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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: 9-101312912-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=101312912&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 101312912,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017753.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.751C>T",
"hgvs_p": "p.Arg251Trp",
"transcript": "NM_207299.2",
"protein_id": "NP_997182.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 325,
"cds_start": 751,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374874.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_207299.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.751C>T",
"hgvs_p": "p.Arg251Trp",
"transcript": "ENST00000374874.8",
"protein_id": "ENSP00000364008.3",
"transcript_support_level": 1,
"aa_start": 251,
"aa_end": null,
"aa_length": 325,
"cds_start": 751,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_207299.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374874.8"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.751C>T",
"hgvs_p": "p.Arg251Trp",
"transcript": "ENST00000395056.2",
"protein_id": "ENSP00000378496.1",
"transcript_support_level": 1,
"aa_start": 251,
"aa_end": null,
"aa_length": 325,
"cds_start": 751,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395056.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.751C>T",
"hgvs_p": "p.Arg251Trp",
"transcript": "NM_017753.3",
"protein_id": "NP_060223.2",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 325,
"cds_start": 751,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017753.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.751C>T",
"hgvs_p": "p.Arg251Trp",
"transcript": "ENST00000883514.1",
"protein_id": "ENSP00000553573.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 325,
"cds_start": 751,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883514.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Trp",
"transcript": "ENST00000883512.1",
"protein_id": "ENSP00000553571.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 304,
"cds_start": 688,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883512.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Arg230Trp",
"transcript": "ENST00000883513.1",
"protein_id": "ENSP00000553572.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 304,
"cds_start": 688,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883513.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188Trp",
"transcript": "ENST00000883511.1",
"protein_id": "ENSP00000553570.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 262,
"cds_start": 562,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883511.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "c.562C>T",
"hgvs_p": "p.Arg188Trp",
"transcript": "ENST00000883515.1",
"protein_id": "ENSP00000553574.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 262,
"cds_start": 562,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883515.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"hgvs_c": "n.*18C>T",
"hgvs_p": null,
"transcript": "ENST00000463206.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000463206.1"
}
],
"gene_symbol": "PLPPR1",
"gene_hgnc_id": 25993,
"dbsnp": "rs780787669",
"frequency_reference_population": 0.00001301112,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.000012997,
"gnomad_genomes_af": 0.0000131472,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9204528331756592,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.744,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7244,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.611,
"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": 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_017753.3",
"gene_symbol": "PLPPR1",
"hgnc_id": 25993,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.751C>T",
"hgvs_p": "p.Arg251Trp"
}
],
"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
}