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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: 19-45163970-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45163970&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 45163970,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024108.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.394T>A",
"hgvs_p": "p.Tyr132Asn",
"transcript": "NM_001270891.2",
"protein_id": "NP_001257820.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 159,
"cds_start": 394,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000585934.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001270891.2"
},
{
"aa_ref": "Y",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.394T>A",
"hgvs_p": "p.Tyr132Asn",
"transcript": "ENST00000585934.1",
"protein_id": "ENSP00000468612.1",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 159,
"cds_start": 394,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001270891.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000585934.1"
},
{
"aa_ref": "Y",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.436T>A",
"hgvs_p": "p.Tyr146Asn",
"transcript": "ENST00000006275.8",
"protein_id": "ENSP00000006275.3",
"transcript_support_level": 1,
"aa_start": 146,
"aa_end": null,
"aa_length": 173,
"cds_start": 436,
"cds_end": null,
"cds_length": 522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000006275.8"
},
{
"aa_ref": "Y",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.436T>A",
"hgvs_p": "p.Tyr146Asn",
"transcript": "NM_024108.3",
"protein_id": "NP_077013.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 173,
"cds_start": 436,
"cds_end": null,
"cds_length": 522,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024108.3"
},
{
"aa_ref": "Y",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.352T>A",
"hgvs_p": "p.Tyr118Asn",
"transcript": "ENST00000940426.1",
"protein_id": "ENSP00000610485.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 145,
"cds_start": 352,
"cds_end": null,
"cds_length": 438,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940426.1"
},
{
"aa_ref": "Y",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.310T>A",
"hgvs_p": "p.Tyr104Asn",
"transcript": "ENST00000879979.1",
"protein_id": "ENSP00000550038.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 131,
"cds_start": 310,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879979.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.368T>A",
"hgvs_p": "p.Leu123Gln",
"transcript": "NM_001270892.2",
"protein_id": "NP_001257821.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 127,
"cds_start": 368,
"cds_end": null,
"cds_length": 384,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001270892.2"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.368T>A",
"hgvs_p": "p.Leu123Gln",
"transcript": "ENST00000592647.1",
"protein_id": "ENSP00000468182.1",
"transcript_support_level": 2,
"aa_start": 123,
"aa_end": null,
"aa_length": 127,
"cds_start": 368,
"cds_end": null,
"cds_length": 384,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592647.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.326T>A",
"hgvs_p": "p.Leu109Gln",
"transcript": "NM_001270893.2",
"protein_id": "NP_001257822.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 113,
"cds_start": 326,
"cds_end": null,
"cds_length": 342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001270893.2"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.326T>A",
"hgvs_p": "p.Leu109Gln",
"transcript": "ENST00000588062.5",
"protein_id": "ENSP00000468363.1",
"transcript_support_level": 2,
"aa_start": 109,
"aa_end": null,
"aa_length": 113,
"cds_start": 326,
"cds_end": null,
"cds_length": 342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588062.5"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.368T>A",
"hgvs_p": "p.Leu123Gln",
"transcript": "XM_047439419.1",
"protein_id": "XP_047295375.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 127,
"cds_start": 368,
"cds_end": null,
"cds_length": 384,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439419.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.326T>A",
"hgvs_p": "p.Leu109Gln",
"transcript": "XM_047439420.1",
"protein_id": "XP_047295376.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 113,
"cds_start": 326,
"cds_end": null,
"cds_length": 342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439420.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.328+194T>A",
"hgvs_p": null,
"transcript": "ENST00000940427.1",
"protein_id": "ENSP00000610486.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": null,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940427.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"hgvs_c": "c.286+194T>A",
"hgvs_p": null,
"transcript": "ENST00000940428.1",
"protein_id": "ENSP00000610487.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 105,
"cds_start": null,
"cds_end": null,
"cds_length": 318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940428.1"
},
{
"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": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MARK4",
"gene_hgnc_id": 13538,
"hgvs_c": "c.-277+84593A>T",
"hgvs_p": null,
"transcript": "ENST00000587566.5",
"protein_id": "ENSP00000465414.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": null,
"cds_end": null,
"cds_length": 187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587566.5"
}
],
"gene_symbol": "TRAPPC6A",
"gene_hgnc_id": 23069,
"dbsnp": "rs774235826",
"frequency_reference_population": 0.000018970988,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000153918,
"gnomad_genomes_af": 0.0000526226,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0603310763835907,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.033,
"revel_prediction": "Benign",
"alphamissense_score": 0.0596,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.972,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_024108.3",
"gene_symbol": "TRAPPC6A",
"hgnc_id": 23069,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.436T>A",
"hgvs_p": "p.Tyr146Asn"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000587566.5",
"gene_symbol": "MARK4",
"hgnc_id": 13538,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-277+84593A>T",
"hgvs_p": null
}
],
"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
}