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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: 11-72106040-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=72106040&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 72106040,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000307198.11",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOMT",
"gene_hgnc_id": 55527,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "NM_001393500.2",
"protein_id": "NP_001380429.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 258,
"cds_start": 89,
"cds_end": null,
"cds_length": 777,
"cdna_start": 117,
"cdna_end": null,
"cdna_length": 1476,
"mane_select": "ENST00000541899.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOMT",
"gene_hgnc_id": 55527,
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met",
"transcript": "ENST00000541899.3",
"protein_id": "ENSP00000494667.1",
"transcript_support_level": 5,
"aa_start": 30,
"aa_end": null,
"aa_length": 258,
"cds_start": 89,
"cds_end": null,
"cds_length": 777,
"cdna_start": 117,
"cdna_end": null,
"cdna_length": 1476,
"mane_select": "NM_001393500.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "c.188C>T",
"hgvs_p": "p.Thr63Met",
"transcript": "ENST00000307198.11",
"protein_id": "ENSP00000305742.7",
"transcript_support_level": 2,
"aa_start": 63,
"aa_end": null,
"aa_length": 291,
"cds_start": 188,
"cds_end": null,
"cds_length": 876,
"cdna_start": 1064,
"cdna_end": null,
"cdna_length": 3604,
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "n.591C>T",
"hgvs_p": null,
"transcript": "ENST00000427369.6",
"protein_id": "ENSP00000409403.2",
"transcript_support_level": 1,
"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": 3299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "n.487-16C>T",
"hgvs_p": null,
"transcript": "ENST00000544409.5",
"protein_id": "ENSP00000440969.1",
"transcript_support_level": 1,
"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": 3182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "c.188C>T",
"hgvs_p": "p.Thr63Met",
"transcript": "NM_001145308.5",
"protein_id": "NP_001138780.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 291,
"cds_start": 188,
"cds_end": null,
"cds_length": 876,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 3090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "c.188C>T",
"hgvs_p": "p.Thr63Met",
"transcript": "NM_001145309.4",
"protein_id": "NP_001138781.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 291,
"cds_start": 188,
"cds_end": null,
"cds_length": 876,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 3311,
"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": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "c.84-16C>T",
"hgvs_p": null,
"transcript": "NM_001145310.4",
"protein_id": "NP_001138782.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": -4,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3191,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "c.438-2565C>T",
"hgvs_p": null,
"transcript": "ENST00000439209.5",
"protein_id": "ENSP00000395139.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": -4,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 801,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "c.438-2565C>T",
"hgvs_p": null,
"transcript": "ENST00000643715.1",
"protein_id": "ENSP00000496019.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": -4,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"hgvs_c": "n.73-16C>T",
"hgvs_p": null,
"transcript": "ENST00000646163.1",
"protein_id": "ENSP00000494749.1",
"transcript_support_level": null,
"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": 773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRTOMT",
"gene_hgnc_id": 25033,
"dbsnp": "rs876657502",
"frequency_reference_population": 0.000007092455,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000643415,
"gnomad_genomes_af": 0.0000131442,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11551040410995483,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.217,
"revel_prediction": "Benign",
"alphamissense_score": 0.1138,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.584,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000307198.11",
"gene_symbol": "LRTOMT",
"hgnc_id": 25033,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.188C>T",
"hgvs_p": "p.Thr63Met"
},
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000541899.3",
"gene_symbol": "TOMT",
"hgnc_id": 55527,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.89C>T",
"hgvs_p": "p.Thr30Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}