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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: X-48893905-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=48893905&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 48893905,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001395498.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.425G>A",
"hgvs_p": "p.Arg142Gln",
"transcript": "NM_001395498.1",
"protein_id": "NP_001382427.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 172,
"cds_start": 425,
"cds_end": null,
"cds_length": 519,
"cdna_start": 444,
"cdna_end": null,
"cdna_length": 818,
"mane_select": "ENST00000696123.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.425G>A",
"hgvs_p": "p.Arg142Gln",
"transcript": "ENST00000696123.1",
"protein_id": "ENSP00000512416.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 172,
"cds_start": 425,
"cds_end": null,
"cds_length": 519,
"cdna_start": 444,
"cdna_end": null,
"cdna_length": 818,
"mane_select": "NM_001395498.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.425G>A",
"hgvs_p": "p.Arg142Gln",
"transcript": "ENST00000376582.7",
"protein_id": "ENSP00000365766.3",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 172,
"cds_start": 425,
"cds_end": null,
"cds_length": 519,
"cdna_start": 574,
"cdna_end": null,
"cdna_length": 950,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.575G>A",
"hgvs_p": "p.Arg192Gln",
"transcript": "NM_001167947.2",
"protein_id": "NP_001161419.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 222,
"cds_start": 575,
"cds_end": null,
"cds_length": 669,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 1100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.575G>A",
"hgvs_p": "p.Arg192Gln",
"transcript": "NM_001395497.1",
"protein_id": "NP_001382426.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 222,
"cds_start": 575,
"cds_end": null,
"cds_length": 669,
"cdna_start": 594,
"cdna_end": null,
"cdna_length": 968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.575G>A",
"hgvs_p": "p.Arg192Gln",
"transcript": "ENST00000396779.7",
"protein_id": "ENSP00000379999.3",
"transcript_support_level": 5,
"aa_start": 192,
"aa_end": null,
"aa_length": 222,
"cds_start": 575,
"cds_end": null,
"cds_length": 669,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 1099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.575G>A",
"hgvs_p": "p.Arg192Gln",
"transcript": "ENST00000465150.6",
"protein_id": "ENSP00000477073.1",
"transcript_support_level": 2,
"aa_start": 192,
"aa_end": null,
"aa_length": 222,
"cds_start": 575,
"cds_end": null,
"cds_length": 669,
"cdna_start": 588,
"cdna_end": null,
"cdna_length": 964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Arg162Gln",
"transcript": "ENST00000495490.6",
"protein_id": "ENSP00000477027.1",
"transcript_support_level": 5,
"aa_start": 162,
"aa_end": null,
"aa_length": 192,
"cds_start": 485,
"cds_end": null,
"cds_length": 579,
"cdna_start": 569,
"cdna_end": null,
"cdna_length": 939,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.446G>A",
"hgvs_p": "p.Arg149Gln",
"transcript": "ENST00000696124.1",
"protein_id": "ENSP00000512417.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 179,
"cds_start": 446,
"cds_end": null,
"cds_length": 540,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"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": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.425G>A",
"hgvs_p": "p.Arg142Gln",
"transcript": "NM_005834.5",
"protein_id": "NP_005825.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 172,
"cds_start": 425,
"cds_end": null,
"cds_length": 519,
"cdna_start": 574,
"cdna_end": null,
"cdna_length": 948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "n.*961G>A",
"hgvs_p": null,
"transcript": "ENST00000466995.5",
"protein_id": "ENSP00000476861.1",
"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": 1528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "n.535G>A",
"hgvs_p": null,
"transcript": "ENST00000472645.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "n.*961G>A",
"hgvs_p": null,
"transcript": "ENST00000466995.5",
"protein_id": "ENSP00000476861.1",
"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": 1528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PQBP1",
"gene_hgnc_id": 9330,
"hgvs_c": "c.-632+3208C>T",
"hgvs_p": null,
"transcript": "ENST00000651767.1",
"protein_id": "ENSP00000498362.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 265,
"cds_start": -4,
"cds_end": null,
"cds_length": 798,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"hgvs_c": "c.*95G>A",
"hgvs_p": null,
"transcript": "ENST00000490755.2",
"protein_id": "ENSP00000477085.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 158,
"cds_start": -4,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TIMM17B",
"gene_hgnc_id": 17310,
"dbsnp": "rs782047781",
"frequency_reference_population": 0.000007466116,
"hom_count_reference_population": 4,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000548893,
"gnomad_genomes_af": 0.0000267054,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06812489032745361,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.038,
"revel_prediction": "Benign",
"alphamissense_score": 0.0616,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.801,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001395498.1",
"gene_symbol": "TIMM17B",
"hgnc_id": 17310,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.425G>A",
"hgvs_p": "p.Arg142Gln"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000651767.1",
"gene_symbol": "PQBP1",
"hgnc_id": 9330,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.-632+3208C>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
}