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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: 12-88153373-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=88153373&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 88153373,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_181783.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"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.272C>T",
"hgvs_p": "p.Ser91Leu",
"transcript": "NM_181783.4",
"protein_id": "NP_861448.2",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 914,
"cds_start": 272,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000266712.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_181783.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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.272C>T",
"hgvs_p": "p.Ser91Leu",
"transcript": "ENST00000266712.11",
"protein_id": "ENSP00000266712.6",
"transcript_support_level": 1,
"aa_start": 91,
"aa_end": null,
"aa_length": 914,
"cds_start": 272,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_181783.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000266712.11"
},
{
"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.272C>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": 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": "ENST00000547034.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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.272C>T",
"hgvs_p": "p.Ser91Leu",
"transcript": "ENST00000869786.1",
"protein_id": "ENSP00000539845.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 914,
"cds_start": 272,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869786.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"hgvs_c": "c.272C>T",
"hgvs_p": "p.Ser91Leu",
"transcript": "ENST00000920416.1",
"protein_id": "ENSP00000590475.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 914,
"cds_start": 272,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920416.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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.272C>T",
"hgvs_p": "p.Ser91Leu",
"transcript": "ENST00000920417.1",
"protein_id": "ENSP00000590476.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 880,
"cds_start": 272,
"cds_end": null,
"cds_length": 2643,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920417.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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.269C>T",
"hgvs_p": "p.Ser90Leu",
"transcript": "ENST00000920415.1",
"protein_id": "ENSP00000590474.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 879,
"cds_start": 269,
"cds_end": null,
"cds_length": 2640,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920415.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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.92C>T",
"hgvs_p": "p.Ser31Leu",
"transcript": "NM_001366574.1",
"protein_id": "NP_001353503.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 854,
"cds_start": 92,
"cds_end": null,
"cds_length": 2565,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366574.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.5C>T",
"hgvs_p": "p.Ser2Leu",
"transcript": "NM_001366580.1",
"protein_id": "NP_001353509.1",
"transcript_support_level": null,
"aa_start": 2,
"aa_end": null,
"aa_length": 825,
"cds_start": 5,
"cds_end": null,
"cds_length": 2478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366580.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"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.272C>T",
"hgvs_p": "p.Ser91Leu",
"transcript": "ENST00000549011.5",
"protein_id": "ENSP00000447640.1",
"transcript_support_level": 4,
"aa_start": 91,
"aa_end": null,
"aa_length": 147,
"cds_start": 272,
"cds_end": null,
"cds_length": 445,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549011.5"
},
{
"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.190-915C>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": null,
"cds_end": null,
"cds_length": 2526,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366579.1"
},
{
"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.-285-915C>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": null,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366583.1"
},
{
"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.190-915C>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": null,
"cds_end": null,
"cds_length": 437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551088.1"
},
{
"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.481C>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": 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_159381.1"
}
],
"gene_symbol": "TMTC3",
"gene_hgnc_id": 26899,
"dbsnp": "rs774374644",
"frequency_reference_population": 0.000004790996,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.000004791,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7091262936592102,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.714,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5131,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.744,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_181783.4",
"gene_symbol": "TMTC3",
"hgnc_id": 26899,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.272C>T",
"hgvs_p": "p.Ser91Leu"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}