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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: 16-13935661-T-TA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=13935661&ref=T&alt=TA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 13935661,
"ref": "T",
"alt": "TA",
"effect": "frameshift_variant,stop_gained",
"transcript": "ENST00000311895.8",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.1730dupA",
"hgvs_p": "p.Tyr577fs",
"transcript": "NM_005236.3",
"protein_id": "NP_005227.1",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 916,
"cds_start": 1731,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 1743,
"cdna_end": null,
"cdna_length": 6764,
"mane_select": "ENST00000311895.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.1730dupA",
"hgvs_p": "p.Tyr577fs",
"transcript": "ENST00000311895.8",
"protein_id": "ENSP00000310520.7",
"transcript_support_level": 1,
"aa_start": 577,
"aa_end": null,
"aa_length": 916,
"cds_start": 1731,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 1743,
"cdna_end": null,
"cdna_length": 6764,
"mane_select": "NM_005236.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.1868dupA",
"hgvs_p": "p.Tyr623fs",
"transcript": "ENST00000682617.1",
"protein_id": "ENSP00000507912.1",
"transcript_support_level": null,
"aa_start": 623,
"aa_end": null,
"aa_length": 962,
"cds_start": 1869,
"cds_end": null,
"cds_length": 2889,
"cdna_start": 1897,
"cdna_end": null,
"cdna_length": 6918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.1868dupA",
"hgvs_p": "p.Tyr623fs",
"transcript": "XM_011522424.4",
"protein_id": "XP_011520726.1",
"transcript_support_level": null,
"aa_start": 623,
"aa_end": null,
"aa_length": 962,
"cds_start": 1869,
"cds_end": null,
"cds_length": 2889,
"cdna_start": 1881,
"cdna_end": null,
"cdna_length": 6902,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.941dupA",
"hgvs_p": "p.Tyr314fs",
"transcript": "XM_047433774.1",
"protein_id": "XP_047289730.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 653,
"cds_start": 942,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 1087,
"cdna_end": null,
"cdna_length": 6108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "c.380dupA",
"hgvs_p": "p.Tyr127fs",
"transcript": "XM_011522427.2",
"protein_id": "XP_011520729.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 466,
"cds_start": 381,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 5739,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.1007dupA",
"hgvs_p": null,
"transcript": "ENST00000389138.7",
"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": 2106,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.1808dupA",
"hgvs_p": null,
"transcript": "ENST00000682568.1",
"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": 2161,
"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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*1044dupA",
"hgvs_p": null,
"transcript": "ENST00000682826.1",
"protein_id": "ENSP00000507274.1",
"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": 4351,
"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": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.3770dupA",
"hgvs_p": null,
"transcript": "ENST00000682909.1",
"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": 6447,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.3375dupA",
"hgvs_p": null,
"transcript": "ENST00000683277.1",
"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": 5930,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.1738dupA",
"hgvs_p": null,
"transcript": "ENST00000683407.1",
"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": 2803,
"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": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*1424dupA",
"hgvs_p": null,
"transcript": "ENST00000683962.1",
"protein_id": "ENSP00000506854.1",
"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": 3925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*1044dupA",
"hgvs_p": null,
"transcript": "ENST00000682826.1",
"protein_id": "ENSP00000507274.1",
"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": 4351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"hgvs_c": "n.*1424dupA",
"hgvs_p": null,
"transcript": "ENST00000683962.1",
"protein_id": "ENSP00000506854.1",
"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": 3925,
"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": "ENSG00000262732",
"gene_hgnc_id": null,
"hgvs_c": "n.-27dupT",
"hgvs_p": null,
"transcript": "ENST00000570663.2",
"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": 398,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000262732",
"gene_hgnc_id": null,
"hgvs_c": "n.-52dupT",
"hgvs_p": null,
"transcript": "ENST00000575137.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 4934,
"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": "ENSG00000262732",
"gene_hgnc_id": null,
"hgvs_c": "n.-43dupT",
"hgvs_p": null,
"transcript": "ENST00000785122.1",
"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": 388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ERCC4",
"gene_hgnc_id": 3436,
"dbsnp": "rs397509404",
"frequency_reference_population": 0.0000027362664,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273627,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"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": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.372,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000311895.8",
"gene_symbol": "ERCC4",
"hgnc_id": 3436,
"effects": [
"frameshift_variant",
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1730dupA",
"hgvs_p": "p.Tyr577fs"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000570663.2",
"gene_symbol": "ENSG00000262732",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-27dupT",
"hgvs_p": null
}
],
"clinvar_disease": " group F, type F/Cockayne syndrome,Cockayne syndrome,Fanconi anemia complementation group Q,Spastic ataxia,Xeroderma pigmentosum",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Xeroderma pigmentosum, type F/Cockayne syndrome|Spastic ataxia|Cockayne syndrome;Xeroderma pigmentosum, group F;Fanconi anemia complementation group Q",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}