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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: 1-171103850-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=171103850&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 171103850,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000367755.9",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.198G>A",
"hgvs_p": "p.Met66Ile",
"transcript": "NM_001002294.3",
"protein_id": "NP_001002294.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 532,
"cds_start": 198,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 281,
"cdna_end": null,
"cdna_length": 2059,
"mane_select": "ENST00000367755.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.198G>A",
"hgvs_p": "p.Met66Ile",
"transcript": "ENST00000367755.9",
"protein_id": "ENSP00000356729.4",
"transcript_support_level": 1,
"aa_start": 66,
"aa_end": null,
"aa_length": 532,
"cds_start": 198,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 281,
"cdna_end": null,
"cdna_length": 2059,
"mane_select": "NM_001002294.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.198G>A",
"hgvs_p": "p.Met66Ile",
"transcript": "ENST00000479749.1",
"protein_id": "ENSP00000477451.1",
"transcript_support_level": 5,
"aa_start": 66,
"aa_end": null,
"aa_length": 217,
"cds_start": 198,
"cds_end": null,
"cds_length": 654,
"cdna_start": 267,
"cdna_end": null,
"cdna_length": 723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.198G>A",
"hgvs_p": "p.Met66Ile",
"transcript": "NM_006894.6",
"protein_id": "NP_008825.4",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 532,
"cds_start": 198,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 264,
"cdna_end": null,
"cdna_length": 2042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.138G>A",
"hgvs_p": "p.Met46Ile",
"transcript": "NM_001319173.2",
"protein_id": "NP_001306102.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 512,
"cds_start": 138,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 391,
"cdna_end": null,
"cdna_length": 2169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.138G>A",
"hgvs_p": "p.Met46Ile",
"transcript": "XM_047416207.1",
"protein_id": "XP_047272163.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 512,
"cds_start": 138,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 2317,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "n.*178G>A",
"hgvs_p": null,
"transcript": "ENST00000472784.5",
"protein_id": "ENSP00000476963.1",
"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": 582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "n.511G>A",
"hgvs_p": null,
"transcript": "ENST00000478457.1",
"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": 713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "n.*178G>A",
"hgvs_p": null,
"transcript": "ENST00000472784.5",
"protein_id": "ENSP00000476963.1",
"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": 582,
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"hgvs_c": "c.133-3825G>A",
"hgvs_p": null,
"transcript": "NM_001319174.2",
"protein_id": "NP_001306103.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 469,
"cds_start": -4,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000231424",
"gene_hgnc_id": 40240,
"hgvs_c": "n.542+64254C>T",
"hgvs_p": null,
"transcript": "ENST00000653116.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000231424",
"gene_hgnc_id": 40240,
"hgvs_c": "n.681+17900C>T",
"hgvs_p": null,
"transcript": "ENST00000664920.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000231424",
"gene_hgnc_id": 40240,
"hgvs_c": "n.533+64254C>T",
"hgvs_p": null,
"transcript": "ENST00000669750.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2208,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000231424",
"gene_hgnc_id": 40240,
"hgvs_c": "n.371+64254C>T",
"hgvs_p": null,
"transcript": "ENST00000670085.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FMO3",
"gene_hgnc_id": 3771,
"dbsnp": "rs72549323",
"frequency_reference_population": 6.841808e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84181e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9445434808731079,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.541,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8208,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.808,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1,PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PS1",
"PM2",
"PP3_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000367755.9",
"gene_symbol": "FMO3",
"hgnc_id": 3771,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.198G>A",
"hgvs_p": "p.Met66Ile"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000653116.1",
"gene_symbol": "ENSG00000231424",
"hgnc_id": 40240,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.542+64254C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}