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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-72205160-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72205160&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 72205160,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_017669.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6L",
"gene_hgnc_id": 20794,
"hgvs_c": "c.3607C>T",
"hgvs_p": "p.Leu1203Phe",
"transcript": "NM_017669.4",
"protein_id": "NP_060139.2",
"transcript_support_level": null,
"aa_start": 1203,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3607,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3723,
"cdna_end": null,
"cdna_length": 4218,
"mane_select": "ENST00000334463.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6L",
"gene_hgnc_id": 20794,
"hgvs_c": "c.3607C>T",
"hgvs_p": "p.Leu1203Phe",
"transcript": "ENST00000334463.4",
"protein_id": "ENSP00000334675.3",
"transcript_support_level": 1,
"aa_start": 1203,
"aa_end": null,
"aa_length": 1250,
"cds_start": 3607,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3723,
"cdna_end": null,
"cdna_length": 4218,
"mane_select": "NM_017669.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"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": "ERCC6L",
"gene_hgnc_id": 20794,
"hgvs_c": "c.3238C>T",
"hgvs_p": "p.Leu1080Phe",
"transcript": "NM_001009954.3",
"protein_id": "NP_001009954.1",
"transcript_support_level": null,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1127,
"cds_start": 3238,
"cds_end": null,
"cds_length": 3384,
"cdna_start": 3841,
"cdna_end": null,
"cdna_length": 4336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"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": "ERCC6L",
"gene_hgnc_id": 20794,
"hgvs_c": "c.3238C>T",
"hgvs_p": "p.Leu1080Phe",
"transcript": "ENST00000373657.2",
"protein_id": "ENSP00000362761.1",
"transcript_support_level": 2,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1127,
"cds_start": 3238,
"cds_end": null,
"cds_length": 3384,
"cdna_start": 3841,
"cdna_end": null,
"cdna_length": 4344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIN4",
"gene_hgnc_id": 8992,
"hgvs_c": "c.312+8256G>A",
"hgvs_p": null,
"transcript": "NM_001170747.1",
"protein_id": "NP_001164218.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": -4,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIN4",
"gene_hgnc_id": 8992,
"hgvs_c": "c.312+8256G>A",
"hgvs_p": null,
"transcript": "ENST00000423432.6",
"protein_id": "ENSP00000409154.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 133,
"cds_start": -4,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIN4",
"gene_hgnc_id": 8992,
"hgvs_c": "c.264+8256G>A",
"hgvs_p": null,
"transcript": "ENST00000652108.2",
"protein_id": "ENSP00000498324.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 117,
"cds_start": -4,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIN4",
"gene_hgnc_id": 8992,
"hgvs_c": "c.237+8256G>A",
"hgvs_p": null,
"transcript": "ENST00000496835.7",
"protein_id": "ENSP00000421676.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 108,
"cds_start": -4,
"cds_end": null,
"cds_length": 327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PIN4",
"gene_hgnc_id": 8992,
"hgvs_c": "n.237+8256G>A",
"hgvs_p": null,
"transcript": "ENST00000439980.7",
"protein_id": "ENSP00000394066.3",
"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": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ERCC6L",
"gene_hgnc_id": 20794,
"dbsnp": "rs1354777511",
"frequency_reference_population": 0.0000018213012,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000018213,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3299003839492798,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.456,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1829,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.309,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_017669.4",
"gene_symbol": "ERCC6L",
"hgnc_id": 20794,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.3607C>T",
"hgvs_p": "p.Leu1203Phe"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001170747.1",
"gene_symbol": "PIN4",
"hgnc_id": 8992,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.312+8256G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}