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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: 3-129556323-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=129556323&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 129556323,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_015103.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.5767A>G",
"hgvs_p": "p.Ser1923Gly",
"transcript": "NM_015103.3",
"protein_id": "NP_055918.3",
"transcript_support_level": null,
"aa_start": 1923,
"aa_end": null,
"aa_length": 1925,
"cds_start": 5767,
"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": "S",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.5767A>G",
"hgvs_p": "p.Ser1923Gly",
"transcript": "ENST00000324093.9",
"protein_id": "ENSP00000317128.4",
"transcript_support_level": 1,
"aa_start": 1923,
"aa_end": null,
"aa_length": 1925,
"cds_start": 5767,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "n.524A>G",
"hgvs_p": null,
"transcript": "ENST00000501038.6",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000501038.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "n.592A>G",
"hgvs_p": null,
"transcript": "ENST00000504524.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000504524.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "n.*416A>G",
"hgvs_p": null,
"transcript": "ENST00000512744.5",
"protein_id": "ENSP00000426540.1",
"transcript_support_level": 1,
"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": "ENST00000512744.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "n.*416A>G",
"hgvs_p": null,
"transcript": "ENST00000512744.5",
"protein_id": "ENSP00000426540.1",
"transcript_support_level": 1,
"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": "ENST00000512744.5"
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.5527A>G",
"hgvs_p": "p.Ser1843Gly",
"transcript": "ENST00000891948.1",
"protein_id": "ENSP00000562007.1",
"transcript_support_level": null,
"aa_start": 1843,
"aa_end": null,
"aa_length": 1845,
"cds_start": 5527,
"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": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.5377A>G",
"hgvs_p": "p.Ser1793Gly",
"transcript": "XM_011512589.2",
"protein_id": "XP_011510891.1",
"transcript_support_level": null,
"aa_start": 1793,
"aa_end": null,
"aa_length": 1795,
"cds_start": 5377,
"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": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.2935A>G",
"hgvs_p": "p.Ser979Gly",
"transcript": "XM_011512592.1",
"protein_id": "XP_011510894.1",
"transcript_support_level": null,
"aa_start": 979,
"aa_end": null,
"aa_length": 981,
"cds_start": 2935,
"cds_end": null,
"cds_length": 2946,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512592.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.*124A>G",
"hgvs_p": null,
"transcript": "XM_011512588.3",
"protein_id": "XP_011510890.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1894,
"cds_start": null,
"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": 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": "PLXND1",
"gene_hgnc_id": 9107,
"hgvs_c": "c.129+294A>G",
"hgvs_p": null,
"transcript": "ENST00000504689.1",
"protein_id": "ENSP00000426162.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 55,
"cds_start": null,
"cds_end": null,
"cds_length": 168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504689.1"
}
],
"gene_symbol": "PLXND1",
"gene_hgnc_id": 9107,
"dbsnp": "rs149917682",
"frequency_reference_population": 0.00006897169,
"hom_count_reference_population": 0,
"allele_count_reference_population": 111,
"gnomad_exomes_af": 0.0000686287,
"gnomad_genomes_af": 0.0000722543,
"gnomad_exomes_ac": 100,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.34541797637939453,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.49000000953674316,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.139,
"revel_prediction": "Benign",
"alphamissense_score": 0.169,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.912,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.49,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_015103.3",
"gene_symbol": "PLXND1",
"hgnc_id": 9107,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.5767A>G",
"hgvs_p": "p.Ser1923Gly"
}
],
"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
}