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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: 1-119034197-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=119034197&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 119034197,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000235521.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.532G>C",
"hgvs_p": "p.Val178Leu",
"transcript": "NM_015836.4",
"protein_id": "NP_056651.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 360,
"cds_start": 532,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 541,
"cdna_end": null,
"cdna_length": 2787,
"mane_select": "ENST00000235521.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.532G>C",
"hgvs_p": "p.Val178Leu",
"transcript": "ENST00000235521.5",
"protein_id": "ENSP00000235521.4",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 360,
"cds_start": 532,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 541,
"cdna_end": null,
"cdna_length": 2787,
"mane_select": "NM_015836.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.532G>C",
"hgvs_p": "p.Val178Leu",
"transcript": "ENST00000369426.9",
"protein_id": "ENSP00000358434.5",
"transcript_support_level": 1,
"aa_start": 178,
"aa_end": null,
"aa_length": 220,
"cds_start": 532,
"cds_end": null,
"cds_length": 663,
"cdna_start": 536,
"cdna_end": null,
"cdna_length": 2811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.463G>C",
"hgvs_p": "p.Val155Leu",
"transcript": "NM_001378226.1",
"protein_id": "NP_001365155.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 337,
"cds_start": 463,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 2872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.463G>C",
"hgvs_p": "p.Val155Leu",
"transcript": "NM_001378227.1",
"protein_id": "NP_001365156.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 337,
"cds_start": 463,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 817,
"cdna_end": null,
"cdna_length": 3063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.361G>C",
"hgvs_p": "p.Val121Leu",
"transcript": "NM_001378228.1",
"protein_id": "NP_001365157.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 303,
"cds_start": 361,
"cds_end": null,
"cds_length": 912,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 2616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.274G>C",
"hgvs_p": "p.Val92Leu",
"transcript": "NM_001378229.1",
"protein_id": "NP_001365158.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 274,
"cds_start": 274,
"cds_end": null,
"cds_length": 825,
"cdna_start": 283,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.250G>C",
"hgvs_p": "p.Val84Leu",
"transcript": "NM_001378230.1",
"protein_id": "NP_001365159.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 266,
"cds_start": 250,
"cds_end": null,
"cds_length": 801,
"cdna_start": 732,
"cdna_end": null,
"cdna_length": 2978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.532G>C",
"hgvs_p": "p.Val178Leu",
"transcript": "NM_201263.2",
"protein_id": "NP_957715.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 220,
"cds_start": 532,
"cds_end": null,
"cds_length": 663,
"cdna_start": 560,
"cdna_end": null,
"cdna_length": 2835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.446G>C",
"hgvs_p": "p.Cys149Ser",
"transcript": "NM_001378231.1",
"protein_id": "NP_001365160.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 192,
"cds_start": 446,
"cds_end": null,
"cds_length": 579,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.478G>C",
"hgvs_p": "p.Val160Leu",
"transcript": "XM_005270350.4",
"protein_id": "XP_005270407.1",
"transcript_support_level": null,
"aa_start": 160,
"aa_end": null,
"aa_length": 342,
"cds_start": 478,
"cds_end": null,
"cds_length": 1029,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 2896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.446G>C",
"hgvs_p": "p.Cys149Ser",
"transcript": "XM_017000038.2",
"protein_id": "XP_016855527.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 341,
"cds_start": 446,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 474,
"cdna_end": null,
"cdna_length": 2749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.463G>C",
"hgvs_p": "p.Val155Leu",
"transcript": "XM_024449826.2",
"protein_id": "XP_024305594.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 337,
"cds_start": 463,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 3159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.275G>C",
"hgvs_p": "p.Cys92Ser",
"transcript": "XM_047429105.1",
"protein_id": "XP_047285061.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 284,
"cds_start": 275,
"cds_end": null,
"cds_length": 855,
"cdna_start": 303,
"cdna_end": null,
"cdna_length": 2578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "c.250G>C",
"hgvs_p": "p.Val84Leu",
"transcript": "XM_024449860.2",
"protein_id": "XP_024305628.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 266,
"cds_start": 250,
"cds_end": null,
"cds_length": 801,
"cdna_start": 828,
"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": 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": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "n.456G>C",
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"hgvs_c": "n.644G>C",
"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
}
],
"gene_symbol": "WARS2",
"gene_hgnc_id": 12730,
"dbsnp": "rs912133959",
"frequency_reference_population": 6.841892e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84189e-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": 0.938274621963501,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.418,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7198,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.607,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000235521.5",
"gene_symbol": "WARS2",
"hgnc_id": 12730,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.532G>C",
"hgvs_p": "p.Val178Leu"
}
],
"clinvar_disease": " mitochondrial, with abnormal movements and lactic acidosis, with or without seizures,Neurodevelopmental disorder",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Neurodevelopmental disorder, mitochondrial, with abnormal movements and lactic acidosis, with or without seizures",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}