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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: 5-446221-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=446221&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EXOC3",
"hgnc_id": 30378,
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_007277.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 37,
"alphamissense_prediction": null,
"alphamissense_score": 0.3241,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.18552371859550476,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 745,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2801,
"cdna_start": 187,
"cds_end": null,
"cds_length": 2238,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_007277.5",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000512944.6",
"protein_coding": true,
"protein_id": "NP_009208.2",
"strand": true,
"transcript": "NM_007277.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 745,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2801,
"cdna_start": 187,
"cds_end": null,
"cds_length": 2238,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000512944.6",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007277.5",
"protein_coding": true,
"protein_id": "ENSP00000425587.1",
"strand": true,
"transcript": "ENST00000512944.6",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 750,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2792,
"cdna_start": 157,
"cds_end": null,
"cds_length": 2253,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000866266.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536325.1",
"strand": true,
"transcript": "ENST00000866266.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 745,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2682,
"cdna_start": 73,
"cds_end": null,
"cds_length": 2238,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000315013.9",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000323377.5",
"strand": true,
"transcript": "ENST00000315013.9",
"transcript_support_level": 2
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 745,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3970,
"cdna_start": 225,
"cds_end": null,
"cds_length": 2238,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000929778.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599837.1",
"strand": true,
"transcript": "ENST00000929778.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 691,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2614,
"cdna_start": 167,
"cds_end": null,
"cds_length": 2076,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000941759.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611818.1",
"strand": true,
"transcript": "ENST00000941759.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 672,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2525,
"cdna_start": 139,
"cds_end": null,
"cds_length": 2019,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000929781.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599840.1",
"strand": true,
"transcript": "ENST00000929781.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 635,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2468,
"cdna_start": 190,
"cds_end": null,
"cds_length": 1908,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000929779.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599838.1",
"strand": true,
"transcript": "ENST00000929779.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 630,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2438,
"cdna_start": 169,
"cds_end": null,
"cds_length": 1893,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000866265.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536324.1",
"strand": true,
"transcript": "ENST00000866265.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 565,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2213,
"cdna_start": 132,
"cds_end": null,
"cds_length": 1698,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000929780.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599839.1",
"strand": true,
"transcript": "ENST00000929780.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 67,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 424,
"cdna_start": 234,
"cds_end": null,
"cds_length": 206,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000508022.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000422596.1",
"strand": true,
"transcript": "ENST00000508022.1",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 431,
"aa_ref": "R",
"aa_start": 6,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1565,
"cdna_start": 187,
"cds_end": null,
"cds_length": 1296,
"cds_start": 16,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047416683.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "c.16C>T",
"hgvs_p": "p.Arg6Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272639.1",
"strand": true,
"transcript": "XM_047416683.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 613,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000510441.1",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "n.188C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000510441.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5748,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000515601.6",
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"hgvs_c": "n.16C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424404.1",
"strand": true,
"transcript": "ENST00000515601.6",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376575084",
"effect": "missense_variant",
"frequency_reference_population": 0.00002292711,
"gene_hgnc_id": 30378,
"gene_symbol": "EXOC3",
"gnomad_exomes_ac": 32,
"gnomad_exomes_af": 0.0000218928,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328645,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.466,
"pos": 446221,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.196,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_007277.5"
}
]
}