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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-119574713-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=119574713&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 119574713,
"ref": "T",
"alt": "G",
"effect": "start_lost",
"transcript": "ENST00000371558.7",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_003336.4",
"protein_id": "NP_003327.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 152,
"cds_start": 2,
"cds_end": null,
"cds_length": 459,
"cdna_start": 151,
"cdna_end": null,
"cdna_length": 1776,
"mane_select": "ENST00000371558.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000371558.7",
"protein_id": "ENSP00000360613.2",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 152,
"cds_start": 2,
"cds_end": null,
"cds_length": 459,
"cdna_start": 151,
"cdna_end": null,
"cdna_length": 1776,
"mane_select": "NM_003336.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000696534.1",
"protein_id": "ENSP00000512695.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 152,
"cds_start": 2,
"cds_end": null,
"cds_length": 459,
"cdna_start": 368,
"cdna_end": null,
"cdna_length": 1993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000346330.6",
"protein_id": "ENSP00000335027.4",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 149,
"cds_start": 2,
"cds_end": null,
"cds_length": 450,
"cdna_start": 178,
"cdna_end": null,
"cdna_length": 718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000631185.2",
"protein_id": "ENSP00000486153.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 123,
"cds_start": 2,
"cds_end": null,
"cds_length": 372,
"cdna_start": 151,
"cdna_end": null,
"cdna_length": 1435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_181762.3",
"protein_id": "NP_861427.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 122,
"cds_start": 2,
"cds_end": null,
"cds_length": 369,
"cdna_start": 151,
"cdna_end": null,
"cdna_length": 1686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000625938.2",
"protein_id": "ENSP00000486599.1",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 122,
"cds_start": 2,
"cds_end": null,
"cds_length": 369,
"cdna_start": 168,
"cdna_end": null,
"cdna_length": 1381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.218T>G",
"hgvs_p": "p.Met73Arg",
"transcript": "ENST00000696533.1",
"protein_id": "ENSP00000512694.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 224,
"cds_start": 218,
"cds_end": null,
"cds_length": 675,
"cdna_start": 468,
"cdna_end": null,
"cdna_length": 2093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.218T>G",
"hgvs_p": "p.Met73Arg",
"transcript": "ENST00000696539.1",
"protein_id": "ENSP00000512700.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 224,
"cds_start": 218,
"cds_end": null,
"cds_length": 675,
"cdna_start": 798,
"cdna_end": null,
"cdna_length": 2423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "n.143T>G",
"hgvs_p": null,
"transcript": "ENST00000469205.2",
"protein_id": null,
"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": 686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "n.165T>G",
"hgvs_p": null,
"transcript": "ENST00000625379.1",
"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": 704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "n.2T>G",
"hgvs_p": null,
"transcript": "ENST00000629303.2",
"protein_id": "ENSP00000486347.1",
"transcript_support_level": 4,
"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": 557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.-91T>G",
"hgvs_p": null,
"transcript": "NM_001282161.2",
"protein_id": "NP_001269090.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": -4,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.-217T>G",
"hgvs_p": null,
"transcript": "ENST00000630695.2",
"protein_id": "ENSP00000486550.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 77,
"cds_start": -4,
"cds_end": null,
"cds_length": 234,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"hgvs_c": "c.-243T>G",
"hgvs_p": null,
"transcript": "ENST00000628549.1",
"protein_id": "ENSP00000487203.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 119,
"cds_start": -4,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124905208",
"gene_hgnc_id": null,
"hgvs_c": "n.-218A>C",
"hgvs_p": null,
"transcript": "XR_007068307.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UBE2A",
"gene_hgnc_id": 12472,
"dbsnp": "rs1556235129",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9926849603652954,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.753,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.742,
"phylop100way_prediction": "Uncertain_significance",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371558.7",
"gene_symbol": "UBE2A",
"hgnc_id": 12472,
"effects": [
"start_lost"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_007068307.1",
"gene_symbol": "LOC124905208",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-218A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}