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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: 11-20638502-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=20638502&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 20638502,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004211.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.1913C>T",
"hgvs_p": "p.Ser638Phe",
"transcript": "NM_004211.5",
"protein_id": "NP_004202.4",
"transcript_support_level": null,
"aa_start": 638,
"aa_end": null,
"aa_length": 797,
"cds_start": 1913,
"cds_end": null,
"cds_length": 2394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000525748.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004211.5"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.1913C>T",
"hgvs_p": "p.Ser638Phe",
"transcript": "ENST00000525748.6",
"protein_id": "ENSP00000434364.2",
"transcript_support_level": 1,
"aa_start": 638,
"aa_end": null,
"aa_length": 797,
"cds_start": 1913,
"cds_end": null,
"cds_length": 2394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004211.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000525748.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.*1210C>T",
"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": 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": "ENST00000298923.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.*1210C>T",
"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": 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": "ENST00000298923.11"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.1211C>T",
"hgvs_p": "p.Ser404Phe",
"transcript": "NM_001318369.2",
"protein_id": "NP_001305298.1",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 563,
"cds_start": 1211,
"cds_end": null,
"cds_length": 1692,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318369.2"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "c.1037C>T",
"hgvs_p": "p.Ser346Phe",
"transcript": "XM_017018544.3",
"protein_id": "XP_016874033.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 505,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018544.3"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.444C>T",
"hgvs_p": null,
"transcript": "ENST00000528440.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000528440.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"hgvs_c": "n.1291C>T",
"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": 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": "XR_007062528.1"
}
],
"gene_symbol": "SLC6A5",
"gene_hgnc_id": 11051,
"dbsnp": "rs753023936",
"frequency_reference_population": 0.0000068172576,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000684276,
"gnomad_genomes_af": 0.00000657229,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8760322332382202,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.602,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9847,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.599,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004211.5",
"gene_symbol": "SLC6A5",
"hgnc_id": 11051,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1913C>T",
"hgvs_p": "p.Ser638Phe"
}
],
"clinvar_disease": "Hyperekplexia 3,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Hyperekplexia 3|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}