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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: 5-116087577-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=116087577&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 116087577,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_016144.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "c.122T>C",
"hgvs_p": "p.Leu41Pro",
"transcript": "NM_016144.4",
"protein_id": "NP_057228.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 202,
"cds_start": 122,
"cds_end": null,
"cds_length": 609,
"cdna_start": 150,
"cdna_end": null,
"cdna_length": 1435,
"mane_select": "ENST00000274458.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016144.4"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "c.122T>C",
"hgvs_p": "p.Leu41Pro",
"transcript": "ENST00000274458.9",
"protein_id": "ENSP00000274458.4",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 202,
"cds_start": 122,
"cds_end": null,
"cds_length": 609,
"cdna_start": 150,
"cdna_end": null,
"cdna_length": 1435,
"mane_select": "NM_016144.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274458.9"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "c.80T>C",
"hgvs_p": "p.Leu27Pro",
"transcript": "ENST00000632434.1",
"protein_id": "ENSP00000488332.1",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 188,
"cds_start": 80,
"cds_end": null,
"cds_length": 567,
"cdna_start": 149,
"cdna_end": null,
"cdna_length": 1433,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000632434.1"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "c.80T>C",
"hgvs_p": "p.Leu27Pro",
"transcript": "NM_001308080.2",
"protein_id": "NP_001295009.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 188,
"cds_start": 80,
"cds_end": null,
"cds_length": 567,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 1511,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308080.2"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "c.80T>C",
"hgvs_p": "p.Leu27Pro",
"transcript": "ENST00000515539.5",
"protein_id": "ENSP00000427319.1",
"transcript_support_level": 3,
"aa_start": 27,
"aa_end": null,
"aa_length": 188,
"cds_start": 80,
"cds_end": null,
"cds_length": 567,
"cdna_start": 214,
"cdna_end": null,
"cdna_length": 869,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515539.5"
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "c.122T>C",
"hgvs_p": "p.Leu41Pro",
"transcript": "ENST00000908482.1",
"protein_id": "ENSP00000578541.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 113,
"cds_start": 122,
"cds_end": null,
"cds_length": 342,
"cdna_start": 168,
"cdna_end": null,
"cdna_length": 1181,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908482.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "n.122T>C",
"hgvs_p": null,
"transcript": "ENST00000507356.5",
"protein_id": "ENSP00000422448.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 870,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000507356.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "n.150T>C",
"hgvs_p": null,
"transcript": "NR_146218.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5296,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_146218.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "n.246T>C",
"hgvs_p": null,
"transcript": "NR_146219.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5392,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_146219.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"hgvs_c": "n.150T>C",
"hgvs_p": null,
"transcript": "NR_146220.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5328,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_146220.2"
}
],
"gene_symbol": "COMMD10",
"gene_hgnc_id": 30201,
"dbsnp": "rs562138361",
"frequency_reference_population": 0.0000065632303,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.00000656323,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9664558172225952,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.724,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9077,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.533,
"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_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_016144.4",
"gene_symbol": "COMMD10",
"hgnc_id": 30201,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.122T>C",
"hgvs_p": "p.Leu41Pro"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}