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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: 11-66284641-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=66284641&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "YIF1A",
"hgnc_id": 16688,
"hgvs_c": "c.878G>A",
"hgvs_p": "p.Arg293Gln",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_020470.3",
"verdict": "Likely_benign"
},
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "CNIH2",
"hgnc_id": 28744,
"hgvs_c": "n.451-458C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "ENST00000530519.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 40,
"alphamissense_prediction": null,
"alphamissense_score": 0.1312,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.14,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08773660659790039,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 293,
"aa_ref": "R",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1097,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 882,
"cds_start": 878,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_020470.3",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.878G>A",
"hgvs_p": "p.Arg293Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000376901.9",
"protein_coding": true,
"protein_id": "NP_065203.2",
"strand": false,
"transcript": "NM_020470.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 293,
"aa_ref": "R",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1097,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 882,
"cds_start": 878,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000376901.9",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.878G>A",
"hgvs_p": "p.Arg293Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020470.3",
"protein_coding": true,
"protein_id": "ENSP00000366098.4",
"strand": false,
"transcript": "ENST00000376901.9",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 293,
"aa_ref": "R",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1146,
"cdna_start": 1077,
"cds_end": null,
"cds_length": 882,
"cds_start": 878,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000715691.1",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.878G>A",
"hgvs_p": "p.Arg293Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000520502.1",
"strand": false,
"transcript": "ENST00000715691.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 241,
"aa_ref": "R",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 941,
"cdna_start": 880,
"cds_end": null,
"cds_length": 726,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001300861.2",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.722G>A",
"hgvs_p": "p.Arg241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001287790.1",
"strand": false,
"transcript": "NM_001300861.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 241,
"aa_ref": "R",
"aa_start": 241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 943,
"cdna_start": 882,
"cds_end": null,
"cds_length": 726,
"cds_start": 722,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000359461.10",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.722G>A",
"hgvs_p": "p.Arg241Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000352437.6",
"strand": false,
"transcript": "ENST00000359461.10",
"transcript_support_level": 2
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 79,
"aa_ref": "R",
"aa_start": 79,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 667,
"cdna_start": 606,
"cds_end": null,
"cds_length": 240,
"cds_start": 236,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000496746.5",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.236G>A",
"hgvs_p": "p.Arg79Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000432185.1",
"strand": false,
"transcript": "ENST00000496746.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 158,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 854,
"cdna_start": null,
"cds_end": null,
"cds_length": 477,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000471387.6",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "c.*61G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000437042.1",
"strand": false,
"transcript": "ENST00000471387.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 653,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000485820.1",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "n.592G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000485820.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 540,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000494836.2",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "n.480G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000494836.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 516,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000526497.5",
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"hgvs_c": "n.455G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000526497.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 653,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000530519.5",
"gene_hgnc_id": 28744,
"gene_symbol": "CNIH2",
"hgvs_c": "n.451-458C>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000530519.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1455781753",
"effect": "missense_variant",
"frequency_reference_population": 0.000024805555,
"gene_hgnc_id": 16688,
"gene_symbol": "YIF1A",
"gnomad_exomes_ac": 37,
"gnomad_exomes_af": 0.000025336,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197148,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.361,
"pos": 66284641,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.151,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020470.3"
}
]
}