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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: 3-129586617-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129586617&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 129586617,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015103.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "NM_015103.3",
"protein_id": "NP_055918.3",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1925,
"cds_start": 1591,
"cds_end": null,
"cds_length": 5778,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000324093.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015103.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "ENST00000324093.9",
"protein_id": "ENSP00000317128.4",
"transcript_support_level": 1,
"aa_start": 531,
"aa_end": null,
"aa_length": 1925,
"cds_start": 1591,
"cds_end": null,
"cds_length": 5778,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015103.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324093.9"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "ENST00000891948.1",
"protein_id": "ENSP00000562007.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1845,
"cds_start": 1591,
"cds_end": null,
"cds_length": 5538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891948.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.280G>A",
"hgvs_p": "p.Gly94Ser",
"transcript": "ENST00000505237.2",
"protein_id": "ENSP00000426241.2",
"transcript_support_level": 5,
"aa_start": 94,
"aa_end": null,
"aa_length": 168,
"cds_start": 280,
"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": "ENST00000505237.2"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "XM_011512588.3",
"protein_id": "XP_011510890.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1894,
"cds_start": 1591,
"cds_end": null,
"cds_length": 5685,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512588.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "XM_011512589.2",
"protein_id": "XP_011510891.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1795,
"cds_start": 1591,
"cds_end": null,
"cds_length": 5388,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512589.2"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "XM_047447765.1",
"protein_id": "XP_047303721.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1728,
"cds_start": 1591,
"cds_end": null,
"cds_length": 5187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447765.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "XM_011512590.3",
"protein_id": "XP_011510892.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1467,
"cds_start": 1591,
"cds_end": null,
"cds_length": 4404,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512590.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser",
"transcript": "XM_047447766.1",
"protein_id": "XP_047303722.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 1007,
"cds_start": 1591,
"cds_end": null,
"cds_length": 3024,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447766.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "n.67G>A",
"hgvs_p": null,
"transcript": "ENST00000505665.5",
"protein_id": "ENSP00000423832.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000505665.5"
}
],
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"dbsnp": "rs2301572",
"frequency_reference_population": 0.041516382,
"hom_count_reference_population": 2174,
"allele_count_reference_population": 65334,
"gnomad_exomes_af": 0.0393169,
"gnomad_genomes_af": 0.0620638,
"gnomad_exomes_ac": 55890,
"gnomad_genomes_ac": 9444,
"gnomad_exomes_homalt": 1730,
"gnomad_genomes_homalt": 444,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0013563930988311768,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.052,
"revel_prediction": "Benign",
"alphamissense_score": 0.0608,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.174,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_015103.3",
"gene_symbol": "PLXND1",
"hgnc_id": 9107,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1591G>A",
"hgvs_p": "p.Gly531Ser"
}
],
"clinvar_disease": "PLXND1-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "PLXND1-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}