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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: 1-117113385-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=117113385&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 117113385,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_025188.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"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": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "c.1568G>A",
"hgvs_p": "p.Arg523His",
"transcript": "NM_025188.4",
"protein_id": "NP_079464.2",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 580,
"cds_start": 1568,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000256649.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025188.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "c.1568G>A",
"hgvs_p": "p.Arg523His",
"transcript": "ENST00000256649.9",
"protein_id": "ENSP00000256649.4",
"transcript_support_level": 1,
"aa_start": 523,
"aa_end": null,
"aa_length": 580,
"cds_start": 1568,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025188.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000256649.9"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "c.1514G>A",
"hgvs_p": "p.Arg505His",
"transcript": "ENST00000369464.7",
"protein_id": "ENSP00000358476.3",
"transcript_support_level": 1,
"aa_start": 505,
"aa_end": null,
"aa_length": 562,
"cds_start": 1514,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369464.7"
},
{
"aa_ref": "R",
"aa_alt": "H",
"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": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "c.1514G>A",
"hgvs_p": "p.Arg505His",
"transcript": "NM_001145635.2",
"protein_id": "NP_001139107.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 562,
"cds_start": 1514,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145635.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "c.1397G>A",
"hgvs_p": "p.Arg466His",
"transcript": "ENST00000369461.3",
"protein_id": "ENSP00000358473.3",
"transcript_support_level": 5,
"aa_start": 466,
"aa_end": null,
"aa_length": 523,
"cds_start": 1397,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369461.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "c.1256G>A",
"hgvs_p": "p.Arg419His",
"transcript": "XM_047430914.1",
"protein_id": "XP_047286870.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 476,
"cds_start": 1256,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047430914.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "n.137G>A",
"hgvs_p": null,
"transcript": "ENST00000497970.5",
"protein_id": "ENSP00000431261.1",
"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": "ENST00000497970.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "n.2062G>A",
"hgvs_p": null,
"transcript": "XR_007063980.1",
"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": "XR_007063980.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM45",
"gene_hgnc_id": 19018,
"hgvs_c": "n.2116G>A",
"hgvs_p": null,
"transcript": "XR_246297.2",
"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": "XR_246297.2"
}
],
"gene_symbol": "TRIM45",
"gene_hgnc_id": 19018,
"dbsnp": "rs199984487",
"frequency_reference_population": 0.000049001366,
"hom_count_reference_population": 1,
"allele_count_reference_population": 79,
"gnomad_exomes_af": 0.0000513754,
"gnomad_genomes_af": 0.000026254,
"gnomad_exomes_ac": 75,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.26583003997802734,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.316,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0795,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.51,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_025188.4",
"gene_symbol": "TRIM45",
"hgnc_id": 19018,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1568G>A",
"hgvs_p": "p.Arg523His"
}
],
"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
}