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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: 11-64599750-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=64599750&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 64599750,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000377574.6",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.1145A>T",
"hgvs_p": "p.Gln382Leu",
"transcript": "NM_144585.4",
"protein_id": "NP_653186.2",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 553,
"cds_start": 1145,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1482,
"cdna_end": null,
"cdna_length": 2792,
"mane_select": "ENST00000377574.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.1145A>T",
"hgvs_p": "p.Gln382Leu",
"transcript": "ENST00000377574.6",
"protein_id": "ENSP00000366797.1",
"transcript_support_level": 1,
"aa_start": 382,
"aa_end": null,
"aa_length": 553,
"cds_start": 1145,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1482,
"cdna_end": null,
"cdna_length": 2792,
"mane_select": "NM_144585.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.1043A>T",
"hgvs_p": "p.Gln348Leu",
"transcript": "ENST00000336464.7",
"protein_id": "ENSP00000336836.7",
"transcript_support_level": 1,
"aa_start": 348,
"aa_end": null,
"aa_length": 519,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1337,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.821A>T",
"hgvs_p": "p.Gln274Leu",
"transcript": "ENST00000377572.5",
"protein_id": "ENSP00000366795.1",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 445,
"cds_start": 821,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1568,
"cdna_end": null,
"cdna_length": 2887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.1043A>T",
"hgvs_p": "p.Gln348Leu",
"transcript": "NM_001276326.2",
"protein_id": "NP_001263255.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 519,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1380,
"cdna_end": null,
"cdna_length": 2690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.821A>T",
"hgvs_p": "p.Gln274Leu",
"transcript": "NM_001276327.2",
"protein_id": "NP_001263256.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 445,
"cds_start": 821,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1158,
"cdna_end": null,
"cdna_length": 2468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.821A>T",
"hgvs_p": "p.Gln274Leu",
"transcript": "ENST00000377567.6",
"protein_id": "ENSP00000366790.2",
"transcript_support_level": 5,
"aa_start": 274,
"aa_end": null,
"aa_length": 445,
"cds_start": 821,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1285,
"cdna_end": null,
"cdna_length": 2599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.482A>T",
"hgvs_p": "p.Gln161Leu",
"transcript": "NM_153378.3",
"protein_id": "NP_700357.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 332,
"cds_start": 482,
"cds_end": null,
"cds_length": 999,
"cdna_start": 1216,
"cdna_end": null,
"cdna_length": 2526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.482A>T",
"hgvs_p": "p.Gln161Leu",
"transcript": "ENST00000473690.5",
"protein_id": "ENSP00000438437.1",
"transcript_support_level": 2,
"aa_start": 161,
"aa_end": null,
"aa_length": 332,
"cds_start": 482,
"cds_end": null,
"cds_length": 999,
"cdna_start": 1208,
"cdna_end": null,
"cdna_length": 2522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.1220A>T",
"hgvs_p": "p.Gln407Leu",
"transcript": "XM_006718430.5",
"protein_id": "XP_006718493.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 578,
"cds_start": 1220,
"cds_end": null,
"cds_length": 1737,
"cdna_start": 1557,
"cdna_end": null,
"cdna_length": 2867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"hgvs_c": "c.1115A>T",
"hgvs_p": "p.Gln372Leu",
"transcript": "XM_006718431.5",
"protein_id": "XP_006718494.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 543,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1632,
"cdna_start": 1446,
"cdna_end": null,
"cdna_length": 2756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC22A12",
"gene_hgnc_id": 17989,
"dbsnp": "rs765990518",
"frequency_reference_population": 0.000030398267,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000287511,
"gnomad_genomes_af": 0.0000463202,
"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": 0.9044153690338135,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.616,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5273,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.731,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000377574.6",
"gene_symbol": "SLC22A12",
"hgnc_id": 17989,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1145A>T",
"hgvs_p": "p.Gln382Leu"
}
],
"clinvar_disease": "Dalmatian hypouricemia,Familial renal hypouricemia,SLC22A12-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:7",
"phenotype_combined": "Dalmatian hypouricemia|Familial renal hypouricemia|SLC22A12-related disorder|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}