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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: X-132082456-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=132082456&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 132082456,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_194277.3",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.812G>A",
"hgvs_p": "p.Cys271Tyr",
"transcript": "NM_194277.3",
"protein_id": "NP_919253.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 714,
"cds_start": 812,
"cds_end": null,
"cds_length": 2145,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000298542.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_194277.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.812G>A",
"hgvs_p": "p.Cys271Tyr",
"transcript": "ENST00000298542.9",
"protein_id": "ENSP00000298542.3",
"transcript_support_level": 1,
"aa_start": 271,
"aa_end": null,
"aa_length": 714,
"cds_start": 812,
"cds_end": null,
"cds_length": 2145,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_194277.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298542.9"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.767G>A",
"hgvs_p": "p.Cys256Tyr",
"transcript": "ENST00000464296.1",
"protein_id": "ENSP00000417996.1",
"transcript_support_level": 1,
"aa_start": 256,
"aa_end": null,
"aa_length": 699,
"cds_start": 767,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000464296.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.452G>A",
"hgvs_p": "p.Cys151Tyr",
"transcript": "ENST00000370879.5",
"protein_id": "ENSP00000359916.1",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 594,
"cds_start": 452,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370879.5"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.767G>A",
"hgvs_p": "p.Cys256Tyr",
"transcript": "NM_001306193.2",
"protein_id": "NP_001293122.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 699,
"cds_start": 767,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001306193.2"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.764G>A",
"hgvs_p": "p.Cys255Tyr",
"transcript": "XM_017029947.3",
"protein_id": "XP_016885436.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 698,
"cds_start": 764,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029947.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.557G>A",
"hgvs_p": "p.Cys186Tyr",
"transcript": "XM_017029948.3",
"protein_id": "XP_016885437.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 629,
"cds_start": 557,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029948.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"hgvs_c": "c.338G>A",
"hgvs_p": "p.Cys113Tyr",
"transcript": "XM_017029949.3",
"protein_id": "XP_016885438.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 556,
"cds_start": 338,
"cds_end": null,
"cds_length": 1671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029949.3"
}
],
"gene_symbol": "FRMD7",
"gene_hgnc_id": 8079,
"dbsnp": "rs387906721",
"frequency_reference_population": 9.1233636e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.12336e-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": 0.987966775894165,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.959,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9985,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.64,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_194277.3",
"gene_symbol": "FRMD7",
"hgnc_id": 8079,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.812G>A",
"hgvs_p": "p.Cys271Tyr"
}
],
"clinvar_disease": " X-linked, congenital,Nystagmus 1",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Nystagmus 1, congenital, X-linked",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}