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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: 1-52414845-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=52414845&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRPF38A",
"hgnc_id": 25930,
"hgvs_c": "c.833G>A",
"hgvs_p": "p.Arg278His",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_032864.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"intron_variant"
],
"gene_symbol": "TUT4",
"hgnc_id": 28981,
"hgvs_c": "c.374-6385C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 1,
"transcript": "ENST00000528457.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 13,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.3328,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.04,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3761810064315796,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 312,
"aa_ref": "R",
"aa_start": 278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5233,
"cdna_start": 981,
"cds_end": null,
"cds_length": 939,
"cds_start": 833,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_032864.4",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.833G>A",
"hgvs_p": "p.Arg278His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000257181.10",
"protein_coding": true,
"protein_id": "NP_116253.2",
"strand": true,
"transcript": "NM_032864.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 312,
"aa_ref": "R",
"aa_start": 278,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5233,
"cdna_start": 981,
"cds_end": null,
"cds_length": 939,
"cds_start": 833,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000257181.10",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.833G>A",
"hgvs_p": "p.Arg278His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032864.4",
"protein_coding": true,
"protein_id": "ENSP00000257181.8",
"strand": true,
"transcript": "ENST00000257181.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1059,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000474048.1",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "n.621G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000474048.1",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 322,
"aa_ref": "R",
"aa_start": 288,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3799,
"cdna_start": 1011,
"cds_end": null,
"cds_length": 969,
"cds_start": 863,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000879463.1",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.863G>A",
"hgvs_p": "p.Arg288His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549522.1",
"strand": true,
"transcript": "ENST00000879463.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 319,
"aa_ref": "R",
"aa_start": 285,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2740,
"cdna_start": 1006,
"cds_end": null,
"cds_length": 960,
"cds_start": 854,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000879464.1",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.854G>A",
"hgvs_p": "p.Arg285His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549523.1",
"strand": true,
"transcript": "ENST00000879464.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 312,
"aa_ref": "R",
"aa_start": 278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1692,
"cdna_start": 1258,
"cds_end": null,
"cds_length": 939,
"cds_start": 833,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000921590.1",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.833G>A",
"hgvs_p": "p.Arg278His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591649.1",
"strand": true,
"transcript": "ENST00000921590.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 310,
"aa_ref": "R",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1404,
"cdna_start": 975,
"cds_end": null,
"cds_length": 933,
"cds_start": 827,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000956531.1",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.827G>A",
"hgvs_p": "p.Arg276His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626590.1",
"strand": true,
"transcript": "ENST00000956531.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 303,
"aa_ref": "R",
"aa_start": 269,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2652,
"cdna_start": 992,
"cds_end": null,
"cds_length": 912,
"cds_start": 806,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000879465.1",
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"hgvs_c": "c.806G>A",
"hgvs_p": "p.Arg269His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549524.1",
"strand": true,
"transcript": "ENST00000879465.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 163,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 553,
"cdna_start": null,
"cds_end": null,
"cds_length": 492,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000528457.5",
"gene_hgnc_id": 28981,
"gene_symbol": "TUT4",
"hgvs_c": "c.374-6385C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000432475.1",
"strand": false,
"transcript": "ENST00000528457.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 691,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000527941.5",
"gene_hgnc_id": 28981,
"gene_symbol": "TUT4",
"hgvs_c": "n.*68-5239C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000436810.1",
"strand": false,
"transcript": "ENST00000527941.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1322447419",
"effect": "missense_variant",
"frequency_reference_population": 0.000008055122,
"gene_hgnc_id": 25930,
"gene_symbol": "PRPF38A",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.0000075251,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131487,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.573,
"pos": 52414845,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.434,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_032864.4"
}
]
}