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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: 22-50731076-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=50731076&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 50731076,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000692848.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.5146C>A",
"hgvs_p": "p.Pro1716Thr",
"transcript": "NM_001372044.2",
"protein_id": "NP_001358973.1",
"transcript_support_level": null,
"aa_start": 1716,
"aa_end": null,
"aa_length": 1793,
"cds_start": 5146,
"cds_end": null,
"cds_length": 5382,
"cdna_start": 5516,
"cdna_end": null,
"cdna_length": 7652,
"mane_select": "ENST00000710353.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.5143C>A",
"hgvs_p": "p.Pro1715Thr",
"transcript": "ENST00000692848.2",
"protein_id": "ENSP00000510794.2",
"transcript_support_level": null,
"aa_start": 1715,
"aa_end": null,
"aa_length": 1792,
"cds_start": 5143,
"cds_end": null,
"cds_length": 5379,
"cdna_start": 5150,
"cdna_end": null,
"cdna_length": 7286,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.4561C>A",
"hgvs_p": "p.Pro1521Thr",
"transcript": "ENST00000262795.8",
"protein_id": "ENSP00000489147.3",
"transcript_support_level": 5,
"aa_start": 1521,
"aa_end": null,
"aa_length": 1598,
"cds_start": 4561,
"cds_end": null,
"cds_length": 4797,
"cdna_start": 5011,
"cdna_end": null,
"cdna_length": 7147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"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": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.3103C>A",
"hgvs_p": "p.Pro1035Thr",
"transcript": "ENST00000664402.3",
"protein_id": "ENSP00000499475.2",
"transcript_support_level": null,
"aa_start": 1035,
"aa_end": null,
"aa_length": 1112,
"cds_start": 3103,
"cds_end": null,
"cds_length": 3339,
"cdna_start": 3507,
"cdna_end": null,
"cdna_length": 5643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "c.403C>A",
"hgvs_p": "p.Pro135Thr",
"transcript": "ENST00000659388.1",
"protein_id": "ENSP00000499632.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 212,
"cds_start": 403,
"cds_end": null,
"cds_length": 639,
"cdna_start": 492,
"cdna_end": null,
"cdna_length": 934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.5145C>A",
"hgvs_p": null,
"transcript": "ENST00000414786.8",
"protein_id": null,
"transcript_support_level": 5,
"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": 7281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.*3559C>A",
"hgvs_p": null,
"transcript": "ENST00000673971.3",
"protein_id": "ENSP00000501192.2",
"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": 7982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"hgvs_c": "n.*3559C>A",
"hgvs_p": null,
"transcript": "ENST00000673971.3",
"protein_id": "ENSP00000501192.2",
"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": 7982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SHANK3",
"gene_hgnc_id": 14294,
"dbsnp": "rs749130556",
"frequency_reference_population": 0.0036642996,
"hom_count_reference_population": 15,
"allele_count_reference_population": 5448,
"gnomad_exomes_af": 0.00373558,
"gnomad_genomes_af": 0.00303115,
"gnomad_exomes_ac": 4992,
"gnomad_genomes_ac": 456,
"gnomad_exomes_homalt": 15,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006612271070480347,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.058,
"revel_prediction": "Benign",
"alphamissense_score": 0.0687,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.676,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000692848.2",
"gene_symbol": "SHANK3",
"hgnc_id": 14294,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5143C>A",
"hgvs_p": "p.Pro1715Thr"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:2",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}