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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: 10-120575220-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=120575220&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 120575220,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001030059.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Leu179Phe",
"transcript": "NM_001030059.3",
"protein_id": "NP_001025230.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 271,
"cds_start": 535,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000398250.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001030059.3"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Leu179Phe",
"transcript": "ENST00000398250.6",
"protein_id": "ENSP00000381302.1",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 271,
"cds_start": 535,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001030059.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398250.6"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Leu116Phe",
"transcript": "NM_001318167.2",
"protein_id": "NP_001305096.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 208,
"cds_start": 346,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318167.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.410C>T",
"hgvs_p": "p.Ala137Val",
"transcript": "NM_001318166.2",
"protein_id": "NP_001305095.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 193,
"cds_start": 410,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318166.2"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.529C>T",
"hgvs_p": "p.Leu177Phe",
"transcript": "XM_011539444.4",
"protein_id": "XP_011537746.1",
"transcript_support_level": null,
"aa_start": 177,
"aa_end": null,
"aa_length": 269,
"cds_start": 529,
"cds_end": null,
"cds_length": 810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011539444.4"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.496C>T",
"hgvs_p": "p.Leu166Phe",
"transcript": "XM_047424709.1",
"protein_id": "XP_047280665.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 258,
"cds_start": 496,
"cds_end": null,
"cds_length": 777,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424709.1"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Leu179Phe",
"transcript": "XM_006717686.5",
"protein_id": "XP_006717749.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 222,
"cds_start": 535,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717686.5"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Leu58Phe",
"transcript": "XM_017015821.3",
"protein_id": "XP_016871310.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 150,
"cds_start": 172,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017015821.3"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Leu58Phe",
"transcript": "XM_017015822.2",
"protein_id": "XP_016871311.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 150,
"cds_start": 172,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017015822.2"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Leu58Phe",
"transcript": "XM_024447862.2",
"protein_id": "XP_024303630.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 150,
"cds_start": 172,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024447862.2"
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Leu58Phe",
"transcript": "XM_047424710.1",
"protein_id": "XP_047280666.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 150,
"cds_start": 172,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424710.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Gly85Gly",
"transcript": "NM_001318168.2",
"protein_id": "NP_001305097.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 96,
"cds_start": 255,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318168.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.255C>T",
"hgvs_p": "p.Gly85Gly",
"transcript": "XM_017015823.2",
"protein_id": "XP_016871312.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 96,
"cds_start": 255,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017015823.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.166-14083C>T",
"hgvs_p": null,
"transcript": "NM_001318169.2",
"protein_id": "NP_001305098.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 96,
"cds_start": null,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318169.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "c.446-14083C>T",
"hgvs_p": null,
"transcript": "XM_005269592.3",
"protein_id": "XP_005269649.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 214,
"cds_start": null,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005269592.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "n.505C>T",
"hgvs_p": null,
"transcript": "ENST00000369073.3",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000369073.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "n.33C>T",
"hgvs_p": null,
"transcript": "ENST00000496437.1",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000496437.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PLPP4",
"gene_hgnc_id": 23531,
"hgvs_c": "n.399C>T",
"hgvs_p": null,
"transcript": "NR_134516.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_134516.1"
}
],
"gene_symbol": "PLPP4",
"gene_hgnc_id": 23531,
"dbsnp": "rs538498909",
"frequency_reference_population": 0.0000075250823,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000752508,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6099307537078857,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.545,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3493,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.841,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001030059.3",
"gene_symbol": "PLPP4",
"hgnc_id": 23531,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Leu179Phe"
}
],
"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
}