_001191376.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204447.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000379567.6",
"protein_id": "ENSP00000368886.2",
"transcript_support_level": 2,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379567.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000455742.6",
"protein_id": "ENSP00000405487.2",
"transcript_support_level": 4,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000455742.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000620777.2",
"protein_id": "ENSP00000520567.1",
"transcript_support_level": 5,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620777.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000870773.1",
"protein_id": "ENSP00000540832.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870773.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000870774.1",
"protein_id": "ENSP00000540833.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870774.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000870775.1",
"protein_id": "ENSP00000540834.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870775.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000927141.1",
"protein_id": "ENSP00000597200.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927141.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp",
"transcript": "ENST00000941770.1",
"protein_id": "ENSP00000611829.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 200,
"cds_start": 148,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941770.1"
}
],
"gene_symbol": "AP5S1",
"gene_hgnc_id": 15875,
"dbsnp": "rs373301302",
"frequency_reference_population": 0.000040272866,
"hom_count_reference_population": 0,
"allele_count_reference_population": 65,
"gnomad_exomes_af": 0.0000355717,
"gnomad_genomes_af": 0.0000854398,
"gnomad_exomes_ac": 52,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2847743332386017,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.218,
"revel_prediction": "Benign",
"alphamissense_score": 0.1455,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.911,
"phylop100way_prediction": "Benign",
"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_018347.3",
"gene_symbol": "AP5S1",
"hgnc_id": 15875,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Trp"
}
],
"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
}