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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: 10-99716419-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=99716419&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 99716419,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000016171.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "NM_078470.6",
"protein_id": "NP_510870.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 410,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 5030,
"mane_select": "ENST00000016171.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "ENST00000016171.6",
"protein_id": "ENSP00000016171.6",
"transcript_support_level": 1,
"aa_start": 344,
"aa_end": null,
"aa_length": 410,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 5030,
"mane_select": "NM_078470.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "ENST00000370483.9",
"protein_id": "ENSP00000359514.5",
"transcript_support_level": 1,
"aa_start": 344,
"aa_end": null,
"aa_length": 388,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 2788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285932",
"gene_hgnc_id": null,
"hgvs_c": "n.*389T>C",
"hgvs_p": null,
"transcript": "ENST00000649102.1",
"protein_id": "ENSP00000497114.1",
"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": 1971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285932",
"gene_hgnc_id": null,
"hgvs_c": "n.*389T>C",
"hgvs_p": null,
"transcript": "ENST00000649102.1",
"protein_id": "ENSP00000497114.1",
"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": 1971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "NM_001372024.1",
"protein_id": "NP_001358953.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 419,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 4276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1048T>C",
"hgvs_p": "p.Ser350Pro",
"transcript": "NM_001372025.1",
"protein_id": "NP_001358954.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 416,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 1126,
"cdna_end": null,
"cdna_length": 5048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1003T>C",
"hgvs_p": "p.Ser335Pro",
"transcript": "NM_001372026.1",
"protein_id": "NP_001358955.1",
"transcript_support_level": null,
"aa_start": 335,
"aa_end": null,
"aa_length": 401,
"cds_start": 1003,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 5003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "NM_001320974.2",
"protein_id": "NP_001307903.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 388,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "NM_004376.7",
"protein_id": "NP_004367.2",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 388,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 3791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro",
"transcript": "NM_001372027.1",
"protein_id": "NP_001358956.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 372,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 5020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"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": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.875T>C",
"hgvs_p": "p.Leu292Pro",
"transcript": "NM_001320975.2",
"protein_id": "NP_001307904.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 298,
"cds_start": 875,
"cds_end": null,
"cds_length": 897,
"cdna_start": 953,
"cdna_end": null,
"cdna_length": 4875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"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": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.875T>C",
"hgvs_p": "p.Leu292Pro",
"transcript": "NM_001372028.1",
"protein_id": "NP_001358957.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 298,
"cds_start": 875,
"cds_end": null,
"cds_length": 897,
"cdna_start": 953,
"cdna_end": null,
"cdna_length": 4121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.493T>C",
"hgvs_p": "p.Ser165Pro",
"transcript": "NM_001320976.2",
"protein_id": "NP_001307905.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 231,
"cds_start": 493,
"cds_end": null,
"cds_length": 696,
"cdna_start": 1025,
"cdna_end": null,
"cdna_length": 4947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"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": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "c.875T>C",
"hgvs_p": "p.Leu292Pro",
"transcript": "XM_006717634.4",
"protein_id": "XP_006717697.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 298,
"cds_start": 875,
"cds_end": null,
"cds_length": 897,
"cdna_start": 953,
"cdna_end": null,
"cdna_length": 3273,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "n.228T>C",
"hgvs_p": null,
"transcript": "ENST00000497381.1",
"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": 366,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"hgvs_c": "n.870T>C",
"hgvs_p": null,
"transcript": "NR_164009.1",
"protein_id": null,
"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": 4792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CUTC",
"gene_hgnc_id": 24271,
"hgvs_c": "n.117-6499A>G",
"hgvs_p": null,
"transcript": "ENST00000493385.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COX15",
"gene_hgnc_id": 2263,
"dbsnp": "rs397514662",
"frequency_reference_population": 0.0000049567216,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000478888,
"gnomad_genomes_af": 0.00000656814,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.925117552280426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.839,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6983,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.769,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000016171.6",
"gene_symbol": "COX15",
"hgnc_id": 2263,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1030T>C",
"hgvs_p": "p.Ser344Pro"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000649102.1",
"gene_symbol": "ENSG00000285932",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*389T>C",
"hgvs_p": null
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000493385.5",
"gene_symbol": "CUTC",
"hgnc_id": 24271,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.117-6499A>G",
"hgvs_p": null
}
],
"clinvar_disease": " due to cytochrome c oxidase deficiency 2, fatal infantile,Cardioencephalomyopathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1",
"phenotype_combined": "Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 2|not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}