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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: 2-19935522-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=19935522&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 19935522,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000281405.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2529A>G",
"hgvs_p": "p.Glu843Glu",
"transcript": "NM_001006657.2",
"protein_id": "NP_001006658.1",
"transcript_support_level": null,
"aa_start": 843,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2529,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2619,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": "ENST00000345530.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2529A>G",
"hgvs_p": "p.Glu843Glu",
"transcript": "ENST00000345530.8",
"protein_id": "ENSP00000314444.5",
"transcript_support_level": 1,
"aa_start": 843,
"aa_end": null,
"aa_length": 1181,
"cds_start": 2529,
"cds_end": null,
"cds_length": 3546,
"cdna_start": 2619,
"cdna_end": null,
"cdna_length": 6931,
"mane_select": null,
"mane_plus": "NM_001006657.2",
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2496A>G",
"hgvs_p": "p.Glu832Glu",
"transcript": "NM_020779.4",
"protein_id": "NP_065830.2",
"transcript_support_level": null,
"aa_start": 832,
"aa_end": null,
"aa_length": 1170,
"cds_start": 2496,
"cds_end": null,
"cds_length": 3513,
"cdna_start": 2586,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": "ENST00000281405.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.2496A>G",
"hgvs_p": "p.Glu832Glu",
"transcript": "ENST00000281405.9",
"protein_id": "ENSP00000281405.5",
"transcript_support_level": 1,
"aa_start": 832,
"aa_end": null,
"aa_length": 1170,
"cds_start": 2496,
"cds_end": null,
"cds_length": 3513,
"cdna_start": 2586,
"cdna_end": null,
"cdna_length": 6898,
"mane_select": "NM_020779.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.1134A>G",
"hgvs_p": "p.Glu378Glu",
"transcript": "ENST00000453014.1",
"protein_id": "ENSP00000404409.1",
"transcript_support_level": 1,
"aa_start": 378,
"aa_end": null,
"aa_length": 406,
"cds_start": 1134,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1134,
"cdna_end": null,
"cdna_length": 1624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "c.1224A>G",
"hgvs_p": "p.Glu408Glu",
"transcript": "XM_011533007.3",
"protein_id": "XP_011531309.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 746,
"cds_start": 1224,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 1329,
"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": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.2529A>G",
"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": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.*1220A>G",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.2586A>G",
"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": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDR35",
"gene_hgnc_id": 29250,
"hgvs_c": "n.*1220A>G",
"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": "rs6741091",
"frequency_reference_population": 0.4449864,
"hom_count_reference_population": 162847,
"allele_count_reference_population": 717521,
"gnomad_exomes_af": 0.443617,
"gnomad_genomes_af": 0.458149,
"gnomad_exomes_ac": 647908,
"gnomad_genomes_ac": 69613,
"gnomad_exomes_homalt": 146678,
"gnomad_genomes_homalt": 16169,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.738,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000281405.9",
"gene_symbol": "WDR35",
"hgnc_id": 29250,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2496A>G",
"hgvs_p": "p.Glu832Glu"
}
],
"clinvar_disease": "Cranioectodermal dysplasia 2,Short-rib thoracic dysplasia 7 with or without polydactyly,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Short-rib thoracic dysplasia 7 with or without polydactyly|Cranioectodermal dysplasia 2|Cranioectodermal dysplasia 2;Short-rib thoracic dysplasia 7 with or without polydactyly|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}