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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: 12-235092-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=235092&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 235092,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000343164.9",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.829C>G",
"hgvs_p": "p.Gln277Glu",
"transcript": "NM_016615.5",
"protein_id": "NP_057699.2",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 602,
"cds_start": 829,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": "ENST00000343164.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.829C>G",
"hgvs_p": "p.Gln277Glu",
"transcript": "ENST00000343164.9",
"protein_id": "ENSP00000339260.4",
"transcript_support_level": 1,
"aa_start": 277,
"aa_end": null,
"aa_length": 602,
"cds_start": 829,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": "NM_016615.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.553C>G",
"hgvs_p": "p.Gln185Glu",
"transcript": "NM_001190997.3",
"protein_id": "NP_001177926.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 510,
"cds_start": 553,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 606,
"cdna_end": null,
"cdna_length": 1912,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.553C>G",
"hgvs_p": "p.Gln185Glu",
"transcript": "ENST00000445055.6",
"protein_id": "ENSP00000407104.2",
"transcript_support_level": 2,
"aa_start": 185,
"aa_end": null,
"aa_length": 510,
"cds_start": 553,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 643,
"cdna_end": null,
"cdna_length": 1950,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.266C>G",
"hgvs_p": "p.Pro89Arg",
"transcript": "XM_017019842.2",
"protein_id": "XP_016875331.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 445,
"cds_start": 266,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 1779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.343C>G",
"hgvs_p": "p.Gln115Glu",
"transcript": "XM_047429420.1",
"protein_id": "XP_047285376.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 440,
"cds_start": 343,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 1916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.100C>G",
"hgvs_p": "p.Gln34Glu",
"transcript": "XM_006719008.4",
"protein_id": "XP_006719071.1",
"transcript_support_level": null,
"aa_start": 34,
"aa_end": null,
"aa_length": 359,
"cds_start": 100,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 1687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.100C>G",
"hgvs_p": "p.Gln34Glu",
"transcript": "XM_017019845.2",
"protein_id": "XP_016875334.1",
"transcript_support_level": null,
"aa_start": 34,
"aa_end": null,
"aa_length": 359,
"cds_start": 100,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 1607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "n.217C>G",
"hgvs_p": null,
"transcript": "ENST00000542379.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 340,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"hgvs_c": "c.*102C>G",
"hgvs_p": null,
"transcript": "ENST00000546319.5",
"protein_id": "ENSP00000444606.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": -4,
"cds_end": null,
"cds_length": 451,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC6A13",
"gene_hgnc_id": 11046,
"dbsnp": "rs1236167026",
"frequency_reference_population": 0.0000068150107,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000684064,
"gnomad_genomes_af": 0.00000656892,
"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": 0.4591395854949951,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10400000214576721,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.384,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0847,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.67,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0222795731051024,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000343164.9",
"gene_symbol": "SLC6A13",
"hgnc_id": 11046,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.829C>G",
"hgvs_p": "p.Gln277Glu"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}