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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: 17-31859160-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=31859160&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 31859160,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018405.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Ala14Thr",
"transcript": "NM_018405.4",
"protein_id": "NP_060875.2",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 184,
"cds_start": 40,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000302362.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018405.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Ala14Thr",
"transcript": "ENST00000302362.11",
"protein_id": "ENSP00000304327.6",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 184,
"cds_start": 40,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018405.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000302362.11"
},
{
"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": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "n.40G>A",
"hgvs_p": null,
"transcript": "ENST00000496655.1",
"protein_id": "ENSP00000464423.1",
"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": "ENST00000496655.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "n.40G>A",
"hgvs_p": null,
"transcript": "ENST00000579984.1",
"protein_id": "ENSP00000464429.1",
"transcript_support_level": 3,
"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": "ENST00000579984.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "c.-340G>A",
"hgvs_p": null,
"transcript": "NM_001330176.2",
"protein_id": "NP_001317105.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330176.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "c.-340G>A",
"hgvs_p": null,
"transcript": "ENST00000378634.6",
"protein_id": "ENSP00000367901.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378634.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"hgvs_c": "c.-390G>A",
"hgvs_p": null,
"transcript": "ENST00000579741.1",
"protein_id": "ENSP00000464425.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 102,
"cds_start": null,
"cds_end": null,
"cds_length": 310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000579741.1"
}
],
"gene_symbol": "COPRS",
"gene_hgnc_id": 28848,
"dbsnp": "rs866914734",
"frequency_reference_population": 0.00003736893,
"hom_count_reference_population": 1,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000390647,
"gnomad_genomes_af": 0.0000268709,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08231908082962036,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.01,
"revel_prediction": "Benign",
"alphamissense_score": 0.1517,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.116,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_018405.4",
"gene_symbol": "COPRS",
"hgnc_id": 28848,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.40G>A",
"hgvs_p": "p.Ala14Thr"
}
],
"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
}