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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: 1-119076564-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119076564&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 119076564,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000235521.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "NM_015836.4",
"protein_id": "NP_056651.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 360,
"cds_start": 134,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 2787,
"mane_select": "ENST00000235521.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "ENST00000235521.5",
"protein_id": "ENSP00000235521.4",
"transcript_support_level": 1,
"aa_start": 45,
"aa_end": null,
"aa_length": 360,
"cds_start": 134,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 2787,
"mane_select": "NM_015836.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "ENST00000369426.9",
"protein_id": "ENSP00000358434.5",
"transcript_support_level": 1,
"aa_start": 45,
"aa_end": null,
"aa_length": 220,
"cds_start": 134,
"cds_end": null,
"cds_length": 663,
"cdna_start": 138,
"cdna_end": null,
"cdna_length": 2811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "NM_001378226.1",
"protein_id": "NP_001365155.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 337,
"cds_start": 65,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 228,
"cdna_end": null,
"cdna_length": 2872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "NM_001378227.1",
"protein_id": "NP_001365156.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 337,
"cds_start": 65,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 419,
"cdna_end": null,
"cdna_length": 3063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "NM_001378228.1",
"protein_id": "NP_001365157.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 303,
"cds_start": 134,
"cds_end": null,
"cds_length": 912,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 2616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "NM_201263.2",
"protein_id": "NP_957715.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 220,
"cds_start": 134,
"cds_end": null,
"cds_length": 663,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "NM_001378231.1",
"protein_id": "NP_001365160.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 192,
"cds_start": 134,
"cds_end": null,
"cds_length": 579,
"cdna_start": 143,
"cdna_end": null,
"cdna_length": 2701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.80G>T",
"hgvs_p": "p.Gly27Val",
"transcript": "XM_005270350.4",
"protein_id": "XP_005270407.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 342,
"cds_start": 80,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 252,
"cdna_end": null,
"cdna_length": 2896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "XM_017000038.2",
"protein_id": "XP_016855527.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 341,
"cds_start": 134,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 2749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.65G>T",
"hgvs_p": "p.Gly22Val",
"transcript": "XM_024449826.2",
"protein_id": "XP_024305594.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 337,
"cds_start": 65,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 515,
"cdna_end": null,
"cdna_length": 3159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val",
"transcript": "XM_047429105.1",
"protein_id": "XP_047285061.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 284,
"cds_start": 134,
"cds_end": null,
"cds_length": 855,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 2578,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "n.144G>T",
"hgvs_p": null,
"transcript": "ENST00000495746.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 621,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "n.246G>T",
"hgvs_p": null,
"transcript": "ENST00000497402.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.-149G>T",
"hgvs_p": null,
"transcript": "NM_001378230.1",
"protein_id": "NP_001365159.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 266,
"cds_start": -4,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.-149G>T",
"hgvs_p": null,
"transcript": "XM_024449860.2",
"protein_id": "XP_024305628.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 266,
"cds_start": -4,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3074,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.91-30902G>T",
"hgvs_p": null,
"transcript": "NM_001378229.1",
"protein_id": "NP_001365158.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 274,
"cds_start": -4,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"dbsnp": "rs1553241795",
"frequency_reference_population": 6.8405535e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84055e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9893813133239746,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.698,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8871,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.394,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000235521.5",
"gene_symbol": "WARS2",
"hgnc_id": 12730,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.134G>T",
"hgvs_p": "p.Gly45Val"
}
],
"clinvar_disease": " mitochondrial, with abnormal movements and lactic acidosis, with or without seizures,Neurodevelopmental disorder",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Neurodevelopmental disorder, mitochondrial, with abnormal movements and lactic acidosis, with or without seizures",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}