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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: 5-1294051-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1294051&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 1294051,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_198253.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr",
"transcript": "NM_198253.3",
"protein_id": "NP_937983.2",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 1132,
"cds_start": 835,
"cds_end": null,
"cds_length": 3399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000310581.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198253.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr",
"transcript": "ENST00000310581.10",
"protein_id": "ENSP00000309572.5",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 1132,
"cds_start": 835,
"cds_end": null,
"cds_length": 3399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_198253.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000310581.10"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr",
"transcript": "ENST00000334602.10",
"protein_id": "ENSP00000334346.6",
"transcript_support_level": 1,
"aa_start": 279,
"aa_end": null,
"aa_length": 1069,
"cds_start": 835,
"cds_end": null,
"cds_length": 3210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334602.10"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.835G>A",
"hgvs_p": null,
"transcript": "ENST00000460137.6",
"protein_id": "ENSP00000425003.1",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000460137.6"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr",
"transcript": "ENST00000922986.1",
"protein_id": "ENSP00000593045.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 1188,
"cds_start": 835,
"cds_end": null,
"cds_length": 3567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922986.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr",
"transcript": "ENST00000922985.1",
"protein_id": "ENSP00000593044.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 1120,
"cds_start": 835,
"cds_end": null,
"cds_length": 3363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922985.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr",
"transcript": "NM_001193376.3",
"protein_id": "NP_001180305.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 1069,
"cds_start": 835,
"cds_end": null,
"cds_length": 3210,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193376.3"
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.835G>A",
"hgvs_p": null,
"transcript": "ENST00000656021.1",
"protein_id": "ENSP00000499759.1",
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000656021.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.914G>A",
"hgvs_p": null,
"transcript": "NR_149162.3",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149162.3"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.914G>A",
"hgvs_p": null,
"transcript": "NR_149163.3",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149163.3"
}
],
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"dbsnp": "rs61748181",
"frequency_reference_population": 0.027116334,
"hom_count_reference_population": 703,
"allele_count_reference_population": 43173,
"gnomad_exomes_af": 0.0276654,
"gnomad_genomes_af": 0.021925,
"gnomad_exomes_ac": 39834,
"gnomad_genomes_ac": 3339,
"gnomad_exomes_homalt": 647,
"gnomad_genomes_homalt": 56,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.030250608921051025,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.162,
"revel_prediction": "Benign",
"alphamissense_score": 0.0743,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.632,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_198253.3",
"gene_symbol": "TERT",
"hgnc_id": 11730,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown,SD,AR",
"hgvs_c": "c.835G>A",
"hgvs_p": "p.Ala279Thr"
}
],
"clinvar_disease": " 1, Telomere-related, autosomal dominant 2,Aplastic anemia,Dyskeratosis congenita,Idiopathic Pulmonary Fibrosis,Malignant tumor of breast,Pulmonary fibrosis and/or bone marrow failure,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:12 O:1",
"phenotype_combined": "Aplastic anemia|not specified|Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1|Dyskeratosis congenita, autosomal dominant 2|not provided|Malignant tumor of breast|Idiopathic Pulmonary Fibrosis;Dyskeratosis congenita, autosomal dominant 2|Dyskeratosis congenita",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}