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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: 5-1279410-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1279410&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 1279410,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000310581.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.2011C>T",
"hgvs_p": "p.Arg671Trp",
"transcript": "NM_198253.3",
"protein_id": "NP_937983.2",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 1132,
"cds_start": 2011,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 2090,
"cdna_end": null,
"cdna_length": 4039,
"mane_select": "ENST00000310581.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.2011C>T",
"hgvs_p": "p.Arg671Trp",
"transcript": "ENST00000310581.10",
"protein_id": "ENSP00000309572.5",
"transcript_support_level": 1,
"aa_start": 671,
"aa_end": null,
"aa_length": 1132,
"cds_start": 2011,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 2090,
"cdna_end": null,
"cdna_length": 4039,
"mane_select": "NM_198253.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.2011C>T",
"hgvs_p": "p.Arg671Trp",
"transcript": "ENST00000334602.10",
"protein_id": "ENSP00000334346.6",
"transcript_support_level": 1,
"aa_start": 671,
"aa_end": null,
"aa_length": 1069,
"cds_start": 2011,
"cds_end": null,
"cds_length": 3210,
"cdna_start": 2011,
"cdna_end": null,
"cdna_length": 3210,
"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": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.2011C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2992,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "c.2011C>T",
"hgvs_p": "p.Arg671Trp",
"transcript": "NM_001193376.3",
"protein_id": "NP_001180305.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 1069,
"cds_start": 2011,
"cds_end": null,
"cds_length": 3210,
"cdna_start": 2090,
"cdna_end": null,
"cdna_length": 3850,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.824C>T",
"hgvs_p": null,
"transcript": "ENST00000484238.6",
"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": 2422,
"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": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.*1557C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5289,
"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": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.2090C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3668,
"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": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.2090C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"hgvs_c": "n.*1557C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TERT",
"gene_hgnc_id": 11730,
"dbsnp": "rs1060503011",
"frequency_reference_population": 0.000005153809,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000499979,
"gnomad_genomes_af": 0.00000657073,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5994177460670471,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.58,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1256,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.403,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM5",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000310581.10",
"gene_symbol": "TERT",
"hgnc_id": 11730,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD,Unknown",
"hgvs_c": "c.2011C>T",
"hgvs_p": "p.Arg671Trp"
}
],
"clinvar_disease": " autosomal dominant 2,Autosomal recessive dyskeratosis congenita 4,Dyskeratosis congenita,Hoyeraal-Hreidarsson syndrome,Idiopathic Pulmonary Fibrosis,Pulmonary fibrosis,Telomere syndrome,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:4",
"phenotype_combined": "Pulmonary fibrosis|Autosomal recessive dyskeratosis congenita 4|Dyskeratosis congenita, autosomal dominant 2;Idiopathic Pulmonary Fibrosis|not provided|Hoyeraal-Hreidarsson syndrome;Autosomal recessive dyskeratosis congenita 4|Telomere syndrome|Dyskeratosis congenita",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}