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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: 19-17360784-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17360784&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 17360784,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_031310.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.1228C>A",
"hgvs_p": "p.Pro410Thr",
"transcript": "NM_031310.3",
"protein_id": "NP_112600.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 442,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": "ENST00000252590.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_031310.3"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.1228C>A",
"hgvs_p": "p.Pro410Thr",
"transcript": "ENST00000252590.9",
"protein_id": "ENSP00000252590.3",
"transcript_support_level": 1,
"aa_start": 410,
"aa_end": null,
"aa_length": 442,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 1282,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": "NM_031310.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252590.9"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.1228C>A",
"hgvs_p": "p.Pro410Thr",
"transcript": "ENST00000962152.1",
"protein_id": "ENSP00000632211.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 466,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 2369,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962152.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.1222C>A",
"hgvs_p": "p.Pro408Thr",
"transcript": "ENST00000962153.1",
"protein_id": "ENSP00000632212.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 440,
"cds_start": 1222,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 1283,
"cdna_end": null,
"cdna_length": 2291,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962153.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.1207C>A",
"hgvs_p": "p.Pro403Thr",
"transcript": "ENST00000962154.1",
"protein_id": "ENSP00000632213.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 435,
"cds_start": 1207,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 1267,
"cdna_end": null,
"cdna_length": 2273,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962154.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.418C>A",
"hgvs_p": "p.Pro140Thr",
"transcript": "ENST00000962151.1",
"protein_id": "ENSP00000632210.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 172,
"cds_start": 418,
"cds_end": null,
"cds_length": 519,
"cdna_start": 486,
"cdna_end": null,
"cdna_length": 1492,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962151.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"hgvs_c": "c.78+5189C>A",
"hgvs_p": null,
"transcript": "ENST00000595816.1",
"protein_id": "ENSP00000469369.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 52,
"cds_start": null,
"cds_end": null,
"cds_length": 159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 272,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595816.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000269350",
"gene_hgnc_id": null,
"hgvs_c": "n.-148G>T",
"hgvs_p": null,
"transcript": "ENST00000597592.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 661,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000597592.1"
}
],
"gene_symbol": "PLVAP",
"gene_hgnc_id": 13635,
"dbsnp": "rs769449142",
"frequency_reference_population": 0.0000018589964,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000136842,
"gnomad_genomes_af": 0.00000656901,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3093855381011963,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.249,
"revel_prediction": "Benign",
"alphamissense_score": 0.0818,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.011,
"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_031310.3",
"gene_symbol": "PLVAP",
"hgnc_id": 13635,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1228C>A",
"hgvs_p": "p.Pro410Thr"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000597592.1",
"gene_symbol": "ENSG00000269350",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-148G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}