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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: 10-13656719-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=13656719&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 13656719,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018027.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"hgvs_c": "c.2870C>T",
"hgvs_p": "p.Ser957Leu",
"transcript": "NM_018027.5",
"protein_id": "NP_060497.3",
"transcript_support_level": null,
"aa_start": 957,
"aa_end": null,
"aa_length": 1039,
"cds_start": 2870,
"cds_end": null,
"cds_length": 3120,
"cdna_start": 3279,
"cdna_end": null,
"cdna_length": 6861,
"mane_select": "ENST00000357447.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"hgvs_c": "c.2870C>T",
"hgvs_p": "p.Ser957Leu",
"transcript": "ENST00000357447.7",
"protein_id": "ENSP00000350032.2",
"transcript_support_level": 1,
"aa_start": 957,
"aa_end": null,
"aa_length": 1039,
"cds_start": 2870,
"cds_end": null,
"cds_length": 3120,
"cdna_start": 3279,
"cdna_end": null,
"cdna_length": 6861,
"mane_select": "NM_018027.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"hgvs_c": "c.2969C>T",
"hgvs_p": "p.Ser990Leu",
"transcript": "NM_001318337.2",
"protein_id": "NP_001305266.1",
"transcript_support_level": null,
"aa_start": 990,
"aa_end": null,
"aa_length": 1072,
"cds_start": 2969,
"cds_end": null,
"cds_length": 3219,
"cdna_start": 3066,
"cdna_end": null,
"cdna_length": 6648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"hgvs_c": "c.2918C>T",
"hgvs_p": "p.Ser973Leu",
"transcript": "NM_001318336.2",
"protein_id": "NP_001305265.1",
"transcript_support_level": null,
"aa_start": 973,
"aa_end": null,
"aa_length": 1055,
"cds_start": 2918,
"cds_end": null,
"cds_length": 3168,
"cdna_start": 3316,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"hgvs_c": "c.2870C>T",
"hgvs_p": "p.Ser957Leu",
"transcript": "ENST00000495956.3",
"protein_id": "ENSP00000488764.2",
"transcript_support_level": 2,
"aa_start": 957,
"aa_end": null,
"aa_length": 1050,
"cds_start": 2870,
"cds_end": null,
"cds_length": 3153,
"cdna_start": 3307,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"hgvs_c": "c.1943C>T",
"hgvs_p": "p.Ser648Leu",
"transcript": "NM_001318338.2",
"protein_id": "NP_001305267.1",
"transcript_support_level": null,
"aa_start": 648,
"aa_end": null,
"aa_length": 730,
"cds_start": 1943,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 2333,
"cdna_end": null,
"cdna_length": 5915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRPF18",
"gene_hgnc_id": 17351,
"hgvs_c": "n.47+8489G>A",
"hgvs_p": null,
"transcript": "ENST00000593351.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FRMD4A",
"gene_hgnc_id": 25491,
"dbsnp": "rs143274194",
"frequency_reference_population": 0.000032734377,
"hom_count_reference_population": 0,
"allele_count_reference_population": 52,
"gnomad_exomes_af": 0.0000341148,
"gnomad_genomes_af": 0.0000197088,
"gnomad_exomes_ac": 49,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5071216225624084,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.486,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.121,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.417,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_018027.5",
"gene_symbol": "FRMD4A",
"hgnc_id": 25491,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2870C>T",
"hgvs_p": "p.Ser957Leu"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000593351.2",
"gene_symbol": "PRPF18",
"hgnc_id": 17351,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.47+8489G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}