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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: 17-6538056-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=6538056&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 6538056,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000262483.13",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "NM_031220.4",
"protein_id": "NP_112497.2",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 974,
"cds_start": 49,
"cds_end": null,
"cds_length": 2925,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 7149,
"mane_select": "ENST00000262483.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "ENST00000262483.13",
"protein_id": "ENSP00000262483.8",
"transcript_support_level": 1,
"aa_start": 17,
"aa_end": null,
"aa_length": 974,
"cds_start": 49,
"cds_end": null,
"cds_length": 2925,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 7149,
"mane_select": "NM_031220.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "NM_001165966.2",
"protein_id": "NP_001159438.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 938,
"cds_start": 49,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 7041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "ENST00000421306.7",
"protein_id": "ENSP00000407882.3",
"transcript_support_level": 2,
"aa_start": 17,
"aa_end": null,
"aa_length": 938,
"cds_start": 49,
"cds_end": null,
"cds_length": 2817,
"cdna_start": 103,
"cdna_end": null,
"cdna_length": 6945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "XM_011524015.4",
"protein_id": "XP_011522317.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 834,
"cds_start": 49,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 3039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "XM_011524016.4",
"protein_id": "XP_011522318.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 801,
"cds_start": 49,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 3890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser",
"transcript": "XM_011524017.4",
"protein_id": "XP_011522319.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 543,
"cds_start": 49,
"cds_end": null,
"cds_length": 1632,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 1869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PITPNM3",
"gene_hgnc_id": 21043,
"dbsnp": "rs28493751",
"frequency_reference_population": 0.091855235,
"hom_count_reference_population": 7452,
"allele_count_reference_population": 148123,
"gnomad_exomes_af": 0.0928877,
"gnomad_genomes_af": 0.0819467,
"gnomad_exomes_ac": 135653,
"gnomad_genomes_ac": 12470,
"gnomad_exomes_homalt": 6854,
"gnomad_genomes_homalt": 598,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00176239013671875,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.102,
"revel_prediction": "Benign",
"alphamissense_score": 0.0726,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.82,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000262483.13",
"gene_symbol": "PITPNM3",
"hgnc_id": 21043,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Pro17Ser"
}
],
"clinvar_disease": "Cone-rod dystrophy 5,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Cone-rod dystrophy 5|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}