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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: 2-19353309-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=19353309&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 19353309,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_145260.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "c.497G>C",
"hgvs_p": "p.Arg166Pro",
"transcript": "NM_145260.3",
"protein_id": "NP_660303.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 266,
"cds_start": 497,
"cds_end": null,
"cds_length": 801,
"cdna_start": 812,
"cdna_end": null,
"cdna_length": 1906,
"mane_select": "ENST00000272223.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "c.497G>C",
"hgvs_p": "p.Arg166Pro",
"transcript": "ENST00000272223.3",
"protein_id": "ENSP00000272223.2",
"transcript_support_level": 1,
"aa_start": 166,
"aa_end": null,
"aa_length": 266,
"cds_start": 497,
"cds_end": null,
"cds_length": 801,
"cdna_start": 812,
"cdna_end": null,
"cdna_length": 1906,
"mane_select": "NM_145260.3",
"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": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "n.3604G>C",
"hgvs_p": null,
"transcript": "ENST00000487581.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 4171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "c.497G>C",
"hgvs_p": "p.Arg166Pro",
"transcript": "XM_006711942.5",
"protein_id": "XP_006712005.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 266,
"cds_start": 497,
"cds_end": null,
"cds_length": 801,
"cdna_start": 1669,
"cdna_end": null,
"cdna_length": 2763,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "n.812G>C",
"hgvs_p": null,
"transcript": "XR_007069636.1",
"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": 7574,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "n.812G>C",
"hgvs_p": null,
"transcript": "XR_007069637.1",
"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": 7278,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"hgvs_c": "n.812G>C",
"hgvs_p": null,
"transcript": "XR_007069638.1",
"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": 7371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OSR1",
"gene_hgnc_id": 8111,
"dbsnp": "rs1457744690",
"frequency_reference_population": 6.8404506e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84045e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.79753577709198,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.227,
"revel_prediction": "Benign",
"alphamissense_score": 0.5696,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.163,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_145260.3",
"gene_symbol": "OSR1",
"hgnc_id": 8111,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.497G>C",
"hgvs_p": "p.Arg166Pro"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}