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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: 2-231737230-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=231737230&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 231737230,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002601.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.328G>C",
"hgvs_p": "p.Glu110Gln",
"transcript": "NM_002601.4",
"protein_id": "NP_002592.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 150,
"cds_start": 328,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000287600.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002601.4"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.328G>C",
"hgvs_p": "p.Glu110Gln",
"transcript": "ENST00000287600.9",
"protein_id": "ENSP00000287600.4",
"transcript_support_level": 1,
"aa_start": 110,
"aa_end": null,
"aa_length": 150,
"cds_start": 328,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002601.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000287600.9"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.202G>C",
"hgvs_p": "p.Glu68Gln",
"transcript": "ENST00000938376.1",
"protein_id": "ENSP00000608435.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 108,
"cds_start": 202,
"cds_end": null,
"cds_length": 327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938376.1"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.271G>C",
"hgvs_p": "p.Glu91Gln",
"transcript": "ENST00000428104.2",
"protein_id": "ENSP00000399098.2",
"transcript_support_level": 3,
"aa_start": 91,
"aa_end": null,
"aa_length": 103,
"cds_start": 271,
"cds_end": null,
"cds_length": 314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428104.2"
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.370G>C",
"hgvs_p": "p.Glu124Gln",
"transcript": "XM_047444726.1",
"protein_id": "XP_047300682.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 164,
"cds_start": 370,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047444726.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.265+783G>C",
"hgvs_p": null,
"transcript": "NM_001291018.2",
"protein_id": "NP_001277947.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 93,
"cds_start": null,
"cds_end": null,
"cds_length": 282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291018.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "c.265+783G>C",
"hgvs_p": null,
"transcript": "ENST00000409772.5",
"protein_id": "ENSP00000387108.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 93,
"cds_start": null,
"cds_end": null,
"cds_length": 282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409772.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"hgvs_c": "n.*192G>C",
"hgvs_p": null,
"transcript": "ENST00000486044.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000486044.1"
}
],
"gene_symbol": "PDE6D",
"gene_hgnc_id": 8788,
"dbsnp": "rs1023549002",
"frequency_reference_population": 0.0000030998024,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 6.84552e-7,
"gnomad_genomes_af": 0.0000262819,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6427533626556396,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.251,
"revel_prediction": "Benign",
"alphamissense_score": 0.5694,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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_002601.4",
"gene_symbol": "PDE6D",
"hgnc_id": 8788,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.328G>C",
"hgvs_p": "p.Glu110Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}