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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-47142420-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47142420&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 47142420,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001135998.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.359G>A",
"hgvs_p": "p.Arg120His",
"transcript": "NM_001135998.3",
"protein_id": "NP_001129470.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 153,
"cds_start": 359,
"cds_end": null,
"cds_length": 462,
"cdna_start": 382,
"cdna_end": null,
"cdna_length": 586,
"mane_select": "ENST00000377811.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.359G>A",
"hgvs_p": "p.Arg120His",
"transcript": "ENST00000377811.4",
"protein_id": "ENSP00000367042.3",
"transcript_support_level": 1,
"aa_start": 120,
"aa_end": null,
"aa_length": 153,
"cds_start": 359,
"cds_end": null,
"cds_length": 462,
"cdna_start": 382,
"cdna_end": null,
"cdna_length": 586,
"mane_select": "NM_001135998.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.*16G>A",
"hgvs_p": null,
"transcript": "ENST00000276062.9",
"protein_id": "ENSP00000276062.9",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 111,
"cds_start": -4,
"cds_end": null,
"cds_length": 336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.389G>A",
"hgvs_p": "p.Arg130His",
"transcript": "NM_019056.7",
"protein_id": "NP_061929.2",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 163,
"cds_start": 389,
"cds_end": null,
"cds_length": 492,
"cdna_start": 1201,
"cdna_end": null,
"cdna_length": 1405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.389G>A",
"hgvs_p": "p.Arg130His",
"transcript": "ENST00000687244.1",
"protein_id": "ENSP00000509334.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 163,
"cds_start": 389,
"cds_end": null,
"cds_length": 492,
"cdna_start": 1176,
"cdna_end": null,
"cdna_length": 1525,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "n.847G>A",
"hgvs_p": null,
"transcript": "ENST00000685599.1",
"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": 1027,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "n.1786G>A",
"hgvs_p": null,
"transcript": "ENST00000690204.1",
"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": 1990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.*160G>A",
"hgvs_p": null,
"transcript": "ENST00000690053.1",
"protein_id": "ENSP00000509556.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 123,
"cds_start": -4,
"cds_end": null,
"cds_length": 372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "c.*16G>A",
"hgvs_p": null,
"transcript": "ENST00000692649.1",
"protein_id": "ENSP00000510488.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 110,
"cds_start": -4,
"cds_end": null,
"cds_length": 333,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"hgvs_c": "n.*405G>A",
"hgvs_p": null,
"transcript": "ENST00000688286.1",
"protein_id": "ENSP00000510534.1",
"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": 537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NDUFB11",
"gene_hgnc_id": 20372,
"dbsnp": "rs782753177",
"frequency_reference_population": 0.00002644755,
"hom_count_reference_population": 9,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000227661,
"gnomad_genomes_af": 0.0000626017,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.46147310733795166,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.416,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1742,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.558,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001135998.3",
"gene_symbol": "NDUFB11",
"hgnc_id": 20372,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.359G>A",
"hgvs_p": "p.Arg120His"
}
],
"clinvar_disease": "Linear skin defects with multiple congenital anomalies 1,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Linear skin defects with multiple congenital anomalies 1|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}