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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: 13-98446628-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=98446628&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 98446628,
"ref": "A",
"alt": "C",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000539966.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK24",
"gene_hgnc_id": 11403,
"hgvs_c": "c.*6545T>G",
"hgvs_p": null,
"transcript": "NM_001032296.4",
"protein_id": "NP_001027467.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 431,
"cds_start": -4,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9605,
"mane_select": "ENST00000539966.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK24",
"gene_hgnc_id": 11403,
"hgvs_c": "c.*6545T>G",
"hgvs_p": null,
"transcript": "ENST00000539966.6",
"protein_id": "ENSP00000442539.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 431,
"cds_start": -4,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9605,
"mane_select": "NM_001032296.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "FARP1",
"gene_hgnc_id": 3591,
"hgvs_c": "c.2905-38A>C",
"hgvs_p": null,
"transcript": "NM_005766.4",
"protein_id": "NP_005757.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1045,
"cds_start": -4,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10419,
"mane_select": "ENST00000319562.11",
"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": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "FARP1",
"gene_hgnc_id": 3591,
"hgvs_c": "c.2905-38A>C",
"hgvs_p": null,
"transcript": "ENST00000319562.11",
"protein_id": "ENSP00000322926.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1045,
"cds_start": -4,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10419,
"mane_select": "NM_005766.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 28,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "FARP1",
"gene_hgnc_id": 3591,
"hgvs_c": "c.2998-38A>C",
"hgvs_p": null,
"transcript": "ENST00000595437.5",
"protein_id": "ENSP00000471242.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1076,
"cds_start": -4,
"cds_end": null,
"cds_length": 3231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4926,
"mane_select": null,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FARP1",
"gene_hgnc_id": 3591,
"hgvs_c": "n.1476A>C",
"hgvs_p": null,
"transcript": "ENST00000594346.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 2692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK24",
"gene_hgnc_id": 11403,
"hgvs_c": "c.*6545T>G",
"hgvs_p": null,
"transcript": "NM_003576.5",
"protein_id": "NP_003567.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 443,
"cds_start": -4,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK24",
"gene_hgnc_id": 11403,
"hgvs_c": "c.*6545T>G",
"hgvs_p": null,
"transcript": "NM_001286649.2",
"protein_id": "NP_001273578.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 28,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "FARP1",
"gene_hgnc_id": 3591,
"hgvs_c": "c.2998-38A>C",
"hgvs_p": null,
"transcript": "NM_001286839.2",
"protein_id": "NP_001273768.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1076,
"cds_start": -4,
"cds_end": null,
"cds_length": 3231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10302,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 28,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "FARP1",
"gene_hgnc_id": 3591,
"hgvs_c": "c.2998-38A>C",
"hgvs_p": null,
"transcript": "ENST00000627049.2",
"protein_id": "ENSP00000486285.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1076,
"cds_start": -4,
"cds_end": null,
"cds_length": 3231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "STK24",
"gene_hgnc_id": 11403,
"dbsnp": "rs2281766",
"frequency_reference_population": 0.7839008,
"hom_count_reference_population": 503237,
"allele_count_reference_population": 1259622,
"gnomad_exomes_af": 0.792715,
"gnomad_genomes_af": 0.699524,
"gnomad_exomes_ac": 1153314,
"gnomad_genomes_ac": 106308,
"gnomad_exomes_homalt": 464204,
"gnomad_genomes_homalt": 39033,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.305,
"phylop100way_prediction": "Benign",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000539966.6",
"gene_symbol": "STK24",
"hgnc_id": 11403,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*6545T>G",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000319562.11",
"gene_symbol": "FARP1",
"hgnc_id": 3591,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2905-38A>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}