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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: 2-32305576-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=32305576&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 32305576,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_032312.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.685C>G",
"hgvs_p": "p.Pro229Ala",
"transcript": "NM_032312.4",
"protein_id": "NP_115688.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 244,
"cds_start": 685,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000238831.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032312.4"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.685C>G",
"hgvs_p": "p.Pro229Ala",
"transcript": "ENST00000238831.9",
"protein_id": "ENSP00000238831.3",
"transcript_support_level": 1,
"aa_start": 229,
"aa_end": null,
"aa_length": 244,
"cds_start": 685,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032312.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000238831.9"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.607C>G",
"hgvs_p": "p.Pro203Ala",
"transcript": "ENST00000856768.1",
"protein_id": "ENSP00000526827.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 218,
"cds_start": 607,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856768.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.571C>G",
"hgvs_p": "p.Pro191Ala",
"transcript": "ENST00000937326.1",
"protein_id": "ENSP00000607385.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 206,
"cds_start": 571,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937326.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.493C>G",
"hgvs_p": "p.Pro165Ala",
"transcript": "ENST00000951423.1",
"protein_id": "ENSP00000621482.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 180,
"cds_start": 493,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951423.1"
},
{
"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": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.52-1528C>G",
"hgvs_p": null,
"transcript": "ENST00000441084.1",
"protein_id": "ENSP00000414267.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 32,
"cds_start": null,
"cds_end": null,
"cds_length": 99,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441084.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.598-1528C>G",
"hgvs_p": null,
"transcript": "XM_005264599.4",
"protein_id": "XP_005264656.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 214,
"cds_start": null,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005264599.4"
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "c.520-1528C>G",
"hgvs_p": null,
"transcript": "XM_024453173.2",
"protein_id": "XP_024308941.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 188,
"cds_start": null,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453173.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "n.*261C>G",
"hgvs_p": null,
"transcript": "ENST00000437765.1",
"protein_id": "ENSP00000394339.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000437765.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"hgvs_c": "n.*261C>G",
"hgvs_p": null,
"transcript": "ENST00000437765.1",
"protein_id": "ENSP00000394339.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000437765.1"
}
],
"gene_symbol": "YIPF4",
"gene_hgnc_id": 28145,
"dbsnp": "rs1051007803",
"frequency_reference_population": 0.0000037287045,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000343146,
"gnomad_genomes_af": 0.00000657756,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8986624479293823,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.854,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.997,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.544,
"phylop100way_prediction": "Pathogenic",
"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": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032312.4",
"gene_symbol": "YIPF4",
"hgnc_id": 28145,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.685C>G",
"hgvs_p": "p.Pro229Ala"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}