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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: 21-42486428-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=42486428&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 42486428,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000291536.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Gly103Asp",
"transcript": "NM_080860.4",
"protein_id": "NP_543136.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 309,
"cds_start": 308,
"cds_end": null,
"cds_length": 930,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 1300,
"mane_select": "ENST00000291536.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Gly103Asp",
"transcript": "ENST00000291536.8",
"protein_id": "ENSP00000291536.3",
"transcript_support_level": 1,
"aa_start": 103,
"aa_end": null,
"aa_length": 309,
"cds_start": 308,
"cds_end": null,
"cds_length": 930,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 1300,
"mane_select": "NM_080860.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.194G>A",
"hgvs_p": "p.Gly65Asp",
"transcript": "NM_001286506.2",
"protein_id": "NP_001273435.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 271,
"cds_start": 194,
"cds_end": null,
"cds_length": 816,
"cdna_start": 232,
"cdna_end": null,
"cdna_length": 1186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.194G>A",
"hgvs_p": "p.Gly65Asp",
"transcript": "ENST00000398352.3",
"protein_id": "ENSP00000381395.3",
"transcript_support_level": 5,
"aa_start": 65,
"aa_end": null,
"aa_length": 271,
"cds_start": 194,
"cds_end": null,
"cds_length": 816,
"cdna_start": 194,
"cdna_end": null,
"cdna_length": 937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Gly103Asp",
"transcript": "XM_011529786.2",
"protein_id": "XP_011528088.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 285,
"cds_start": 308,
"cds_end": null,
"cds_length": 858,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 1228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "c.101G>A",
"hgvs_p": "p.Gly34Asp",
"transcript": "XM_005261208.3",
"protein_id": "XP_005261265.1",
"transcript_support_level": null,
"aa_start": 34,
"aa_end": null,
"aa_length": 240,
"cds_start": 101,
"cds_end": null,
"cds_length": 723,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 1093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"hgvs_c": "n.368G>A",
"hgvs_p": null,
"transcript": "ENST00000493019.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RSPH1",
"gene_hgnc_id": 12371,
"dbsnp": "rs587777060",
"frequency_reference_population": 0.000008674295,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000889336,
"gnomad_genomes_af": 0.0000065703,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9940786957740784,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.891,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9954,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.71,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000291536.8",
"gene_symbol": "RSPH1",
"hgnc_id": 12371,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.308G>A",
"hgvs_p": "p.Gly103Asp"
}
],
"clinvar_disease": "Primary ciliary dyskinesia 24,RSPH1-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Primary ciliary dyskinesia 24|RSPH1-related disorder",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}