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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: 11-20628056-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=20628056&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 20628056,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000525748.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.1472A>G",
"hgvs_p": "p.Tyr491Cys",
"transcript": "NM_004211.5",
"protein_id": "NP_004202.4",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 797,
"cds_start": 1472,
"cds_end": null,
"cds_length": 2394,
"cdna_start": 1537,
"cdna_end": null,
"cdna_length": 6876,
"mane_select": "ENST00000525748.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.1472A>G",
"hgvs_p": "p.Tyr491Cys",
"transcript": "ENST00000525748.6",
"protein_id": "ENSP00000434364.2",
"transcript_support_level": 1,
"aa_start": 491,
"aa_end": null,
"aa_length": 797,
"cds_start": 1472,
"cds_end": null,
"cds_length": 2394,
"cdna_start": 1537,
"cdna_end": null,
"cdna_length": 6876,
"mane_select": "NM_004211.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.*769A>G",
"hgvs_p": null,
"transcript": "ENST00000298923.11",
"protein_id": "ENSP00000298923.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.*769A>G",
"hgvs_p": null,
"transcript": "ENST00000298923.11",
"protein_id": "ENSP00000298923.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.770A>G",
"hgvs_p": "p.Tyr257Cys",
"transcript": "NM_001318369.2",
"protein_id": "NP_001305298.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 563,
"cds_start": 770,
"cds_end": null,
"cds_length": 1692,
"cdna_start": 1398,
"cdna_end": null,
"cdna_length": 6737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.596A>G",
"hgvs_p": "p.Tyr199Cys",
"transcript": "XM_017018544.3",
"protein_id": "XP_016874033.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 505,
"cds_start": 596,
"cds_end": null,
"cds_length": 1518,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 6015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297872",
"gene_hgnc_id": null,
"hgvs_c": "n.241T>C",
"hgvs_p": null,
"transcript": "ENST00000751475.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.850A>G",
"hgvs_p": null,
"transcript": "XR_007062528.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3927,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"dbsnp": "rs121908494",
"frequency_reference_population": 0.00001796865,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000164183,
"gnomad_genomes_af": 0.000032864,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9913111925125122,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.954,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9953,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.321,
"phylop100way_prediction": "Pathogenic",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000525748.6",
"gene_symbol": "SLC6A5",
"hgnc_id": 11051,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1472A>G",
"hgvs_p": "p.Tyr491Cys"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000751475.1",
"gene_symbol": "ENSG00000297872",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.241T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hyperekplexia 3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Hyperekplexia 3",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}