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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: 3-119190989-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119190989&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "UPK1B",
"hgnc_id": 12578,
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_006952.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 11,
"alphamissense_prediction": null,
"alphamissense_score": 0.7144,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "3",
"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": 0.3300741910934448,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 260,
"aa_ref": "P",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2028,
"cdna_start": 422,
"cds_end": null,
"cds_length": 783,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_006952.4",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264234.8",
"protein_coding": true,
"protein_id": "NP_008883.2",
"strand": true,
"transcript": "NM_006952.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 260,
"aa_ref": "P",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2028,
"cdna_start": 422,
"cds_end": null,
"cds_length": 783,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000264234.8",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006952.4",
"protein_coding": true,
"protein_id": "ENSP00000264234.3",
"strand": true,
"transcript": "ENST00000264234.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 252,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1937,
"cdna_start": null,
"cds_end": null,
"cds_length": 759,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000460625.1",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.346-17C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418116.1",
"strand": true,
"transcript": "ENST00000460625.1",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 260,
"aa_ref": "P",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1323,
"cdna_start": 593,
"cds_end": null,
"cds_length": 783,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000863546.1",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533605.1",
"strand": true,
"transcript": "ENST00000863546.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 235,
"aa_ref": "P",
"aa_start": 93,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1949,
"cdna_start": 345,
"cds_end": null,
"cds_length": 708,
"cds_start": 278,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000863545.1",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.278C>T",
"hgvs_p": "p.Pro93Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533604.1",
"strand": true,
"transcript": "ENST00000863545.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 232,
"aa_ref": "P",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1969,
"cdna_start": 438,
"cds_end": null,
"cds_length": 699,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000863543.1",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533602.1",
"strand": true,
"transcript": "ENST00000863543.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 188,
"aa_ref": "P",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 670,
"cdna_start": 455,
"cds_end": null,
"cds_length": 568,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000494855.5",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418597.1",
"strand": true,
"transcript": "ENST00000494855.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 180,
"aa_ref": "P",
"aa_start": 38,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 981,
"cdna_start": 406,
"cds_end": null,
"cds_length": 543,
"cds_start": 113,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000497685.5",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Pro38Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418972.1",
"strand": true,
"transcript": "ENST00000497685.5",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 168,
"aa_ref": "P",
"aa_start": 118,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 687,
"cdna_start": 532,
"cds_end": null,
"cds_length": 508,
"cds_start": 353,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000479520.5",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.353C>T",
"hgvs_p": "p.Pro118Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418399.1",
"strand": true,
"transcript": "ENST00000479520.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 251,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2020,
"cdna_start": null,
"cds_end": null,
"cds_length": 756,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000863544.1",
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"hgvs_c": "c.346-20C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533603.1",
"strand": true,
"transcript": "ENST00000863544.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs965985398",
"effect": "missense_variant",
"frequency_reference_population": 0.000006816379,
"gene_hgnc_id": 12578,
"gene_symbol": "UPK1B",
"gnomad_exomes_ac": 10,
"gnomad_exomes_af": 0.00000684155,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657454,
"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": "Benign",
"phylop100way_score": 2.42,
"pos": 119190989,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.314,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07999999821186066,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.08,
"transcript": "NM_006952.4"
}
]
}