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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: 2-19933479-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=19933479&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 19933479,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000281405.9",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2613G>A",
"hgvs_p": "p.Met871Ile",
"transcript": "NM_001006657.2",
"protein_id": "NP_001006658.1",
"transcript_support_level": null,
"aa_start": 871,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2613,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2703,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": "ENST00000345530.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2613G>A",
"hgvs_p": "p.Met871Ile",
"transcript": "ENST00000345530.8",
"protein_id": "ENSP00000314444.5",
"transcript_support_level": 1,
"aa_start": 871,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2613,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2703,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": "NM_001006657.2",
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2580G>A",
"hgvs_p": "p.Met860Ile",
"transcript": "NM_020779.4",
"protein_id": "NP_065830.2",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 1170,
"cds_start": 2580,
"cds_end": null,
"cds_length": 3513,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": "ENST00000281405.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2580G>A",
"hgvs_p": "p.Met860Ile",
"transcript": "ENST00000281405.9",
"protein_id": "ENSP00000281405.5",
"transcript_support_level": 1,
"aa_start": 860,
"aa_end": null,
"aa_length": 1170,
"cds_start": 2580,
"cds_end": null,
"cds_length": 3513,
"cdna_start": 2670,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": "NM_020779.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.1308G>A",
"hgvs_p": "p.Met436Ile",
"transcript": "XM_011533007.3",
"protein_id": "XP_011531309.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 746,
"cds_start": 1308,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 5641,
"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": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.2617G>A",
"hgvs_p": null,
"transcript": "ENST00000414212.5",
"protein_id": "ENSP00000390802.1",
"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": 3483,
"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": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.2670G>A",
"hgvs_p": null,
"transcript": "XR_426989.4",
"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": 3061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.*1271+1992G>A",
"hgvs_p": null,
"transcript": "ENST00000445063.5",
"protein_id": "ENSP00000390105.1",
"transcript_support_level": 2,
"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": 2788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"dbsnp": "rs201443916",
"frequency_reference_population": 0.000019208344,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.000020526,
"gnomad_genomes_af": 0.00000656495,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.36991360783576965,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.195,
"revel_prediction": "Benign",
"alphamissense_score": 0.7911,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.57,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000281405.9",
"gene_symbol": "WDR35",
"hgnc_id": 29250,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2580G>A",
"hgvs_p": "p.Met860Ile"
}
],
"clinvar_disease": "Cranioectodermal dysplasia 2,Short-rib thoracic dysplasia 7 with or without polydactyly",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Short-rib thoracic dysplasia 7 with or without polydactyly;Cranioectodermal dysplasia 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}