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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: 2-3388304-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=3388304&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 3388304,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000324266.10",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "NM_016030.6",
"protein_id": "NP_057114.5",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 735,
"cds_start": 681,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 2499,
"mane_select": "ENST00000324266.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "ENST00000324266.10",
"protein_id": "ENSP00000324318.5",
"transcript_support_level": 1,
"aa_start": 227,
"aa_end": null,
"aa_length": 735,
"cds_start": 681,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 2499,
"mane_select": "NM_016030.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "NM_001321102.2",
"protein_id": "NP_001308031.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 735,
"cds_start": 681,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 831,
"cdna_end": null,
"cdna_length": 2462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "ENST00000382110.6",
"protein_id": "ENSP00000371544.2",
"transcript_support_level": 2,
"aa_start": 227,
"aa_end": null,
"aa_length": 735,
"cds_start": 681,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 2483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_011510350.3",
"protein_id": "XP_011508652.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 697,
"cds_start": 681,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 2385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_047444637.1",
"protein_id": "XP_047300593.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 697,
"cds_start": 681,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 831,
"cdna_end": null,
"cdna_length": 2348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_011510352.3",
"protein_id": "XP_011508654.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 578,
"cds_start": 681,
"cds_end": null,
"cds_length": 1737,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 3819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_047444638.1",
"protein_id": "XP_047300594.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 578,
"cds_start": 681,
"cds_end": null,
"cds_length": 1737,
"cdna_start": 831,
"cdna_end": null,
"cdna_length": 3782,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_047444639.1",
"protein_id": "XP_047300595.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 540,
"cds_start": 681,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 3705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_011510353.3",
"protein_id": "XP_011508655.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 537,
"cds_start": 681,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 2385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe",
"transcript": "XM_011510354.3",
"protein_id": "XP_011508656.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 517,
"cds_start": 681,
"cds_end": null,
"cds_length": 1554,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 2691,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "n.177T>C",
"hgvs_p": null,
"transcript": "ENST00000411973.3",
"protein_id": "ENSP00000405626.1",
"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": 838,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "n.842T>C",
"hgvs_p": null,
"transcript": "ENST00000482645.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1538,
"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": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "n.868T>C",
"hgvs_p": null,
"transcript": "XR_001738761.2",
"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": 2604,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "n.868T>C",
"hgvs_p": null,
"transcript": "XR_007076381.1",
"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": 4692,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "n.868T>C",
"hgvs_p": null,
"transcript": "XR_007076382.1",
"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": 1530,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"hgvs_c": "n.868T>C",
"hgvs_p": null,
"transcript": "XR_426956.4",
"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": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRAPPC12",
"gene_hgnc_id": 24284,
"dbsnp": "rs10865541",
"frequency_reference_population": 0.5933976,
"hom_count_reference_population": 284338,
"allele_count_reference_population": 953228,
"gnomad_exomes_af": 0.59052,
"gnomad_genomes_af": 0.620945,
"gnomad_exomes_ac": 858899,
"gnomad_genomes_ac": 94329,
"gnomad_exomes_homalt": 254773,
"gnomad_genomes_homalt": 29565,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6100000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.715,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000324266.10",
"gene_symbol": "TRAPPC12",
"hgnc_id": 24284,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.681T>C",
"hgvs_p": "p.Phe227Phe"
}
],
"clinvar_disease": "Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome,TRAPPC12-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|TRAPPC12-related disorder|Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}