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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: 1-32810939-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=32810939&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 32810939,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000373477.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.176T>C",
"hgvs_p": "p.Ile59Thr",
"transcript": "NM_003680.4",
"protein_id": "NP_003671.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 528,
"cds_start": 176,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 2443,
"mane_select": "ENST00000373477.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.176T>C",
"hgvs_p": "p.Ile59Thr",
"transcript": "ENST00000373477.9",
"protein_id": "ENSP00000362576.4",
"transcript_support_level": 1,
"aa_start": 59,
"aa_end": null,
"aa_length": 528,
"cds_start": 176,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 2443,
"mane_select": "NM_003680.4",
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.709T>C",
"hgvs_p": null,
"transcript": "ENST00000472692.1",
"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": 773,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.176T>C",
"hgvs_p": null,
"transcript": "ENST00000481895.6",
"protein_id": "ENSP00000502016.1",
"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": 2521,
"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": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.176T>C",
"hgvs_p": null,
"transcript": "ENST00000616261.2",
"protein_id": "ENSP00000484192.2",
"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": 1018,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.176T>C",
"hgvs_p": null,
"transcript": "ENST00000674654.1",
"protein_id": "ENSP00000501729.1",
"transcript_support_level": null,
"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": 2784,
"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": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.176T>C",
"hgvs_p": null,
"transcript": "ENST00000676297.1",
"protein_id": "ENSP00000501596.1",
"transcript_support_level": null,
"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": 3263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.58-173T>C",
"hgvs_p": null,
"transcript": "ENST00000675785.2",
"protein_id": "ENSP00000502019.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 479,
"cds_start": -4,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.58-4328T>C",
"hgvs_p": null,
"transcript": "ENST00000674629.1",
"protein_id": "ENSP00000502470.1",
"transcript_support_level": null,
"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": 2075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.-250-4328T>C",
"hgvs_p": null,
"transcript": "XM_011542347.3",
"protein_id": "XP_011540649.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 318,
"cds_start": -4,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"dbsnp": "rs774466323",
"frequency_reference_population": 0.000029740257,
"hom_count_reference_population": 0,
"allele_count_reference_population": 48,
"gnomad_exomes_af": 0.000031466,
"gnomad_genomes_af": 0.000013151,
"gnomad_exomes_ac": 46,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8957984447479248,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.667,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7342,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.909,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000373477.9",
"gene_symbol": "YARS1",
"hgnc_id": 12840,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.176T>C",
"hgvs_p": "p.Ile59Thr"
}
],
"clinvar_disease": " and pancreatic disease, endocrine, infantile-onset 2, multisystem,Charcot-Marie-Tooth disease dominant intermediate C,Neurodevelopmental delay,Neurologic,recessive ARS-related multisystem disease",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1",
"phenotype_combined": "Charcot-Marie-Tooth disease dominant intermediate C|Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset 2|recessive ARS-related multisystem disease|Neurodevelopmental delay",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}