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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: 20-46560194-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=46560194&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 46560194,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000279027.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1637G>A",
"hgvs_p": "p.Arg546Gln",
"transcript": "NM_022829.6",
"protein_id": "NP_073740.2",
"transcript_support_level": null,
"aa_start": 546,
"aa_end": null,
"aa_length": 602,
"cds_start": 1637,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 1675,
"cdna_end": null,
"cdna_length": 4041,
"mane_select": "ENST00000279027.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1637G>A",
"hgvs_p": "p.Arg546Gln",
"transcript": "ENST00000279027.9",
"protein_id": "ENSP00000279027.4",
"transcript_support_level": 1,
"aa_start": 546,
"aa_end": null,
"aa_length": 602,
"cds_start": 1637,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 1675,
"cdna_end": null,
"cdna_length": 4041,
"mane_select": "NM_022829.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1496G>A",
"hgvs_p": "p.Arg499Gln",
"transcript": "ENST00000495082.5",
"protein_id": "ENSP00000419621.1",
"transcript_support_level": 1,
"aa_start": 499,
"aa_end": null,
"aa_length": 555,
"cds_start": 1496,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1687,
"cdna_end": null,
"cdna_length": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1496G>A",
"hgvs_p": "p.Arg499Gln",
"transcript": "NM_001011554.3",
"protein_id": "NP_001011554.1",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 555,
"cds_start": 1496,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1713,
"cdna_end": null,
"cdna_length": 4079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1496G>A",
"hgvs_p": "p.Arg499Gln",
"transcript": "ENST00000290317.9",
"protein_id": "ENSP00000290317.5",
"transcript_support_level": 5,
"aa_start": 499,
"aa_end": null,
"aa_length": 555,
"cds_start": 1496,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1623,
"cdna_end": null,
"cdna_length": 3994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1487G>A",
"hgvs_p": "p.Arg496Gln",
"transcript": "NM_001193339.2",
"protein_id": "NP_001180268.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 552,
"cds_start": 1487,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1525,
"cdna_end": null,
"cdna_length": 3891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1487G>A",
"hgvs_p": "p.Arg496Gln",
"transcript": "ENST00000413164.6",
"protein_id": "ENSP00000415852.2",
"transcript_support_level": 2,
"aa_start": 496,
"aa_end": null,
"aa_length": 552,
"cds_start": 1487,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1525,
"cdna_end": null,
"cdna_length": 2008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1391G>A",
"hgvs_p": "p.Arg464Gln",
"transcript": "NM_001193340.2",
"protein_id": "NP_001180269.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 520,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1608,
"cdna_end": null,
"cdna_length": 3974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1391G>A",
"hgvs_p": "p.Arg464Gln",
"transcript": "ENST00000472148.5",
"protein_id": "ENSP00000420177.1",
"transcript_support_level": 5,
"aa_start": 464,
"aa_end": null,
"aa_length": 520,
"cds_start": 1391,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1518,
"cdna_end": null,
"cdna_length": 3283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"hgvs_c": "c.1343G>A",
"hgvs_p": "p.Arg448Gln",
"transcript": "NM_001193342.2",
"protein_id": "NP_001180271.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 504,
"cds_start": 1343,
"cds_end": null,
"cds_length": 1515,
"cdna_start": 1502,
"cdna_end": null,
"cdna_length": 3868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC13A3",
"gene_hgnc_id": 14430,
"dbsnp": "rs188700676",
"frequency_reference_population": 0.00016914394,
"hom_count_reference_population": 0,
"allele_count_reference_population": 273,
"gnomad_exomes_af": 0.00017171,
"gnomad_genomes_af": 0.000144505,
"gnomad_exomes_ac": 251,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03153678774833679,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.252,
"revel_prediction": "Benign",
"alphamissense_score": 0.1101,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.976,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000279027.9",
"gene_symbol": "SLC13A3",
"hgnc_id": 14430,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1637G>A",
"hgvs_p": "p.Arg546Gln"
}
],
"clinvar_disease": " acute reversible, with increased urinary alpha-ketoglutarate,Leukoencephalopathy,Prostate cancer,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Prostate cancer|not provided|Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}