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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: 12-32750046-A-ACTCCTGATCAGACATGAC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=32750046&ref=A&alt=ACTCCTGATCAGACATGAC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 32750046,
"ref": "A",
"alt": "ACTCCTGATCAGACATGAC",
"effect": "conservative_inframe_insertion",
"transcript": "ENST00000324868.13",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "EVMSDQE",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS2",
"gene_hgnc_id": 24249,
"hgvs_c": "c.1147_1164dupGTCATGTCTGATCAGGAG",
"hgvs_p": "p.Glu388_Leu389insValMetSerAspGlnGlu",
"transcript": "NM_001040436.3",
"protein_id": "NP_001035526.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 477,
"cds_start": 1164,
"cds_end": null,
"cds_length": 1434,
"cdna_start": 1187,
"cdna_end": null,
"cdna_length": 2117,
"mane_select": "ENST00000324868.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "EVMSDQE",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS2",
"gene_hgnc_id": 24249,
"hgvs_c": "c.1147_1164dupGTCATGTCTGATCAGGAG",
"hgvs_p": "p.Glu388_Leu389insValMetSerAspGlnGlu",
"transcript": "ENST00000324868.13",
"protein_id": "ENSP00000320658.8",
"transcript_support_level": 1,
"aa_start": 388,
"aa_end": null,
"aa_length": 477,
"cds_start": 1164,
"cds_end": null,
"cds_length": 1434,
"cdna_start": 1187,
"cdna_end": null,
"cdna_length": 2117,
"mane_select": "NM_001040436.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS2",
"gene_hgnc_id": 24249,
"hgvs_c": "n.*158_*175dupGTCATGTCTGATCAGGAG",
"hgvs_p": null,
"transcript": "ENST00000548490.1",
"protein_id": "ENSP00000447710.1",
"transcript_support_level": 5,
"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": 1321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS2",
"gene_hgnc_id": 24249,
"hgvs_c": "n.44_61dupGTCATGTCTGATCAGGAG",
"hgvs_p": null,
"transcript": "ENST00000551673.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS2",
"gene_hgnc_id": 24249,
"hgvs_c": "n.*158_*175dupGTCATGTCTGATCAGGAG",
"hgvs_p": null,
"transcript": "ENST00000548490.1",
"protein_id": "ENSP00000447710.1",
"transcript_support_level": 5,
"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": 1321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "YARS2",
"gene_hgnc_id": 24249,
"dbsnp": "rs775256289",
"frequency_reference_population": 0.00005130366,
"hom_count_reference_population": 0,
"allele_count_reference_population": 75,
"gnomad_exomes_af": 0.0000513037,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 75,
"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": 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": 1.745,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM4",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000324868.13",
"gene_symbol": "YARS2",
"hgnc_id": 24249,
"effects": [
"conservative_inframe_insertion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1147_1164dupGTCATGTCTGATCAGGAG",
"hgvs_p": "p.Glu388_Leu389insValMetSerAspGlnGlu"
}
],
"clinvar_disease": "Mitochondrial disease",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mitochondrial disease",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}