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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: 19-55157103-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=55157103&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 55157103,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000363.5",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "c.55A>C",
"hgvs_p": "p.Ile19Leu",
"transcript": "NM_000363.5",
"protein_id": "NP_000354.4",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 210,
"cds_start": 55,
"cds_end": null,
"cds_length": 633,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 843,
"mane_select": "ENST00000344887.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "c.55A>C",
"hgvs_p": "p.Ile19Leu",
"transcript": "ENST00000344887.10",
"protein_id": "ENSP00000341838.5",
"transcript_support_level": 1,
"aa_start": 19,
"aa_end": null,
"aa_length": 210,
"cds_start": 55,
"cds_end": null,
"cds_length": 633,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 843,
"mane_select": "NM_000363.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267110",
"gene_hgnc_id": null,
"hgvs_c": "n.*157A>C",
"hgvs_p": null,
"transcript": "ENST00000587871.1",
"protein_id": "ENSP00000473050.1",
"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": 975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267110",
"gene_hgnc_id": null,
"hgvs_c": "n.*157A>C",
"hgvs_p": null,
"transcript": "ENST00000587871.1",
"protein_id": "ENSP00000473050.1",
"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": 975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "c.55A>C",
"hgvs_p": "p.Ile19Leu",
"transcript": "ENST00000665070.1",
"protein_id": "ENSP00000499482.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 221,
"cds_start": 55,
"cds_end": null,
"cds_length": 666,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "c.55A>C",
"hgvs_p": "p.Ile19Leu",
"transcript": "ENST00000714238.1",
"protein_id": "ENSP00000519518.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 206,
"cds_start": 55,
"cds_end": null,
"cds_length": 621,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "c.55A>C",
"hgvs_p": "p.Ile19Leu",
"transcript": "ENST00000714236.1",
"protein_id": "ENSP00000519516.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 196,
"cds_start": 55,
"cds_end": null,
"cds_length": 591,
"cdna_start": 198,
"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": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "n.197A>C",
"hgvs_p": null,
"transcript": "ENST00000586446.1",
"protein_id": null,
"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": 571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "n.63A>C",
"hgvs_p": null,
"transcript": "ENST00000586669.5",
"protein_id": null,
"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": 477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "n.239A>C",
"hgvs_p": null,
"transcript": "ENST00000587176.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 992,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "n.227A>C",
"hgvs_p": null,
"transcript": "ENST00000590463.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 539,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"hgvs_c": "c.24+193A>C",
"hgvs_p": null,
"transcript": "ENST00000714237.1",
"protein_id": "ENSP00000519517.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 182,
"cds_start": -4,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TNNI3",
"gene_hgnc_id": 11947,
"dbsnp": "rs755862334",
"frequency_reference_population": 0.0000020677876,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000206779,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04295000433921814,
"computational_prediction_selected": "Benign",
"computational_source_selected": "CardioboostCm",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.261,
"revel_prediction": "Benign",
"alphamissense_score": 0.0702,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.899,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": "PM1,PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2",
"BP4_Strong"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000363.5",
"gene_symbol": "TNNI3",
"hgnc_id": 11947,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.55A>C",
"hgvs_p": "p.Ile19Leu"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000587871.1",
"gene_symbol": "ENSG00000267110",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*157A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Cardiomyopathy,Cardiovascular phenotype,Hypertrophic cardiomyopathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Cardiomyopathy|Cardiovascular phenotype|Hypertrophic cardiomyopathy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}