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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: 5-151521647-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=151521647&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 151521647,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000261800.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "NM_001447.3",
"protein_id": "NP_001438.1",
"transcript_support_level": null,
"aa_start": 3649,
"aa_end": null,
"aa_length": 4349,
"cds_start": 10946,
"cds_end": null,
"cds_length": 13050,
"cdna_start": 11133,
"cdna_end": null,
"cdna_length": 14710,
"mane_select": "ENST00000261800.6",
"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": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "ENST00000261800.6",
"protein_id": "ENSP00000261800.5",
"transcript_support_level": 1,
"aa_start": 3649,
"aa_end": null,
"aa_length": 4349,
"cds_start": 10946,
"cds_end": null,
"cds_length": 13050,
"cdna_start": 11133,
"cdna_end": null,
"cdna_length": 14710,
"mane_select": "NM_001447.3",
"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": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Arg507Gln",
"transcript": "ENST00000520200.5",
"protein_id": "ENSP00000429678.1",
"transcript_support_level": 1,
"aa_start": 507,
"aa_end": null,
"aa_length": 1121,
"cds_start": 1520,
"cds_end": null,
"cds_length": 3366,
"cdna_start": 1521,
"cdna_end": null,
"cdna_length": 4839,
"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": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "XM_011537600.3",
"protein_id": "XP_011535902.1",
"transcript_support_level": null,
"aa_start": 3649,
"aa_end": null,
"aa_length": 4349,
"cds_start": 10946,
"cds_end": null,
"cds_length": 13050,
"cdna_start": 11295,
"cdna_end": null,
"cdna_length": 14872,
"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": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "XM_011537603.2",
"protein_id": "XP_011535905.1",
"transcript_support_level": null,
"aa_start": 3649,
"aa_end": null,
"aa_length": 4349,
"cds_start": 10946,
"cds_end": null,
"cds_length": 13050,
"cdna_start": 11231,
"cdna_end": null,
"cdna_length": 14808,
"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": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "XM_017009224.2",
"protein_id": "XP_016864713.1",
"transcript_support_level": null,
"aa_start": 3649,
"aa_end": null,
"aa_length": 4349,
"cds_start": 10946,
"cds_end": null,
"cds_length": 13050,
"cdna_start": 11297,
"cdna_end": null,
"cdna_length": 14874,
"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": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "XM_017009225.2",
"protein_id": "XP_016864714.1",
"transcript_support_level": null,
"aa_start": 3649,
"aa_end": null,
"aa_length": 4349,
"cds_start": 10946,
"cds_end": null,
"cds_length": 13050,
"cdna_start": 11139,
"cdna_end": null,
"cdna_length": 14716,
"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": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln",
"transcript": "XM_047416934.1",
"protein_id": "XP_047272890.1",
"transcript_support_level": null,
"aa_start": 3649,
"aa_end": null,
"aa_length": 3886,
"cds_start": 10946,
"cds_end": null,
"cds_length": 11661,
"cdna_start": 11133,
"cdna_end": null,
"cdna_length": 12053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SLC36A1",
"gene_hgnc_id": 18761,
"hgvs_c": "c.1253-17606C>T",
"hgvs_p": null,
"transcript": "XM_047416925.1",
"protein_id": "XP_047272881.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 449,
"cds_start": -4,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SLC36A1",
"gene_hgnc_id": 18761,
"hgvs_c": "c.1253-17606C>T",
"hgvs_p": null,
"transcript": "XM_011537595.3",
"protein_id": "XP_011535897.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 447,
"cds_start": -4,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "SLC36A1",
"gene_hgnc_id": 18761,
"hgvs_c": "c.1160-17606C>T",
"hgvs_p": null,
"transcript": "XM_017009217.2",
"protein_id": "XP_016864706.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 418,
"cds_start": -4,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"dbsnp": "rs201335279",
"frequency_reference_population": 0.000010533334,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.00000889352,
"gnomad_genomes_af": 0.0000262836,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6521545052528381,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.282,
"revel_prediction": "Benign",
"alphamissense_score": 0.2161,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.021,
"phylop100way_prediction": "Uncertain_significance",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000261800.6",
"gene_symbol": "FAT2",
"hgnc_id": 3596,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.10946G>A",
"hgvs_p": "p.Arg3649Gln"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XM_047416925.1",
"gene_symbol": "SLC36A1",
"hgnc_id": 18761,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1253-17606C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Spinocerebellar ataxia 45",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Spinocerebellar ataxia 45",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}