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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: 2-218680624-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=218680624&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 218680624,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000295709.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "NM_015690.5",
"protein_id": "NP_056505.2",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 1315,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3948,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 4873,
"mane_select": "ENST00000295709.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "ENST00000295709.8",
"protein_id": "ENSP00000295709.3",
"transcript_support_level": 1,
"aa_start": 386,
"aa_end": null,
"aa_length": 1315,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3948,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 4873,
"mane_select": "NM_015690.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "ENST00000392105.7",
"protein_id": "ENSP00000375954.3",
"transcript_support_level": 1,
"aa_start": 386,
"aa_end": null,
"aa_length": 1294,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3885,
"cdna_start": 1394,
"cdna_end": null,
"cdna_length": 4821,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "NM_001369423.1",
"protein_id": "NP_001356352.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 1315,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3948,
"cdna_start": 1295,
"cdna_end": null,
"cdna_length": 4793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "ENST00000440309.5",
"protein_id": "ENSP00000394095.1",
"transcript_support_level": 5,
"aa_start": 386,
"aa_end": null,
"aa_length": 1315,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3948,
"cdna_start": 1317,
"cdna_end": null,
"cdna_length": 4721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "NM_001243313.2",
"protein_id": "NP_001230242.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 1294,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3885,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 4810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "XM_011510959.3",
"protein_id": "XP_011509261.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 1306,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 4848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "XM_047443931.1",
"protein_id": "XP_047299887.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 1306,
"cds_start": 1158,
"cds_end": null,
"cds_length": 3921,
"cdna_start": 1295,
"cdna_end": null,
"cdna_length": 4766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "XM_017003804.3",
"protein_id": "XP_016859293.2",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 851,
"cds_start": 1158,
"cds_end": null,
"cds_length": 2556,
"cdna_start": 1295,
"cdna_end": null,
"cdna_length": 3056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp",
"transcript": "XM_047443932.1",
"protein_id": "XP_047299888.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 851,
"cds_start": 1158,
"cds_end": null,
"cds_length": 2556,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 3138,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "n.51T>C",
"hgvs_p": null,
"transcript": "ENST00000414413.5",
"protein_id": "ENSP00000406184.1",
"transcript_support_level": 5,
"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": 563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"hgvs_c": "n.-70T>C",
"hgvs_p": null,
"transcript": "ENST00000422778.1",
"protein_id": "ENSP00000409688.1",
"transcript_support_level": 5,
"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": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "STK36",
"gene_hgnc_id": 17209,
"dbsnp": "rs55839518",
"frequency_reference_population": 0.004409805,
"hom_count_reference_population": 20,
"allele_count_reference_population": 7115,
"gnomad_exomes_af": 0.00451291,
"gnomad_genomes_af": 0.00342066,
"gnomad_exomes_ac": 6594,
"gnomad_genomes_ac": 521,
"gnomad_exomes_homalt": 17,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"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": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.324,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000295709.8",
"gene_symbol": "STK36",
"hgnc_id": 17209,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1158T>C",
"hgvs_p": "p.Asp386Asp"
}
],
"clinvar_disease": "STK36-related disorder,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "not specified|not provided|STK36-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}