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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: 3-41463106-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=41463106&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 41463106,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_017886.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.3374T>C",
"hgvs_p": "p.Ile1125Thr",
"transcript": "NM_017886.4",
"protein_id": "NP_060356.2",
"transcript_support_level": null,
"aa_start": 1125,
"aa_end": null,
"aa_length": 1275,
"cds_start": 3374,
"cds_end": null,
"cds_length": 3828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000301831.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017886.4"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.3374T>C",
"hgvs_p": "p.Ile1125Thr",
"transcript": "ENST00000301831.9",
"protein_id": "ENSP00000301831.4",
"transcript_support_level": 2,
"aa_start": 1125,
"aa_end": null,
"aa_length": 1275,
"cds_start": 3374,
"cds_end": null,
"cds_length": 3828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017886.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000301831.9"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.3371T>C",
"hgvs_p": "p.Ile1124Thr",
"transcript": "ENST00000951851.1",
"protein_id": "ENSP00000621910.1",
"transcript_support_level": null,
"aa_start": 1124,
"aa_end": null,
"aa_length": 1274,
"cds_start": 3371,
"cds_end": null,
"cds_length": 3825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951851.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.3290T>C",
"hgvs_p": "p.Ile1097Thr",
"transcript": "ENST00000889811.1",
"protein_id": "ENSP00000559870.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1247,
"cds_start": 3290,
"cds_end": null,
"cds_length": 3744,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889811.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.3374T>C",
"hgvs_p": "p.Ile1125Thr",
"transcript": "NM_001322500.2",
"protein_id": "NP_001309429.1",
"transcript_support_level": null,
"aa_start": 1125,
"aa_end": null,
"aa_length": 1235,
"cds_start": 3374,
"cds_end": null,
"cds_length": 3708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001322500.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.2468T>C",
"hgvs_p": "p.Ile823Thr",
"transcript": "NM_001322501.2",
"protein_id": "NP_001309430.1",
"transcript_support_level": null,
"aa_start": 823,
"aa_end": null,
"aa_length": 973,
"cds_start": 2468,
"cds_end": null,
"cds_length": 2922,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001322501.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.1547T>C",
"hgvs_p": "p.Ile516Thr",
"transcript": "XM_047448417.1",
"protein_id": "XP_047304373.1",
"transcript_support_level": null,
"aa_start": 516,
"aa_end": null,
"aa_length": 666,
"cds_start": 1547,
"cds_end": null,
"cds_length": 2001,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448417.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.1505T>C",
"hgvs_p": "p.Ile502Thr",
"transcript": "XM_024453612.2",
"protein_id": "XP_024309380.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 652,
"cds_start": 1505,
"cds_end": null,
"cds_length": 1959,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453612.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "n.3345T>C",
"hgvs_p": null,
"transcript": "NR_136342.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_136342.2"
}
],
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"dbsnp": "rs560135771",
"frequency_reference_population": 0.00002540792,
"hom_count_reference_population": 0,
"allele_count_reference_population": 41,
"gnomad_exomes_af": 0.0000109487,
"gnomad_genomes_af": 0.000164139,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 25,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22882938385009766,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.171,
"revel_prediction": "Benign",
"alphamissense_score": 0.1108,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.786,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_017886.4",
"gene_symbol": "ULK4",
"hgnc_id": 15784,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3374T>C",
"hgvs_p": "p.Ile1125Thr"
}
],
"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
}