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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: 11-119639934-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=119639934&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 119639934,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_203285.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN1",
"gene_hgnc_id": 9706,
"hgvs_c": "n.1082T>G",
"hgvs_p": null,
"transcript": "ENST00000341398.6",
"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": "ENST00000341398.6"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN1",
"gene_hgnc_id": 9706,
"hgvs_c": "c.1082T>G",
"hgvs_p": "p.Val361Gly",
"transcript": "ENST00000531468.2",
"protein_id": "ENSP00000513010.1",
"transcript_support_level": 3,
"aa_start": 361,
"aa_end": null,
"aa_length": 493,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000531468.2"
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN1",
"gene_hgnc_id": 9706,
"hgvs_c": "c.1082T>G",
"hgvs_p": "p.Val361Gly",
"transcript": "NM_203285.2",
"protein_id": "NP_976030.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 458,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_203285.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP2-AS1",
"gene_hgnc_id": 48673,
"hgvs_c": "n.953A>C",
"hgvs_p": null,
"transcript": "ENST00000706364.1",
"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": "ENST00000706364.1"
},
{
"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": 4,
"intron_rank_end": null,
"gene_symbol": "USP2-AS1",
"gene_hgnc_id": 48673,
"hgvs_c": "n.574-14089A>C",
"hgvs_p": null,
"transcript": "ENST00000706418.1",
"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": "ENST00000706418.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "USP2-AS1",
"gene_hgnc_id": 48673,
"hgvs_c": "n.129+2906A>C",
"hgvs_p": null,
"transcript": "ENST00000706430.1",
"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": "ENST00000706430.1"
}
],
"gene_symbol": "NECTIN1",
"gene_hgnc_id": 9706,
"dbsnp": "rs7940667",
"frequency_reference_population": 0.9203811,
"hom_count_reference_population": 685633,
"allele_count_reference_population": 1485543,
"gnomad_exomes_af": 0.925506,
"gnomad_genomes_af": 0.871164,
"gnomad_exomes_ac": 1352931,
"gnomad_genomes_ac": 132612,
"gnomad_exomes_homalt": 627170,
"gnomad_genomes_homalt": 58463,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000003309156227260246,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.088,
"revel_prediction": "Benign",
"alphamissense_score": 0.0765,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.354,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_203285.2",
"gene_symbol": "NECTIN1",
"hgnc_id": 9706,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1082T>G",
"hgvs_p": "p.Val361Gly"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000706364.1",
"gene_symbol": "USP2-AS1",
"hgnc_id": 48673,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.953A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Cleft lip/palate-ectodermal dysplasia syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Cleft lip/palate-ectodermal dysplasia syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}