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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: 9-128371385-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128371385&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 128371385,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001135947.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "NM_030914.4",
"protein_id": "NP_112176.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 101,
"cds_start": 5,
"cds_end": null,
"cds_length": 306,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372853.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_030914.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000372853.9",
"protein_id": "ENSP00000361944.4",
"transcript_support_level": 1,
"aa_start": 2,
"aa_end": null,
"aa_length": 101,
"cds_start": 5,
"cds_end": null,
"cds_length": 306,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_030914.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372853.9"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000372850.5",
"protein_id": "ENSP00000361941.1",
"transcript_support_level": 1,
"aa_start": 2,
"aa_end": null,
"aa_length": 63,
"cds_start": 5,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372850.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000928501.1",
"protein_id": "ENSP00000598560.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 173,
"cds_start": 5,
"cds_end": null,
"cds_length": 522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928501.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "NM_001135947.2",
"protein_id": "NP_001129419.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 146,
"cds_start": 5,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001135947.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000483206.2",
"protein_id": "ENSP00000501135.1",
"transcript_support_level": 2,
"aa_start": 2,
"aa_end": null,
"aa_length": 146,
"cds_start": 5,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483206.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000899715.1",
"protein_id": "ENSP00000569774.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 144,
"cds_start": 5,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899715.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "NM_001265582.1",
"protein_id": "NP_001252511.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 63,
"cds_start": 5,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001265582.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val",
"transcript": "ENST00000372847.1",
"protein_id": "ENSP00000361938.1",
"transcript_support_level": 3,
"aa_start": 2,
"aa_end": null,
"aa_length": 63,
"cds_start": 5,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372847.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "n.5C>T",
"hgvs_p": null,
"transcript": "ENST00000470840.5",
"protein_id": "ENSP00000435186.1",
"transcript_support_level": 2,
"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": "ENST00000470840.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "URM1",
"gene_hgnc_id": 28378,
"hgvs_c": "n.12C>T",
"hgvs_p": null,
"transcript": "NR_049743.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_049743.2"
}
],
"gene_symbol": "URM1",
"gene_hgnc_id": 28378,
"dbsnp": "rs757588357",
"frequency_reference_population": 0.000032857213,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000157447,
"gnomad_genomes_af": 0.000197068,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 30,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23013383150100708,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.159,
"revel_prediction": "Benign",
"alphamissense_score": 0.4852,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.939,
"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": -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_001135947.2",
"gene_symbol": "URM1",
"hgnc_id": 28378,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5C>T",
"hgvs_p": "p.Ala2Val"
}
],
"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
}