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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: 19-39459893-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=39459893&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 39459893,
"ref": "T",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_003169.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "NM_001111020.3",
"protein_id": "NP_001104490.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 700,
"cdna_end": null,
"cdna_length": 3678,
"mane_select": "ENST00000432763.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001111020.3"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "ENST00000432763.7",
"protein_id": "ENSP00000404029.4",
"transcript_support_level": 1,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 700,
"cdna_end": null,
"cdna_length": 3678,
"mane_select": "NM_001111020.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000432763.7"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "ENST00000598725.5",
"protein_id": "ENSP00000469090.1",
"transcript_support_level": 1,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 764,
"cdna_end": null,
"cdna_length": 3742,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000598725.5"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.545T>C",
"hgvs_p": "p.Ile182Thr",
"transcript": "ENST00000359191.10",
"protein_id": "ENSP00000352117.6",
"transcript_support_level": 1,
"aa_start": 182,
"aa_end": null,
"aa_length": 1083,
"cds_start": 545,
"cds_end": null,
"cds_length": 3252,
"cdna_start": 792,
"cdna_end": null,
"cdna_length": 3770,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359191.10"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.545T>C",
"hgvs_p": "p.Ile182Thr",
"transcript": "ENST00000402194.6",
"protein_id": "ENSP00000384505.2",
"transcript_support_level": 1,
"aa_start": 182,
"aa_end": null,
"aa_length": 1083,
"cds_start": 545,
"cds_end": null,
"cds_length": 3252,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 3698,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402194.6"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "NM_001130824.2",
"protein_id": "NP_001124296.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 3603,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130824.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "NM_001319990.2",
"protein_id": "NP_001306919.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 622,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319990.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "NM_003169.4",
"protein_id": "NP_003160.2",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 3782,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003169.4"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "ENST00000599117.5",
"protein_id": "ENSP00000470252.1",
"transcript_support_level": 5,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 924,
"cdna_end": null,
"cdna_length": 3902,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000599117.5"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "ENST00000946279.1",
"protein_id": "ENSP00000616338.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 722,
"cdna_end": null,
"cdna_length": 3700,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946279.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr",
"transcript": "ENST00000946280.1",
"protein_id": "ENSP00000616339.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 1087,
"cds_start": 557,
"cds_end": null,
"cds_length": 3264,
"cdna_start": 583,
"cdna_end": null,
"cdna_length": 3557,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946280.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.545T>C",
"hgvs_p": "p.Ile182Thr",
"transcript": "NM_001130825.2",
"protein_id": "NP_001124297.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 1083,
"cds_start": 545,
"cds_end": null,
"cds_length": 3252,
"cdna_start": 688,
"cdna_end": null,
"cdna_length": 3666,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130825.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.545T>C",
"hgvs_p": "p.Ile182Thr",
"transcript": "NM_001319991.2",
"protein_id": "NP_001306920.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 1083,
"cds_start": 545,
"cds_end": null,
"cds_length": 3252,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 3588,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001319991.2"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.545T>C",
"hgvs_p": "p.Ile182Thr",
"transcript": "ENST00000917285.1",
"protein_id": "ENSP00000587344.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 1062,
"cds_start": 545,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 3699,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917285.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Ile97Thr",
"transcript": "ENST00000593727.1",
"protein_id": "ENSP00000469915.1",
"transcript_support_level": 3,
"aa_start": 97,
"aa_end": null,
"aa_length": 163,
"cds_start": 290,
"cds_end": null,
"cds_length": 493,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 493,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593727.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "n.316T>C",
"hgvs_p": null,
"transcript": "ENST00000598459.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 548,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000598459.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"hgvs_c": "n.704T>C",
"hgvs_p": null,
"transcript": "ENST00000599907.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 859,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000599907.1"
}
],
"gene_symbol": "SUPT5H",
"gene_hgnc_id": 11469,
"dbsnp": "rs1044402481",
"frequency_reference_population": 0.000013631187,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.000014366,
"gnomad_genomes_af": 0.00000657212,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.75342857837677,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3799999952316284,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.657,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8363,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.651,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.364386699929502,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_003169.4",
"gene_symbol": "SUPT5H",
"hgnc_id": 11469,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.557T>C",
"hgvs_p": "p.Ile186Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}