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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: 5-65664567-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=65664567&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 65664567,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001093755.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1210G>T",
"hgvs_p": "p.Ala404Ser",
"transcript": "NM_024941.4",
"protein_id": "NP_079217.2",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 417,
"cds_start": 1210,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000399438.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024941.4"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1210G>T",
"hgvs_p": "p.Ala404Ser",
"transcript": "ENST00000399438.8",
"protein_id": "ENSP00000382367.3",
"transcript_support_level": 2,
"aa_start": 404,
"aa_end": null,
"aa_length": 417,
"cds_start": 1210,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024941.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399438.8"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1213G>T",
"hgvs_p": "p.Ala405Ser",
"transcript": "ENST00000438419.6",
"protein_id": "ENSP00000409231.2",
"transcript_support_level": 1,
"aa_start": 405,
"aa_end": null,
"aa_length": 418,
"cds_start": 1213,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000438419.6"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1195G>T",
"hgvs_p": "p.Ala399Ser",
"transcript": "ENST00000505553.5",
"protein_id": "ENSP00000423405.1",
"transcript_support_level": 1,
"aa_start": 399,
"aa_end": null,
"aa_length": 412,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505553.5"
},
{
"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": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.330G>T",
"hgvs_p": null,
"transcript": "ENST00000415825.2",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000415825.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1213G>T",
"hgvs_p": "p.Ala405Ser",
"transcript": "NM_001093755.2",
"protein_id": "NP_001087224.1",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 418,
"cds_start": 1213,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001093755.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1210G>T",
"hgvs_p": "p.Ala404Ser",
"transcript": "ENST00000715762.1",
"protein_id": "ENSP00000520517.1",
"transcript_support_level": null,
"aa_start": 404,
"aa_end": null,
"aa_length": 417,
"cds_start": 1210,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000715762.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1195G>T",
"hgvs_p": "p.Ala399Ser",
"transcript": "NM_001243737.2",
"protein_id": "NP_001230666.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 412,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001243737.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1192G>T",
"hgvs_p": "p.Ala398Ser",
"transcript": "NM_001093756.2",
"protein_id": "NP_001087225.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 411,
"cds_start": 1192,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001093756.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.1192G>T",
"hgvs_p": "p.Ala398Ser",
"transcript": "ENST00000231526.8",
"protein_id": "ENSP00000231526.4",
"transcript_support_level": 5,
"aa_start": 398,
"aa_end": null,
"aa_length": 411,
"cds_start": 1192,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000231526.8"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.724G>T",
"hgvs_p": "p.Ala242Ser",
"transcript": "NM_001365342.1",
"protein_id": "NP_001352271.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 255,
"cds_start": 724,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365342.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.721G>T",
"hgvs_p": "p.Ala241Ser",
"transcript": "NM_001365343.1",
"protein_id": "NP_001352272.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 254,
"cds_start": 721,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365343.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.647G>T",
"hgvs_p": null,
"transcript": "ENST00000505108.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000505108.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.4487G>T",
"hgvs_p": null,
"transcript": "ENST00000512009.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000512009.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.*186G>T",
"hgvs_p": null,
"transcript": "ENST00000509234.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000509234.1"
}
],
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"dbsnp": "rs201524074",
"frequency_reference_population": 0.0000037213272,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000342413,
"gnomad_genomes_af": 0.00000657445,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5413982272148132,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.183,
"revel_prediction": "Benign",
"alphamissense_score": 0.1452,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.526,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001093755.2",
"gene_symbol": "TRAPPC13",
"hgnc_id": 25828,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1213G>T",
"hgvs_p": "p.Ala405Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}