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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: 5-65658419-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=65658419&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 65658419,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001093755.2",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.616A>G",
"hgvs_p": "p.Met206Val",
"transcript": "NM_024941.4",
"protein_id": "NP_079217.2",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 417,
"cds_start": 616,
"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": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.616A>G",
"hgvs_p": "p.Met206Val",
"transcript": "ENST00000399438.8",
"protein_id": "ENSP00000382367.3",
"transcript_support_level": 2,
"aa_start": 206,
"aa_end": null,
"aa_length": 417,
"cds_start": 616,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.616A>G",
"hgvs_p": "p.Met206Val",
"transcript": "ENST00000438419.6",
"protein_id": "ENSP00000409231.2",
"transcript_support_level": 1,
"aa_start": 206,
"aa_end": null,
"aa_length": 418,
"cds_start": 616,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.598A>G",
"hgvs_p": "p.Met200Val",
"transcript": "ENST00000505553.5",
"protein_id": "ENSP00000423405.1",
"transcript_support_level": 1,
"aa_start": 200,
"aa_end": null,
"aa_length": 412,
"cds_start": 598,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.616A>G",
"hgvs_p": "p.Met206Val",
"transcript": "NM_001093755.2",
"protein_id": "NP_001087224.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 418,
"cds_start": 616,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.616A>G",
"hgvs_p": "p.Met206Val",
"transcript": "ENST00000715762.1",
"protein_id": "ENSP00000520517.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 417,
"cds_start": 616,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.598A>G",
"hgvs_p": "p.Met200Val",
"transcript": "NM_001243737.2",
"protein_id": "NP_001230666.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 412,
"cds_start": 598,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.598A>G",
"hgvs_p": "p.Met200Val",
"transcript": "NM_001093756.2",
"protein_id": "NP_001087225.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 411,
"cds_start": 598,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.598A>G",
"hgvs_p": "p.Met200Val",
"transcript": "ENST00000231526.8",
"protein_id": "ENSP00000231526.4",
"transcript_support_level": 5,
"aa_start": 200,
"aa_end": null,
"aa_length": 411,
"cds_start": 598,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.127A>G",
"hgvs_p": "p.Met43Val",
"transcript": "NM_001365342.1",
"protein_id": "NP_001352271.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 255,
"cds_start": 127,
"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": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "c.127A>G",
"hgvs_p": "p.Met43Val",
"transcript": "NM_001365343.1",
"protein_id": "NP_001352272.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 254,
"cds_start": 127,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.*285A>G",
"hgvs_p": null,
"transcript": "ENST00000504243.5",
"protein_id": "ENSP00000429396.1",
"transcript_support_level": 5,
"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": "ENST00000504243.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.*267A>G",
"hgvs_p": null,
"transcript": "ENST00000504751.5",
"protein_id": "ENSP00000424343.1",
"transcript_support_level": 4,
"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": "ENST00000504751.5"
},
{
"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": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.449A>G",
"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"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.655A>G",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.72A>G",
"hgvs_p": null,
"transcript": "ENST00000520525.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000520525.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.*285A>G",
"hgvs_p": null,
"transcript": "ENST00000504243.5",
"protein_id": "ENSP00000429396.1",
"transcript_support_level": 5,
"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": "ENST00000504243.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"hgvs_c": "n.*267A>G",
"hgvs_p": null,
"transcript": "ENST00000504751.5",
"protein_id": "ENSP00000424343.1",
"transcript_support_level": 4,
"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": "ENST00000504751.5"
}
],
"gene_symbol": "TRAPPC13",
"gene_hgnc_id": 25828,
"dbsnp": "rs1312624222",
"frequency_reference_population": 0.0000013847883,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000138479,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3982836604118347,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.439,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1991,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.835,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001093755.2",
"gene_symbol": "TRAPPC13",
"hgnc_id": 25828,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.616A>G",
"hgvs_p": "p.Met206Val"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}