← Back to variant description
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: 4-4862574-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=4862574&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 4862574,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000382723.5",
"consequences": [
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MSX1",
"gene_hgnc_id": 7391,
"hgvs_c": "c.470-127C>A",
"hgvs_p": null,
"transcript": "NM_002448.3",
"protein_id": "NP_002439.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 303,
"cds_start": -4,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1940,
"mane_select": "ENST00000382723.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MSX1",
"gene_hgnc_id": 7391,
"hgvs_c": "c.470-127C>A",
"hgvs_p": null,
"transcript": "ENST00000382723.5",
"protein_id": "ENSP00000372170.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 303,
"cds_start": -4,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1940,
"mane_select": "NM_002448.3",
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSX1",
"gene_hgnc_id": 7391,
"hgvs_c": "n.147C>A",
"hgvs_p": null,
"transcript": "ENST00000468421.1",
"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": 509,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000308455",
"gene_hgnc_id": null,
"hgvs_c": "n.304-5785G>T",
"hgvs_p": null,
"transcript": "ENST00000834195.1",
"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": 532,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000308455",
"gene_hgnc_id": null,
"hgvs_c": "n.48+5089G>T",
"hgvs_p": null,
"transcript": "ENST00000834196.1",
"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": 277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MSX1",
"gene_hgnc_id": 7391,
"dbsnp": "rs33946149",
"frequency_reference_population": 0.1451919,
"hom_count_reference_population": 12626,
"allele_count_reference_population": 163642,
"gnomad_exomes_af": 0.145642,
"gnomad_genomes_af": 0.142309,
"gnomad_exomes_ac": 141966,
"gnomad_genomes_ac": 21676,
"gnomad_exomes_homalt": 11025,
"gnomad_genomes_homalt": 1601,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04699999839067459,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.047,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.364,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000382723.5",
"gene_symbol": "MSX1",
"hgnc_id": 7391,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.470-127C>A",
"hgvs_p": null
},
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000834195.1",
"gene_symbol": "ENSG00000308455",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.304-5785G>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}