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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: 1-161076355-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=161076355&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 161076355,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000368012.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln",
"transcript": "NM_030916.3",
"protein_id": "NP_112178.2",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 510,
"cds_start": 851,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": "ENST00000368012.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln",
"transcript": "ENST00000368012.4",
"protein_id": "ENSP00000356991.3",
"transcript_support_level": 1,
"aa_start": 284,
"aa_end": null,
"aa_length": 510,
"cds_start": 851,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": "NM_030916.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln",
"transcript": "XM_011510021.3",
"protein_id": "XP_011508323.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 511,
"cds_start": 851,
"cds_end": null,
"cds_length": 1536,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 3461,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln",
"transcript": "XM_011510022.3",
"protein_id": "XP_011508324.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 486,
"cds_start": 851,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 3386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln",
"transcript": "XM_005245508.4",
"protein_id": "XP_005245565.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 485,
"cds_start": 851,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln",
"transcript": "XM_047431288.1",
"protein_id": "XP_047287244.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 459,
"cds_start": 851,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 3525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NECTIN4",
"gene_hgnc_id": 19688,
"dbsnp": "rs267606991",
"frequency_reference_population": 0.000013137497,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131375,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.641638994216919,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9940000176429749,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.255,
"revel_prediction": "Benign",
"alphamissense_score": 0.3222,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.955,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.48,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.999985930335359,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000368012.4",
"gene_symbol": "NECTIN4",
"hgnc_id": 19688,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.851G>A",
"hgvs_p": "p.Arg284Gln"
}
],
"clinvar_disease": "Ectodermal dysplasia-syndactyly syndrome 1",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Ectodermal dysplasia-syndactyly syndrome 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}