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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: 3-140459539-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=140459539&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 140459539,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000458420.7",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLSTN2",
"gene_hgnc_id": 17448,
"hgvs_c": "c.992T>C",
"hgvs_p": "p.Ile331Thr",
"transcript": "NM_022131.3",
"protein_id": "NP_071414.2",
"transcript_support_level": null,
"aa_start": 331,
"aa_end": null,
"aa_length": 955,
"cds_start": 992,
"cds_end": null,
"cds_length": 2868,
"cdna_start": 1182,
"cdna_end": null,
"cdna_length": 14202,
"mane_select": "ENST00000458420.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLSTN2",
"gene_hgnc_id": 17448,
"hgvs_c": "c.992T>C",
"hgvs_p": "p.Ile331Thr",
"transcript": "ENST00000458420.7",
"protein_id": "ENSP00000402460.2",
"transcript_support_level": 1,
"aa_start": 331,
"aa_end": null,
"aa_length": 955,
"cds_start": 992,
"cds_end": null,
"cds_length": 2868,
"cdna_start": 1182,
"cdna_end": null,
"cdna_length": 14202,
"mane_select": "NM_022131.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLSTN2",
"gene_hgnc_id": 17448,
"hgvs_c": "c.917T>C",
"hgvs_p": "p.Ile306Thr",
"transcript": "XM_017007022.3",
"protein_id": "XP_016862511.1",
"transcript_support_level": null,
"aa_start": 306,
"aa_end": null,
"aa_length": 930,
"cds_start": 917,
"cds_end": null,
"cds_length": 2793,
"cdna_start": 1221,
"cdna_end": null,
"cdna_length": 14241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLSTN2",
"gene_hgnc_id": 17448,
"hgvs_c": "n.1180T>C",
"hgvs_p": null,
"transcript": "ENST00000511524.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000249290",
"gene_hgnc_id": null,
"hgvs_c": "n.100+713A>G",
"hgvs_p": null,
"transcript": "ENST00000503357.1",
"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": 478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC105374132",
"gene_hgnc_id": null,
"hgvs_c": "n.49-4786A>G",
"hgvs_p": null,
"transcript": "XR_007096117.1",
"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": 226,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLSTN2",
"gene_hgnc_id": 17448,
"dbsnp": "rs17348572",
"frequency_reference_population": 0.049445402,
"hom_count_reference_population": 2107,
"allele_count_reference_population": 79803,
"gnomad_exomes_af": 0.050447,
"gnomad_genomes_af": 0.0398292,
"gnomad_exomes_ac": 73739,
"gnomad_genomes_ac": 6064,
"gnomad_exomes_homalt": 1961,
"gnomad_genomes_homalt": 146,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.002151787281036377,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.045,
"revel_prediction": "Benign",
"alphamissense_score": 0.0808,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.615,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000458420.7",
"gene_symbol": "CLSTN2",
"hgnc_id": 17448,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.992T>C",
"hgvs_p": "p.Ile331Thr"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000503357.1",
"gene_symbol": "ENSG00000249290",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.100+713A>G",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_007096117.1",
"gene_symbol": "LOC105374132",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.49-4786A>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}