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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: 2-108008651-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=108008651&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 108008651,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000264047.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "NM_021815.5",
"protein_id": "NP_068587.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 580,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1373,
"cdna_end": null,
"cdna_length": 5167,
"mane_select": "ENST00000264047.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "ENST00000264047.3",
"protein_id": "ENSP00000264047.2",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 580,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1373,
"cdna_end": null,
"cdna_length": 5167,
"mane_select": "NM_021815.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "ENST00000409059.5",
"protein_id": "ENSP00000387346.1",
"transcript_support_level": 1,
"aa_start": 361,
"aa_end": null,
"aa_length": 580,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1371,
"cdna_end": null,
"cdna_length": 2032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "NM_001305005.3",
"protein_id": "NP_001291934.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 580,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1370,
"cdna_end": null,
"cdna_length": 5164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.767G>A",
"hgvs_p": "p.Arg256Gln",
"transcript": "NM_001305006.3",
"protein_id": "NP_001291935.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 475,
"cds_start": 767,
"cds_end": null,
"cds_length": 1428,
"cdna_start": 1144,
"cdna_end": null,
"cdna_length": 4938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.341G>A",
"hgvs_p": "p.Arg114Gln",
"transcript": "NM_001305007.3",
"protein_id": "NP_001291936.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 333,
"cds_start": 341,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 1336,
"cdna_end": null,
"cdna_length": 5130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln",
"transcript": "XM_047445369.1",
"protein_id": "XP_047301325.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 580,
"cds_start": 1082,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1491,
"cdna_end": null,
"cdna_length": 5285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.968G>A",
"hgvs_p": "p.Arg323Gln",
"transcript": "XM_047445370.1",
"protein_id": "XP_047301326.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 542,
"cds_start": 968,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 5053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.830G>A",
"hgvs_p": "p.Arg277Gln",
"transcript": "XM_011511580.3",
"protein_id": "XP_011509882.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 496,
"cds_start": 830,
"cds_end": null,
"cds_length": 1491,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 4728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"hgvs_c": "c.767G>A",
"hgvs_p": "p.Arg256Gln",
"transcript": "XM_017004629.3",
"protein_id": "XP_016860118.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 475,
"cds_start": 767,
"cds_end": null,
"cds_length": 1428,
"cdna_start": 919,
"cdna_end": null,
"cdna_length": 4713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC5A7",
"gene_hgnc_id": 14025,
"dbsnp": "rs147656110",
"frequency_reference_population": 0.000004960133,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000479048,
"gnomad_genomes_af": 0.00000659509,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8224815130233765,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.734,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2399,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.917,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,PP5",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000264047.3",
"gene_symbol": "SLC5A7",
"hgnc_id": 14025,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361Gln"
}
],
"clinvar_disease": "Congenital myasthenic syndrome 20",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Congenital myasthenic syndrome 20",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}