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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: 19-17888397-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17888397&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 17888397,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000222248.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "c.1593C>T",
"hgvs_p": "p.Tyr531Tyr",
"transcript": "NM_000453.3",
"protein_id": "NP_000444.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 643,
"cds_start": 1593,
"cds_end": null,
"cds_length": 1932,
"cdna_start": 1968,
"cdna_end": null,
"cdna_length": 3604,
"mane_select": "ENST00000222248.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "c.1593C>T",
"hgvs_p": "p.Tyr531Tyr",
"transcript": "ENST00000222248.4",
"protein_id": "ENSP00000222248.2",
"transcript_support_level": 1,
"aa_start": 531,
"aa_end": null,
"aa_length": 643,
"cds_start": 1593,
"cds_end": null,
"cds_length": 1932,
"cdna_start": 1968,
"cdna_end": null,
"cdna_length": 3604,
"mane_select": "NM_000453.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "c.1326C>T",
"hgvs_p": "p.Tyr442Tyr",
"transcript": "NM_001440707.1",
"protein_id": "NP_001427636.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 554,
"cds_start": 1326,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 1476,
"cdna_end": null,
"cdna_length": 3112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "c.1626C>T",
"hgvs_p": "p.Tyr542Tyr",
"transcript": "XM_011528192.3",
"protein_id": "XP_011526494.1",
"transcript_support_level": null,
"aa_start": 542,
"aa_end": null,
"aa_length": 654,
"cds_start": 1626,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 2001,
"cdna_end": null,
"cdna_length": 3637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "c.1359C>T",
"hgvs_p": "p.Tyr453Tyr",
"transcript": "XM_011528193.4",
"protein_id": "XP_011526495.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 565,
"cds_start": 1359,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1509,
"cdna_end": null,
"cdna_length": 3145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "c.1260C>T",
"hgvs_p": "p.Tyr420Tyr",
"transcript": "XM_011528194.4",
"protein_id": "XP_011526496.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 532,
"cds_start": 1260,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 1461,
"cdna_end": null,
"cdna_length": 3097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"hgvs_c": "n.*19C>T",
"hgvs_p": null,
"transcript": "ENST00000597109.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC5A5",
"gene_hgnc_id": 11040,
"dbsnp": "rs121909177",
"frequency_reference_population": 0.00001982954,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000171033,
"gnomad_genomes_af": 0.0000460393,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5899999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.031,
"phylop100way_prediction": "Benign",
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000222248.4",
"gene_symbol": "SLC5A5",
"hgnc_id": 11040,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1593C>T",
"hgvs_p": "p.Tyr531Tyr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}