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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: 22-46689996-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=46689996&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CERK",
"hgnc_id": 19256,
"hgvs_c": "c.1537G>T",
"hgvs_p": "p.Val513Phe",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_022766.6",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 12,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.4028,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.01,
"chr": "22",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7145059704780579,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 537,
"aa_ref": "V",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4442,
"cdna_start": 1641,
"cds_end": null,
"cds_length": 1614,
"cds_start": 1537,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_022766.6",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1537G>T",
"hgvs_p": "p.Val513Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000216264.13",
"protein_coding": true,
"protein_id": "NP_073603.2",
"strand": false,
"transcript": "NM_022766.6",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 537,
"aa_ref": "V",
"aa_start": 513,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4442,
"cdna_start": 1641,
"cds_end": null,
"cds_length": 1614,
"cds_start": 1537,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000216264.13",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1537G>T",
"hgvs_p": "p.Val513Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_022766.6",
"protein_coding": true,
"protein_id": "ENSP00000216264.8",
"strand": false,
"transcript": "ENST00000216264.13",
"transcript_support_level": 1
},
{
"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": 1760,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000443629.5",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "n.*915G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000400859.1",
"strand": false,
"transcript": "ENST00000443629.5",
"transcript_support_level": 1
},
{
"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": 1760,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000443629.5",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "n.*915G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000400859.1",
"strand": false,
"transcript": "ENST00000443629.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 544,
"aa_ref": "V",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3270,
"cdna_start": 1665,
"cds_end": null,
"cds_length": 1635,
"cds_start": 1558,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000951513.1",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1558G>T",
"hgvs_p": "p.Val520Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621572.1",
"strand": false,
"transcript": "ENST00000951513.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 532,
"aa_ref": "V",
"aa_start": 508,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4421,
"cdna_start": 1626,
"cds_end": null,
"cds_length": 1599,
"cds_start": 1522,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000951512.1",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1522G>T",
"hgvs_p": "p.Val508Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621571.1",
"strand": false,
"transcript": "ENST00000951512.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 496,
"aa_ref": "V",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4331,
"cdna_start": 1533,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1414,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000918417.1",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1414G>T",
"hgvs_p": "p.Val472Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588476.1",
"strand": false,
"transcript": "ENST00000918417.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 496,
"aa_ref": "V",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4319,
"cdna_start": 1518,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1414,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000951510.1",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1414G>T",
"hgvs_p": "p.Val472Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621569.1",
"strand": false,
"transcript": "ENST00000951510.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 495,
"aa_ref": "V",
"aa_start": 471,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4313,
"cdna_start": 1515,
"cds_end": null,
"cds_length": 1488,
"cds_start": 1411,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000951511.1",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "c.1411G>T",
"hgvs_p": "p.Val471Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621570.1",
"strand": false,
"transcript": "ENST00000951511.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 567,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000471929.1",
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"hgvs_c": "n.*59G>T",
"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": "ENST00000471929.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs774060048",
"effect": "missense_variant",
"frequency_reference_population": 0.0000074855807,
"gene_hgnc_id": 19256,
"gene_symbol": "CERK",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.0000075797,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000658597,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.212,
"pos": 46689996,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.184,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_022766.6"
}
]
}