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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-119542514-CTCCTCT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=119542514&ref=CTCCTCT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 119542514,
"ref": "CTCCTCT",
"alt": "C",
"effect": "disruptive_inframe_deletion",
"transcript": "NM_022101.4",
"consequences": [
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.498_503delAGAGGA",
"hgvs_p": "p.Glu167_Glu168del",
"transcript": "NM_022101.4",
"protein_id": "NP_071384.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 222,
"cds_start": 498,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000644802.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022101.4"
},
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.498_503delAGAGGA",
"hgvs_p": "p.Glu167_Glu168del",
"transcript": "ENST00000644802.2",
"protein_id": "ENSP00000494123.2",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 222,
"cds_start": 498,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022101.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644802.2"
},
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.498_503delAGAGGA",
"hgvs_p": "p.Glu167_Glu168del",
"transcript": "ENST00000868973.1",
"protein_id": "ENSP00000539032.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 222,
"cds_start": 498,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868973.1"
},
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.456_461delAGAGGA",
"hgvs_p": "p.Glu153_Glu154del",
"transcript": "NM_001170570.2",
"protein_id": "NP_001164041.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 208,
"cds_start": 456,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001170570.2"
},
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.456_461delAGAGGA",
"hgvs_p": "p.Glu153_Glu154del",
"transcript": "ENST00000536133.2",
"protein_id": "ENSP00000441786.1",
"transcript_support_level": 2,
"aa_start": 152,
"aa_end": null,
"aa_length": 208,
"cds_start": 456,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000536133.2"
},
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.351_356delAGAGGA",
"hgvs_p": "p.Glu118_Glu119del",
"transcript": "NM_001170569.1",
"protein_id": "NP_001164040.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 173,
"cds_start": 351,
"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_001170569.1"
},
{
"aa_ref": "EEE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "c.351_356delAGAGGA",
"hgvs_p": "p.Glu118_Glu119del",
"transcript": "ENST00000320339.8",
"protein_id": "ENSP00000320345.4",
"transcript_support_level": 2,
"aa_start": 117,
"aa_end": null,
"aa_length": 173,
"cds_start": 351,
"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": "ENST00000320339.8"
},
{
"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": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.-157-31120_-157-31115delCTCTTC",
"hgvs_p": null,
"transcript": "ENST00000696533.1",
"protein_id": "ENSP00000512694.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696533.1"
},
{
"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": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.-487-17_-487-12delCTCTTC",
"hgvs_p": null,
"transcript": "ENST00000696539.1",
"protein_id": "ENSP00000512700.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000696539.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"hgvs_c": "n.248_253delAGAGGA",
"hgvs_p": null,
"transcript": "ENST00000469448.1",
"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": "pseudogene",
"feature": "ENST00000469448.1"
}
],
"gene_symbol": "STEEP1",
"gene_hgnc_id": 26239,
"dbsnp": "rs2053171807",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.114,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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_pathogenic",
"acmg_criteria": "PM2,PM4,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM4",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_022101.4",
"gene_symbol": "STEEP1",
"hgnc_id": 26239,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "XL",
"hgvs_c": "c.498_503delAGAGGA",
"hgvs_p": "p.Glu167_Glu168del"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000696533.1",
"gene_symbol": "UBE2A",
"hgnc_id": 12472,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.-157-31120_-157-31115delCTCTTC",
"hgvs_p": null
}
],
"clinvar_disease": " X-linked 107,Intellectual disability",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Intellectual disability, X-linked 107",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}