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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: 20-763866-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=763866&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 763866,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000645534.1",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "NM_033409.4",
"protein_id": "NP_212134.3",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 2611,
"mane_select": "ENST00000645534.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "ENST00000645534.1",
"protein_id": "ENSP00000494193.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 2611,
"mane_select": "NM_033409.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "NM_001370085.1",
"protein_id": "NP_001357014.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 973,
"cdna_end": null,
"cdna_length": 2624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "NM_001370086.1",
"protein_id": "NP_001357015.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1482,
"cdna_end": null,
"cdna_length": 3133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "ENST00000217254.11",
"protein_id": "ENSP00000217254.7",
"transcript_support_level": 5,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1003,
"cdna_end": null,
"cdna_length": 2654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "ENST00000488495.3",
"protein_id": "ENSP00000494009.1",
"transcript_support_level": 3,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1469,
"cdna_end": null,
"cdna_length": 3106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "ENST00000381944.5",
"protein_id": "ENSP00000371370.3",
"transcript_support_level": 2,
"aa_start": 235,
"aa_end": null,
"aa_length": 415,
"cds_start": 705,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 1093,
"cdna_end": null,
"cdna_length": 3206,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "ENST00000675066.1",
"protein_id": "ENSP00000501902.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 364,
"cds_start": 705,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 884,
"cdna_end": null,
"cdna_length": 2674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "XM_024451821.1",
"protein_id": "XP_024307589.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 1004,
"cdna_end": null,
"cdna_length": 2655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "XM_047439867.1",
"protein_id": "XP_047295823.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 964,
"cdna_end": null,
"cdna_length": 2615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "XM_047439868.1",
"protein_id": "XP_047295824.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 469,
"cds_start": 705,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 964,
"cdna_end": null,
"cdna_length": 2615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.567+1342C>T",
"hgvs_p": null,
"transcript": "ENST00000473664.2",
"protein_id": "ENSP00000502741.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 336,
"cds_start": -4,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"hgvs_c": "c.*21C>T",
"hgvs_p": null,
"transcript": "ENST00000676154.1",
"protein_id": "ENSP00000501807.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": -4,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC52A3",
"gene_hgnc_id": 16187,
"dbsnp": "rs3746806",
"frequency_reference_population": 0.0018306781,
"hom_count_reference_population": 29,
"allele_count_reference_population": 2955,
"gnomad_exomes_af": 0.00101581,
"gnomad_genomes_af": 0.00965416,
"gnomad_exomes_ac": 1485,
"gnomad_genomes_ac": 1470,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 15,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.562,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000645534.1",
"gene_symbol": "SLC52A3",
"hgnc_id": 16187,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.705C>T",
"hgvs_p": "p.Leu235Leu"
}
],
"clinvar_disease": "Brown-Vialetto-van Laere syndrome 1,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "Brown-Vialetto-van Laere syndrome 1|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}