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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: 4-1056882-C-CG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1056882&ref=C&alt=CG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 1056882,
"ref": "C",
"alt": "CG",
"effect": "frameshift_variant",
"transcript": "NM_001366919.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "c.769dupC",
"hgvs_p": "p.Arg257fs",
"transcript": "NM_001366919.1",
"protein_id": "NP_001353848.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 272,
"cds_start": 769,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366919.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "c.769dupC",
"hgvs_p": "p.Arg257fs",
"transcript": "ENST00000698262.1",
"protein_id": "ENSP00000513634.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 272,
"cds_start": 769,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698262.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "c.667dupC",
"hgvs_p": "p.Arg223fs",
"transcript": "XM_047450083.1",
"protein_id": "XP_047306039.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 238,
"cds_start": 667,
"cds_end": null,
"cds_length": 717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450083.1"
},
{
"aa_ref": "R",
"aa_alt": "P?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "c.505dupC",
"hgvs_p": "p.Arg169fs",
"transcript": "XM_011513446.2",
"protein_id": "XP_011511748.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 184,
"cds_start": 505,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513446.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "c.648-380dupC",
"hgvs_p": null,
"transcript": "NM_001366918.1",
"protein_id": "NP_001353847.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": null,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001366918.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "n.696dupC",
"hgvs_p": null,
"transcript": "ENST00000505693.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000505693.5"
},
{
"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": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "n.351dupC",
"hgvs_p": null,
"transcript": "ENST00000508633.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000508633.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "n.229dupC",
"hgvs_p": null,
"transcript": "ENST00000514024.5",
"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": "retained_intron",
"feature": "ENST00000514024.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "n.696dupC",
"hgvs_p": null,
"transcript": "ENST00000514757.5",
"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": "retained_intron",
"feature": "ENST00000514757.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "n.221-380dupC",
"hgvs_p": null,
"transcript": "ENST00000503206.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000503206.5"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294272",
"gene_hgnc_id": null,
"hgvs_c": "n.815-207dupG",
"hgvs_p": null,
"transcript": "ENST00000722332.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000722332.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "c.*156dupC",
"hgvs_p": null,
"transcript": "XM_047450082.1",
"protein_id": "XP_047306038.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 270,
"cds_start": null,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450082.1"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"hgvs_c": "n.*548dupC",
"hgvs_p": null,
"transcript": "ENST00000506730.5",
"protein_id": "ENSP00000425843.1",
"transcript_support_level": 3,
"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": "nonsense_mediated_decay",
"feature": "ENST00000506730.5"
}
],
"gene_symbol": "RNF212",
"gene_hgnc_id": 27729,
"dbsnp": "rs572675416",
"frequency_reference_population": 0.0042639985,
"hom_count_reference_population": 5,
"allele_count_reference_population": 4202,
"gnomad_exomes_af": 0.00443041,
"gnomad_genomes_af": 0.00335244,
"gnomad_exomes_ac": 3692,
"gnomad_genomes_ac": 510,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 2,
"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": -1.1,
"phylop100way_prediction": "Benign",
"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": -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_001366919.1",
"gene_symbol": "RNF212",
"hgnc_id": 27729,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.769dupC",
"hgvs_p": "p.Arg257fs"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000722332.1",
"gene_symbol": "ENSG00000294272",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.815-207dupG",
"hgvs_p": null
}
],
"clinvar_disease": "Spermatogenic failure 62",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Spermatogenic failure 62",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}