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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-54467901-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=54467901&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 54467901,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004463.3",
"consequences": [
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln",
"transcript": "NM_004463.3",
"protein_id": "NP_004454.2",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 961,
"cds_start": 1223,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375135.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004463.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln",
"transcript": "ENST00000375135.4",
"protein_id": "ENSP00000364277.3",
"transcript_support_level": 1,
"aa_start": 408,
"aa_end": null,
"aa_length": 961,
"cds_start": 1223,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004463.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375135.4"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln",
"transcript": "ENST00000934021.1",
"protein_id": "ENSP00000604080.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 961,
"cds_start": 1223,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934021.1"
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln",
"transcript": "ENST00000934019.1",
"protein_id": "ENSP00000604078.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 960,
"cds_start": 1223,
"cds_end": null,
"cds_length": 2883,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934019.1"
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln",
"transcript": "ENST00000934020.1",
"protein_id": "ENSP00000604079.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 959,
"cds_start": 1223,
"cds_end": null,
"cds_length": 2880,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934020.1"
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln",
"transcript": "ENST00000934022.1",
"protein_id": "ENSP00000604081.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 907,
"cds_start": 1223,
"cds_end": null,
"cds_length": 2724,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934022.1"
}
],
"gene_symbol": "FGD1",
"gene_hgnc_id": 3663,
"dbsnp": "rs137853265",
"frequency_reference_population": 0.000021262318,
"hom_count_reference_population": 9,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000225599,
"gnomad_genomes_af": 0.00000893232,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8708391189575195,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.427,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1108,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.983,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004463.3",
"gene_symbol": "FGD1",
"hgnc_id": 3663,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,XL",
"hgvs_c": "c.1223G>A",
"hgvs_p": "p.Arg408Gln"
}
],
"clinvar_disease": "Aarskog syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Aarskog syndrome|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}