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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: 2-19937944-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=19937944&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 19937944,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000281405.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2099G>A",
"hgvs_p": "p.Arg700His",
"transcript": "NM_001006657.2",
"protein_id": "NP_001006658.1",
"transcript_support_level": null,
"aa_start": 700,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2099,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2189,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": "ENST00000345530.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2099G>A",
"hgvs_p": "p.Arg700His",
"transcript": "ENST00000345530.8",
"protein_id": "ENSP00000314444.5",
"transcript_support_level": 1,
"aa_start": 700,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2099,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2189,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": "NM_001006657.2",
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2066G>A",
"hgvs_p": "p.Arg689His",
"transcript": "NM_020779.4",
"protein_id": "NP_065830.2",
"transcript_support_level": null,
"aa_start": 689,
"aa_end": null,
"aa_length": 1170,
"cds_start": 2066,
"cds_end": null,
"cds_length": 3513,
"cdna_start": 2156,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": "ENST00000281405.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2066G>A",
"hgvs_p": "p.Arg689His",
"transcript": "ENST00000281405.9",
"protein_id": "ENSP00000281405.5",
"transcript_support_level": 1,
"aa_start": 689,
"aa_end": null,
"aa_length": 1170,
"cds_start": 2066,
"cds_end": null,
"cds_length": 3513,
"cdna_start": 2156,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": "NM_020779.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.704G>A",
"hgvs_p": "p.Arg235His",
"transcript": "ENST00000453014.1",
"protein_id": "ENSP00000404409.1",
"transcript_support_level": 1,
"aa_start": 235,
"aa_end": null,
"aa_length": 406,
"cds_start": 704,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 704,
"cdna_end": null,
"cdna_length": 1624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Arg265His",
"transcript": "XM_011533007.3",
"protein_id": "XP_011531309.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 746,
"cds_start": 794,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 899,
"cdna_end": null,
"cdna_length": 5641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2010G>A",
"hgvs_p": "p.Ala670Ala",
"transcript": "XM_047445199.1",
"protein_id": "XP_047301155.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 673,
"cds_start": 2010,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 2100,
"cdna_end": null,
"cdna_length": 2216,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.2099G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.*790G>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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.2156G>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": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.*790G>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": "rs74470618",
"frequency_reference_population": 0.00038105602,
"hom_count_reference_population": 0,
"allele_count_reference_population": 615,
"gnomad_exomes_af": 0.000262706,
"gnomad_genomes_af": 0.00151746,
"gnomad_exomes_ac": 384,
"gnomad_genomes_ac": 231,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.013697594404220581,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.659,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.0901,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.981,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000281405.9",
"gene_symbol": "WDR35",
"hgnc_id": 29250,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2066G>A",
"hgvs_p": "p.Arg689His"
}
],
"clinvar_disease": "Cranioectodermal dysplasia 2,Short-rib thoracic dysplasia 7 with or without polydactyly,WDR35-related disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:4",
"phenotype_combined": "not specified|Short-rib thoracic dysplasia 7 with or without polydactyly;Cranioectodermal dysplasia 2|Short-rib thoracic dysplasia 7 with or without polydactyly|Cranioectodermal dysplasia 2|not provided|WDR35-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}