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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: 11-72106043-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=72106043&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 72106043,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000307198.11",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "G",
"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.92T>G",
"hgvs_p": "p.Val31Gly",
"transcript": "NM_001393500.2",
"protein_id": "NP_001380429.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 258,
"cds_start": 92,
"cds_end": null,
"cds_length": 777,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 1476,
"mane_select": "ENST00000541899.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"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.92T>G",
"hgvs_p": "p.Val31Gly",
"transcript": "ENST00000541899.3",
"protein_id": "ENSP00000494667.1",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 258,
"cds_start": 92,
"cds_end": null,
"cds_length": 777,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 1476,
"mane_select": "NM_001393500.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"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.191T>G",
"hgvs_p": "p.Val64Gly",
"transcript": "ENST00000307198.11",
"protein_id": "ENSP00000305742.7",
"transcript_support_level": 2,
"aa_start": 64,
"aa_end": null,
"aa_length": 291,
"cds_start": 191,
"cds_end": null,
"cds_length": 876,
"cdna_start": 1067,
"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.594T>G",
"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.487-13T>G",
"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": "V",
"aa_alt": "G",
"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.191T>G",
"hgvs_p": "p.Val64Gly",
"transcript": "NM_001145308.5",
"protein_id": "NP_001138780.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 291,
"cds_start": 191,
"cds_end": null,
"cds_length": 876,
"cdna_start": 548,
"cdna_end": null,
"cdna_length": 3090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"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.191T>G",
"hgvs_p": "p.Val64Gly",
"transcript": "NM_001145309.4",
"protein_id": "NP_001138781.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 291,
"cds_start": 191,
"cds_end": null,
"cds_length": 876,
"cdna_start": 769,
"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.84-13T>G",
"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.438-2562T>G",
"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.438-2562T>G",
"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.73-13T>G",
"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": "rs574631765",
"frequency_reference_population": 0.000043843076,
"hom_count_reference_population": 1,
"allele_count_reference_population": 68,
"gnomad_exomes_af": 0.000043609,
"gnomad_genomes_af": 0.0000459945,
"gnomad_exomes_ac": 61,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6861308813095093,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.706,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2024,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.86,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000307198.11",
"gene_symbol": "LRTOMT",
"hgnc_id": 25033,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.191T>G",
"hgvs_p": "p.Val64Gly"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000541899.3",
"gene_symbol": "TOMT",
"hgnc_id": 55527,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.92T>G",
"hgvs_p": "p.Val31Gly"
}
],
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 63,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases|Autosomal recessive nonsyndromic hearing loss 63",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}