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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: 12-14613124-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=14613124&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 14613124,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004963.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GUCY2C",
"gene_hgnc_id": 4688,
"hgvs_c": "c.3215A>G",
"hgvs_p": "p.Tyr1072Cys",
"transcript": "NM_004963.4",
"protein_id": "NP_004954.2",
"transcript_support_level": null,
"aa_start": 1072,
"aa_end": null,
"aa_length": 1073,
"cds_start": 3215,
"cds_end": null,
"cds_length": 3222,
"cdna_start": 3366,
"cdna_end": null,
"cdna_length": 3858,
"mane_select": "ENST00000261170.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GUCY2C",
"gene_hgnc_id": 4688,
"hgvs_c": "c.3215A>G",
"hgvs_p": "p.Tyr1072Cys",
"transcript": "ENST00000261170.5",
"protein_id": "ENSP00000261170.3",
"transcript_support_level": 1,
"aa_start": 1072,
"aa_end": null,
"aa_length": 1073,
"cds_start": 3215,
"cds_end": null,
"cds_length": 3222,
"cdna_start": 3366,
"cdna_end": null,
"cdna_length": 3858,
"mane_select": "NM_004963.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GUCY2C",
"gene_hgnc_id": 4688,
"hgvs_c": "c.2969A>G",
"hgvs_p": "p.Tyr990Cys",
"transcript": "XM_011520631.3",
"protein_id": "XP_011518933.1",
"transcript_support_level": null,
"aa_start": 990,
"aa_end": null,
"aa_length": 991,
"cds_start": 2969,
"cds_end": null,
"cds_length": 2976,
"cdna_start": 3224,
"cdna_end": null,
"cdna_length": 3716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLBD1-AS1",
"gene_hgnc_id": 51143,
"hgvs_c": "n.848+198T>C",
"hgvs_p": null,
"transcript": "ENST00000542401.2",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLBD1-AS1",
"gene_hgnc_id": 51143,
"hgvs_c": "n.279+198T>C",
"hgvs_p": null,
"transcript": "ENST00000545424.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLBD1-AS1",
"gene_hgnc_id": 51143,
"hgvs_c": "n.732-6028T>C",
"hgvs_p": null,
"transcript": "ENST00000660979.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLBD1-AS1",
"gene_hgnc_id": 51143,
"hgvs_c": "n.160+89T>C",
"hgvs_p": null,
"transcript": "ENST00000746767.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 208,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLBD1-AS1",
"gene_hgnc_id": 51143,
"hgvs_c": "n.297+198T>C",
"hgvs_p": null,
"transcript": "NR_120465.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GUCY2C",
"gene_hgnc_id": 4688,
"dbsnp": "rs35179392",
"frequency_reference_population": 0.00016741778,
"hom_count_reference_population": 2,
"allele_count_reference_population": 270,
"gnomad_exomes_af": 0.000148586,
"gnomad_genomes_af": 0.000347997,
"gnomad_exomes_ac": 217,
"gnomad_genomes_ac": 53,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01121559739112854,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.567,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0628,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.49,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004963.4",
"gene_symbol": "GUCY2C",
"hgnc_id": 4688,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3215A>G",
"hgvs_p": "p.Tyr1072Cys"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000545424.5",
"gene_symbol": "PLBD1-AS1",
"hgnc_id": 51143,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.279+198T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}