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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: 3-122285045-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=122285045&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 122285045,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000639785.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser",
"transcript": "NM_000388.4",
"protein_id": "NP_000379.3",
"transcript_support_level": null,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3091,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3478,
"cdna_end": null,
"cdna_length": 10062,
"mane_select": "ENST00000639785.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser",
"transcript": "ENST00000639785.2",
"protein_id": "ENSP00000491584.2",
"transcript_support_level": 1,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3091,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3478,
"cdna_end": null,
"cdna_length": 10062,
"mane_select": "NM_000388.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3121G>A",
"hgvs_p": "p.Gly1041Ser",
"transcript": "ENST00000498619.4",
"protein_id": "ENSP00000420194.1",
"transcript_support_level": 1,
"aa_start": 1041,
"aa_end": null,
"aa_length": 1088,
"cds_start": 3121,
"cds_end": null,
"cds_length": 3267,
"cdna_start": 3559,
"cdna_end": null,
"cdna_length": 5009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3121G>A",
"hgvs_p": "p.Gly1041Ser",
"transcript": "NM_001178065.2",
"protein_id": "NP_001171536.2",
"transcript_support_level": null,
"aa_start": 1041,
"aa_end": null,
"aa_length": 1088,
"cds_start": 3121,
"cds_end": null,
"cds_length": 3267,
"cdna_start": 3566,
"cdna_end": null,
"cdna_length": 10150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser",
"transcript": "ENST00000638421.1",
"protein_id": "ENSP00000492190.1",
"transcript_support_level": 5,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3091,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3630,
"cdna_end": null,
"cdna_length": 5088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2860G>A",
"hgvs_p": "p.Gly954Ser",
"transcript": "ENST00000490131.7",
"protein_id": "ENSP00000418685.2",
"transcript_support_level": 5,
"aa_start": 954,
"aa_end": null,
"aa_length": 1001,
"cds_start": 2860,
"cds_end": null,
"cds_length": 3006,
"cdna_start": 3102,
"cdna_end": null,
"cdna_length": 4015,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser",
"transcript": "XM_006713789.4",
"protein_id": "XP_006713852.1",
"transcript_support_level": null,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3091,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3536,
"cdna_end": null,
"cdna_length": 10120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser",
"transcript": "XM_017007324.2",
"protein_id": "XP_016862813.1",
"transcript_support_level": null,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3091,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 5410,
"cdna_end": null,
"cdna_length": 11994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser",
"transcript": "XM_017007325.2",
"protein_id": "XP_016862814.1",
"transcript_support_level": null,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1078,
"cds_start": 3091,
"cds_end": null,
"cds_length": 3237,
"cdna_start": 3435,
"cdna_end": null,
"cdna_length": 10019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"hgvs_c": "c.2608G>A",
"hgvs_p": "p.Gly870Ser",
"transcript": "XM_047449065.1",
"protein_id": "XP_047305021.1",
"transcript_support_level": null,
"aa_start": 870,
"aa_end": null,
"aa_length": 917,
"cds_start": 2608,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 3229,
"cdna_end": null,
"cdna_length": 9813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CASR",
"gene_hgnc_id": 1514,
"dbsnp": "rs142704083",
"frequency_reference_population": 0.000104694525,
"hom_count_reference_population": 1,
"allele_count_reference_population": 169,
"gnomad_exomes_af": 0.0000560916,
"gnomad_genomes_af": 0.000571143,
"gnomad_exomes_ac": 82,
"gnomad_genomes_ac": 87,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009535402059555054,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.145,
"revel_prediction": "Benign",
"alphamissense_score": 0.0677,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.522,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000639785.2",
"gene_symbol": "CASR",
"hgnc_id": 1514,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3091G>A",
"hgvs_p": "p.Gly1031Ser"
}
],
"clinvar_disease": "Autosomal dominant hypocalcemia 1,Familial hypocalciuric hypercalcemia,Familial hypocalciuric hypercalcemia 1,Nephrolithiasis/nephrocalcinosis,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:3",
"phenotype_combined": "Familial hypocalciuric hypercalcemia 1|not specified|Familial hypocalciuric hypercalcemia;Autosomal dominant hypocalcemia 1|Nephrolithiasis/nephrocalcinosis",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}