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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: 19-282753-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=282753&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 282753,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000434325.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.539C>G",
"hgvs_p": "p.Ala180Gly",
"transcript": "NM_003712.4",
"protein_id": "NP_003703.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 288,
"cds_start": 539,
"cds_end": null,
"cds_length": 867,
"cdna_start": 606,
"cdna_end": null,
"cdna_length": 1279,
"mane_select": "ENST00000434325.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.539C>G",
"hgvs_p": "p.Ala180Gly",
"transcript": "ENST00000434325.7",
"protein_id": "ENSP00000388565.2",
"transcript_support_level": 1,
"aa_start": 180,
"aa_end": null,
"aa_length": 288,
"cds_start": 539,
"cds_end": null,
"cds_length": 867,
"cdna_start": 606,
"cdna_end": null,
"cdna_length": 1279,
"mane_select": "NM_003712.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.602C>G",
"hgvs_p": "p.Ala201Gly",
"transcript": "NM_177543.3",
"protein_id": "NP_808211.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 309,
"cds_start": 602,
"cds_end": null,
"cds_length": 930,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 1348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.602C>G",
"hgvs_p": "p.Ala201Gly",
"transcript": "ENST00000327790.7",
"protein_id": "ENSP00000329697.1",
"transcript_support_level": 5,
"aa_start": 201,
"aa_end": null,
"aa_length": 309,
"cds_start": 602,
"cds_end": null,
"cds_length": 930,
"cdna_start": 721,
"cdna_end": null,
"cdna_length": 1397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.371C>G",
"hgvs_p": "p.Ala124Gly",
"transcript": "NM_177526.3",
"protein_id": "NP_803545.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 232,
"cds_start": 371,
"cds_end": null,
"cds_length": 699,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 1238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.371C>G",
"hgvs_p": "p.Ala124Gly",
"transcript": "ENST00000269812.7",
"protein_id": "ENSP00000269812.2",
"transcript_support_level": 3,
"aa_start": 124,
"aa_end": null,
"aa_length": 232,
"cds_start": 371,
"cds_end": null,
"cds_length": 699,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 1228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.371C>G",
"hgvs_p": "p.Ala124Gly",
"transcript": "ENST00000633125.1",
"protein_id": "ENSP00000488312.1",
"transcript_support_level": 5,
"aa_start": 124,
"aa_end": null,
"aa_length": 207,
"cds_start": 371,
"cds_end": null,
"cds_length": 624,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.218C>G",
"hgvs_p": "p.Ala73Gly",
"transcript": "ENST00000586998.3",
"protein_id": "ENSP00000466947.1",
"transcript_support_level": 2,
"aa_start": 73,
"aa_end": null,
"aa_length": 135,
"cds_start": 218,
"cds_end": null,
"cds_length": 408,
"cdna_start": 220,
"cdna_end": null,
"cdna_length": 541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.557C>G",
"hgvs_p": "p.Ala186Gly",
"transcript": "XM_011528396.3",
"protein_id": "XP_011526698.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 294,
"cds_start": 557,
"cds_end": null,
"cds_length": 885,
"cdna_start": 624,
"cdna_end": null,
"cdna_length": 1297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "n.5785C>G",
"hgvs_p": null,
"transcript": "ENST00000621795.1",
"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": 6455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"hgvs_c": "c.*22C>G",
"hgvs_p": null,
"transcript": "ENST00000591572.2",
"protein_id": "ENSP00000466545.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 177,
"cds_start": -4,
"cds_end": null,
"cds_length": 535,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLPP2",
"gene_hgnc_id": 9230,
"dbsnp": "rs1138439",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 0,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5875145792961121,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.11400000005960464,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.414,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2548,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.187,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0010935108009943,
"dbscsnv_ada_prediction": "Benign",
"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": "ENST00000434325.7",
"gene_symbol": "PLPP2",
"hgnc_id": 9230,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.539C>G",
"hgvs_p": "p.Ala180Gly"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}