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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: 12-88153300-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=88153300&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 88153300,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000266712.11",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.199C>T",
"hgvs_p": "p.His67Tyr",
"transcript": "NM_181783.4",
"protein_id": "NP_861448.2",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 914,
"cds_start": 199,
"cds_end": null,
"cds_length": 2745,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 7192,
"mane_select": "ENST00000266712.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.199C>T",
"hgvs_p": "p.His67Tyr",
"transcript": "ENST00000266712.11",
"protein_id": "ENSP00000266712.6",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 914,
"cds_start": 199,
"cds_end": null,
"cds_length": 2745,
"cdna_start": 408,
"cdna_end": null,
"cdna_length": 7192,
"mane_select": "NM_181783.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "n.199C>T",
"hgvs_p": null,
"transcript": "ENST00000547034.5",
"protein_id": "ENSP00000448733.1",
"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": 1842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.His7Tyr",
"transcript": "NM_001366574.1",
"protein_id": "NP_001353503.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 854,
"cds_start": 19,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 277,
"cdna_end": null,
"cdna_length": 7061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.199C>T",
"hgvs_p": "p.His67Tyr",
"transcript": "ENST00000549011.5",
"protein_id": "ENSP00000447640.1",
"transcript_support_level": 4,
"aa_start": 67,
"aa_end": null,
"aa_length": 147,
"cds_start": 199,
"cds_end": null,
"cds_length": 445,
"cdna_start": 328,
"cdna_end": null,
"cdna_length": 574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "n.408C>T",
"hgvs_p": null,
"transcript": "NR_159381.1",
"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": 7316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.-69C>T",
"hgvs_p": null,
"transcript": "NM_001366580.1",
"protein_id": "NP_001353509.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 825,
"cds_start": -4,
"cds_end": null,
"cds_length": 2478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.190-988C>T",
"hgvs_p": null,
"transcript": "NM_001366579.1",
"protein_id": "NP_001353508.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 841,
"cds_start": -4,
"cds_end": null,
"cds_length": 2526,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.-285-988C>T",
"hgvs_p": null,
"transcript": "NM_001366583.1",
"protein_id": "NP_001353512.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 683,
"cds_start": -4,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.190-988C>T",
"hgvs_p": null,
"transcript": "ENST00000551088.1",
"protein_id": "ENSP00000448566.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": -4,
"cds_end": null,
"cds_length": 437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"dbsnp": "rs754200057",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8847717046737671,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.821,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.55,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000266712.11",
"gene_symbol": "TMTC3",
"hgnc_id": 26899,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.199C>T",
"hgvs_p": "p.His67Tyr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}