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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: 2-167955560-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=167955560&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "STK39",
"hgnc_id": 17717,
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Cys525Tyr",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_013233.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 10,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.2122,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.03,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5341299176216125,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 545,
"aa_ref": "C",
"aa_start": 525,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3272,
"cdna_start": 1734,
"cds_end": null,
"cds_length": 1638,
"cds_start": 1574,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "NM_013233.3",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Cys525Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000355999.5",
"protein_coding": true,
"protein_id": "NP_037365.2",
"strand": false,
"transcript": "NM_013233.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 545,
"aa_ref": "C",
"aa_start": 525,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3272,
"cdna_start": 1734,
"cds_end": null,
"cds_length": 1638,
"cds_start": 1574,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000355999.5",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Cys525Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_013233.3",
"protein_coding": true,
"protein_id": "ENSP00000348278.4",
"strand": false,
"transcript": "ENST00000355999.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2214,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000487143.5",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "n.674G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000487143.5",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 545,
"aa_ref": "C",
"aa_start": 525,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3467,
"cdna_start": 1689,
"cds_end": null,
"cds_length": 1638,
"cds_start": 1574,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000952313.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Cys525Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622372.1",
"strand": false,
"transcript": "ENST00000952313.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 524,
"aa_ref": "C",
"aa_start": 504,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3209,
"cdna_start": 1671,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1511,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001410961.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Cys504Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397890.1",
"strand": false,
"transcript": "NM_001410961.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 524,
"aa_ref": "C",
"aa_start": 504,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3047,
"cdna_start": 1511,
"cds_end": null,
"cds_length": 1575,
"cds_start": 1511,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000697205.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Cys504Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513185.1",
"strand": false,
"transcript": "ENST00000697205.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 521,
"aa_ref": "C",
"aa_start": 501,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3180,
"cdna_start": 1643,
"cds_end": null,
"cds_length": 1566,
"cds_start": 1502,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000952314.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1502G>A",
"hgvs_p": "p.Cys501Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622373.1",
"strand": false,
"transcript": "ENST00000952314.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 514,
"aa_ref": "C",
"aa_start": 494,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3321,
"cdna_start": 1785,
"cds_end": null,
"cds_length": 1545,
"cds_start": 1481,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000940691.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1481G>A",
"hgvs_p": "p.Cys494Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610750.1",
"strand": false,
"transcript": "ENST00000940691.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 511,
"aa_ref": "C",
"aa_start": 491,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3146,
"cdna_start": 1606,
"cds_end": null,
"cds_length": 1536,
"cds_start": 1472,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000940693.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1472G>A",
"hgvs_p": "p.Cys491Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610752.1",
"strand": false,
"transcript": "ENST00000940693.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 494,
"aa_ref": "C",
"aa_start": 474,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3093,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1485,
"cds_start": 1421,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000940694.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1421G>A",
"hgvs_p": "p.Cys474Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610753.1",
"strand": false,
"transcript": "ENST00000940694.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 490,
"aa_ref": "C",
"aa_start": 470,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3088,
"cdna_start": 1550,
"cds_end": null,
"cds_length": 1473,
"cds_start": 1409,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000940692.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1409G>A",
"hgvs_p": "p.Cys470Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610751.1",
"strand": false,
"transcript": "ENST00000940692.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 411,
"aa_ref": "C",
"aa_start": 391,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2790,
"cdna_start": 1251,
"cds_end": null,
"cds_length": 1236,
"cds_start": 1172,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000952315.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1172G>A",
"hgvs_p": "p.Cys391Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622374.1",
"strand": false,
"transcript": "ENST00000952315.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 443,
"aa_ref": "C",
"aa_start": 423,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4412,
"cdna_start": 2874,
"cds_end": null,
"cds_length": 1332,
"cds_start": 1268,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047443944.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1268G>A",
"hgvs_p": "p.Cys423Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299900.1",
"strand": false,
"transcript": "XM_047443944.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 381,
"aa_ref": "C",
"aa_start": 361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2631,
"cdna_start": 1093,
"cds_end": null,
"cds_length": 1146,
"cds_start": 1082,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_017003817.3",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Cys361Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016859306.1",
"strand": false,
"transcript": "XM_017003817.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 535,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9493,
"cdna_start": null,
"cds_end": null,
"cds_length": 1608,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017003813.3",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.*7742G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016859302.1",
"strand": true,
"transcript": "XM_017003813.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 514,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9430,
"cdna_start": null,
"cds_end": null,
"cds_length": 1545,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047443941.1",
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"hgvs_c": "c.*7742G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299897.1",
"strand": true,
"transcript": "XM_047443941.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs541206860",
"effect": "missense_variant",
"frequency_reference_population": 0.000006197507,
"gene_hgnc_id": 17717,
"gene_symbol": "STK39",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000479005,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197125,
"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": "Uncertain_significance",
"phylop100way_score": 6.706,
"pos": 167955560,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.225,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_013233.3"
}
]
}