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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: 1-42700869-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=42700869&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 42700869,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004559.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.829C>A",
"hgvs_p": "p.Pro277Thr",
"transcript": "NM_004559.5",
"protein_id": "NP_004550.2",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 324,
"cds_start": 829,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000321358.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004559.5"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.829C>A",
"hgvs_p": "p.Pro277Thr",
"transcript": "ENST00000321358.12",
"protein_id": "ENSP00000361626.3",
"transcript_support_level": 1,
"aa_start": 277,
"aa_end": null,
"aa_length": 324,
"cds_start": 829,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004559.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000321358.12"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.976C>A",
"hgvs_p": "p.Pro326Thr",
"transcript": "ENST00000436427.1",
"protein_id": "ENSP00000389639.1",
"transcript_support_level": 1,
"aa_start": 326,
"aa_end": null,
"aa_length": 373,
"cds_start": 976,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000436427.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.934C>A",
"hgvs_p": "p.Pro312Thr",
"transcript": "ENST00000936897.1",
"protein_id": "ENSP00000606956.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 359,
"cds_start": 934,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936897.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.829C>A",
"hgvs_p": "p.Pro277Thr",
"transcript": "ENST00000886270.1",
"protein_id": "ENSP00000556329.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 324,
"cds_start": 829,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886270.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.829C>A",
"hgvs_p": "p.Pro277Thr",
"transcript": "ENST00000886274.1",
"protein_id": "ENSP00000556333.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 324,
"cds_start": 829,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886274.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.814C>A",
"hgvs_p": "p.Pro272Thr",
"transcript": "ENST00000886271.1",
"protein_id": "ENSP00000556330.1",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 319,
"cds_start": 814,
"cds_end": null,
"cds_length": 960,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886271.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.811C>A",
"hgvs_p": "p.Pro271Thr",
"transcript": "ENST00000886273.1",
"protein_id": "ENSP00000556332.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 318,
"cds_start": 811,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886273.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Pro181Thr",
"transcript": "ENST00000953953.1",
"protein_id": "ENSP00000624012.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 228,
"cds_start": 541,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953953.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.526C>A",
"hgvs_p": "p.Pro176Thr",
"transcript": "ENST00000886272.1",
"protein_id": "ENSP00000556331.1",
"transcript_support_level": null,
"aa_start": 176,
"aa_end": null,
"aa_length": 223,
"cds_start": 526,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886272.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.436C>A",
"hgvs_p": "p.Pro146Thr",
"transcript": "ENST00000886269.1",
"protein_id": "ENSP00000556328.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 193,
"cds_start": 436,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886269.1"
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "c.739C>A",
"hgvs_p": "p.Pro247Thr",
"transcript": "XM_047421495.1",
"protein_id": "XP_047277451.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 294,
"cds_start": 739,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421495.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"hgvs_c": "n.829C>A",
"hgvs_p": null,
"transcript": "NR_132737.2",
"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": "NR_132737.2"
}
],
"gene_symbol": "YBX1",
"gene_hgnc_id": 8014,
"dbsnp": "rs754064164",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3879135251045227,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.404,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1442,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.234,
"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_004559.5",
"gene_symbol": "YBX1",
"hgnc_id": 8014,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.829C>A",
"hgvs_p": "p.Pro277Thr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}