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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: 19-45348003-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45348003&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 45348003,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000391946.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"hgvs_c": "c.622C>T",
"hgvs_p": "p.Arg208Trp",
"transcript": "NM_177417.3",
"protein_id": "NP_803136.2",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 504,
"cds_start": 622,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 727,
"cdna_end": null,
"cdna_length": 1782,
"mane_select": "ENST00000391946.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"hgvs_c": "c.622C>T",
"hgvs_p": "p.Arg208Trp",
"transcript": "ENST00000391946.7",
"protein_id": "ENSP00000375810.2",
"transcript_support_level": 1,
"aa_start": 208,
"aa_end": null,
"aa_length": 504,
"cds_start": 622,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 727,
"cdna_end": null,
"cdna_length": 1782,
"mane_select": "NM_177417.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"hgvs_c": "c.664C>T",
"hgvs_p": "p.Arg222Trp",
"transcript": "ENST00000470402.1",
"protein_id": "ENSP00000436019.1",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 518,
"cds_start": 664,
"cds_end": null,
"cds_length": 1557,
"cdna_start": 764,
"cdna_end": null,
"cdna_length": 1820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"hgvs_c": "c.619C>T",
"hgvs_p": "p.Arg207Trp",
"transcript": "ENST00000585434.5",
"protein_id": "ENSP00000466067.1",
"transcript_support_level": 1,
"aa_start": 207,
"aa_end": null,
"aa_length": 503,
"cds_start": 619,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 713,
"cdna_end": null,
"cdna_length": 1764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"hgvs_c": "c.622C>T",
"hgvs_p": "p.Arg208Trp",
"transcript": "ENST00000589373.5",
"protein_id": "ENSP00000465950.1",
"transcript_support_level": 5,
"aa_start": 208,
"aa_end": null,
"aa_length": 395,
"cds_start": 622,
"cds_end": null,
"cds_length": 1190,
"cdna_start": 1438,
"cdna_end": null,
"cdna_length": 2006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"hgvs_c": "c.574C>T",
"hgvs_p": "p.Arg192Trp",
"transcript": "ENST00000589837.5",
"protein_id": "ENSP00000466974.1",
"transcript_support_level": 5,
"aa_start": 192,
"aa_end": null,
"aa_length": 296,
"cds_start": 574,
"cds_end": null,
"cds_length": 892,
"cdna_start": 655,
"cdna_end": null,
"cdna_length": 973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KLC3",
"gene_hgnc_id": 20717,
"dbsnp": "rs367618092",
"frequency_reference_population": 0.000030456347,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000288326,
"gnomad_genomes_af": 0.000046,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7772281169891357,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.262,
"revel_prediction": "Benign",
"alphamissense_score": 0.8792,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.004,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000391946.7",
"gene_symbol": "KLC3",
"hgnc_id": 20717,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.622C>T",
"hgvs_p": "p.Arg208Trp"
}
],
"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
}