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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-110453979-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=110453979&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 110453979,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000520821.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "NM_001385449.1",
"protein_id": "NP_001372378.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3598,
"cdna_end": null,
"cdna_length": 5416,
"mane_select": "ENST00000520821.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "ENST00000520821.6",
"protein_id": "ENSP00000430395.2",
"transcript_support_level": 4,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3598,
"cdna_end": null,
"cdna_length": 5416,
"mane_select": "NM_001385449.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "ENST00000465301.2",
"protein_id": "ENSP00000419786.2",
"transcript_support_level": 1,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3608,
"cdna_end": null,
"cdna_length": 5426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "NM_020769.2",
"protein_id": "NP_065820.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3608,
"cdna_end": null,
"cdna_length": 5426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "ENST00000540313.1",
"protein_id": "ENSP00000441452.1",
"transcript_support_level": 2,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3415,
"cdna_end": null,
"cdna_length": 5225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_011530999.3",
"protein_id": "XP_011529301.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3732,
"cdna_end": null,
"cdna_length": 5550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_017029695.2",
"protein_id": "XP_016885184.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3865,
"cdna_end": null,
"cdna_length": 5683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_047442283.1",
"protein_id": "XP_047298239.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3895,
"cdna_end": null,
"cdna_length": 5713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_047442284.1",
"protein_id": "XP_047298240.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3903,
"cdna_end": null,
"cdna_length": 5721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_047442285.1",
"protein_id": "XP_047298241.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3770,
"cdna_end": null,
"cdna_length": 5588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_047442286.1",
"protein_id": "XP_047298242.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3636,
"cdna_end": null,
"cdna_length": 5454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_047442287.1",
"protein_id": "XP_047298243.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3628,
"cdna_end": null,
"cdna_length": 5446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu",
"transcript": "XM_047442288.1",
"protein_id": "XP_047298244.1",
"transcript_support_level": null,
"aa_start": 1121,
"aa_end": null,
"aa_length": 1388,
"cds_start": 3362,
"cds_end": null,
"cds_length": 4167,
"cdna_start": 3762,
"cdna_end": null,
"cdna_length": 5580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RTL9",
"gene_hgnc_id": 29245,
"dbsnp": "rs771130284",
"frequency_reference_population": 0.000016525579,
"hom_count_reference_population": 7,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000173009,
"gnomad_genomes_af": 0.00000892554,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.069857656955719,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.039,
"revel_prediction": "Benign",
"alphamissense_score": 0.0857,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.415,
"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": "ENST00000520821.6",
"gene_symbol": "RTL9",
"hgnc_id": 29245,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.3362C>T",
"hgvs_p": "p.Ser1121Leu"
}
],
"clinvar_disease": " X-linked,Spinocerebellar ataxia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Spinocerebellar ataxia, X-linked",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}