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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: 19-55154109-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=55154109&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TNNI3",
"hgnc_id": 11947,
"hgvs_c": "c.470C>T",
"hgvs_p": "p.Ala157Val",
"inheritance_mode": "AR,AD",
"pathogenic_score": 22,
"score": 22,
"transcript": "NM_000363.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_score": 22,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": 0.3822,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.05,
"chr": "19",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Cardiomyopathy,Cardiovascular phenotype,Hypertrophic cardiomyopathy,Hypertrophic cardiomyopathy 7,Primary familial hypertrophic cardiomyopathy,TNNI3-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:11 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9739320278167725,
"computational_source_selected": "CardioboostCm",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 210,
"aa_ref": "A",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 843,
"cdna_start": 613,
"cds_end": null,
"cds_length": 633,
"cds_start": 470,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_000363.5",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.470C>T",
"hgvs_p": "p.Ala157Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000344887.10",
"protein_coding": true,
"protein_id": "NP_000354.4",
"strand": false,
"transcript": "NM_000363.5",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 210,
"aa_ref": "A",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 843,
"cdna_start": 613,
"cds_end": null,
"cds_length": 633,
"cds_start": 470,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000344887.10",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.470C>T",
"hgvs_p": "p.Ala157Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000363.5",
"protein_coding": true,
"protein_id": "ENSP00000341838.5",
"strand": false,
"transcript": "ENST00000344887.10",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 221,
"aa_ref": "A",
"aa_start": 168,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 871,
"cdna_start": 646,
"cds_end": null,
"cds_length": 666,
"cds_start": 503,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000665070.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.503C>T",
"hgvs_p": "p.Ala168Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499482.1",
"strand": false,
"transcript": "ENST00000665070.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 206,
"aa_ref": "A",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 831,
"cdna_start": 601,
"cds_end": null,
"cds_length": 621,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000714238.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.458C>T",
"hgvs_p": "p.Ala153Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519518.1",
"strand": false,
"transcript": "ENST00000714238.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 202,
"aa_ref": "A",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 816,
"cdna_start": 613,
"cds_end": null,
"cds_length": 609,
"cds_start": 470,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000955280.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.470C>T",
"hgvs_p": "p.Ala157Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625339.1",
"strand": false,
"transcript": "ENST00000955280.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 196,
"aa_ref": "A",
"aa_start": 143,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 801,
"cdna_start": 571,
"cds_end": null,
"cds_length": 591,
"cds_start": 428,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000714236.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.428C>T",
"hgvs_p": "p.Ala143Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519516.1",
"strand": false,
"transcript": "ENST00000714236.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 193,
"aa_ref": "A",
"aa_start": 140,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 714,
"cdna_start": 487,
"cds_end": null,
"cds_length": 582,
"cds_start": 419,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000955282.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Ala140Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625341.1",
"strand": false,
"transcript": "ENST00000955282.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 191,
"aa_ref": "A",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 787,
"cdna_start": 557,
"cds_end": null,
"cds_length": 576,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000955279.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.413C>T",
"hgvs_p": "p.Ala138Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625338.1",
"strand": false,
"transcript": "ENST00000955279.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 185,
"aa_ref": "A",
"aa_start": 132,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 669,
"cdna_start": 443,
"cds_end": null,
"cds_length": 558,
"cds_start": 395,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000588882.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Ala132Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466729.1",
"strand": false,
"transcript": "ENST00000588882.1",
"transcript_support_level": 2
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 182,
"aa_ref": "A",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 759,
"cdna_start": 529,
"cds_end": null,
"cds_length": 549,
"cds_start": 386,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000714237.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.386C>T",
"hgvs_p": "p.Ala129Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519517.1",
"strand": false,
"transcript": "ENST00000714237.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 176,
"aa_ref": "A",
"aa_start": 123,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 736,
"cdna_start": 511,
"cds_end": null,
"cds_length": 531,
"cds_start": 368,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000955281.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Ala123Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625340.1",
"strand": false,
"transcript": "ENST00000955281.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 141,
"aa_ref": "A",
"aa_start": 88,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 537,
"cdna_start": 311,
"cds_end": null,
"cds_length": 426,
"cds_start": 263,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000714240.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "c.263C>T",
"hgvs_p": "p.Ala88Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519520.1",
"strand": false,
"transcript": "ENST00000714240.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 699,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000585806.5",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.469C>T",
"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": "ENST00000585806.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 774,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000586858.2",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.*241C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465258.2",
"strand": false,
"transcript": "ENST00000586858.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 525,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000589864.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.298C>T",
"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": "ENST00000589864.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 787,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000714239.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.*144C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519519.1",
"strand": false,
"transcript": "ENST00000714239.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 774,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000586858.2",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.*241C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465258.2",
"strand": false,
"transcript": "ENST00000586858.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 787,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000714239.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.*144C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519519.1",
"strand": false,
"transcript": "ENST00000714239.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 397,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000714235.1",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.371+632C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000714235.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 477,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000586669.5",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.*1C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000586669.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 992,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000587176.5",
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"hgvs_c": "n.*196C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000587176.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs397516353",
"effect": "missense_variant",
"frequency_reference_population": 0.0000034222057,
"gene_hgnc_id": 11947,
"gene_symbol": "TNNI3",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000342221,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "not provided|Hypertrophic cardiomyopathy 7|Hypertrophic cardiomyopathy|Primary familial hypertrophic cardiomyopathy|Cardiovascular phenotype|TNNI3-related disorder|Cardiomyopathy",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.883,
"pos": 55154109,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.652,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_000363.5"
}
]
}