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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: 4-1001517-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1001517&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 1001517,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000514224.2",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.543T>C",
"hgvs_p": "p.Asn181Asn",
"transcript": "NM_000203.5",
"protein_id": "NP_000194.2",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 653,
"cds_start": 543,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": "ENST00000514224.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.543T>C",
"hgvs_p": "p.Asn181Asn",
"transcript": "ENST00000514224.2",
"protein_id": "ENSP00000425081.2",
"transcript_support_level": 2,
"aa_start": 181,
"aa_end": null,
"aa_length": 653,
"cds_start": 543,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": "NM_000203.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.543T>C",
"hgvs_p": "p.Asn181Asn",
"transcript": "ENST00000247933.9",
"protein_id": "ENSP00000247933.4",
"transcript_support_level": 1,
"aa_start": 181,
"aa_end": null,
"aa_length": 653,
"cds_start": 543,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 2186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.147T>C",
"hgvs_p": "p.Asn49Asn",
"transcript": "NM_001363576.1",
"protein_id": "NP_001350505.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 521,
"cds_start": 147,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 599,
"cdna_end": null,
"cdna_length": 2182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.402T>C",
"hgvs_p": "p.Asn134Asn",
"transcript": "ENST00000502910.5",
"protein_id": "ENSP00000422952.1",
"transcript_support_level": 3,
"aa_start": 134,
"aa_end": null,
"aa_length": 223,
"cds_start": 402,
"cds_end": null,
"cds_length": 673,
"cdna_start": 443,
"cdna_end": null,
"cdna_length": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.501T>C",
"hgvs_p": "p.Asn167Asn",
"transcript": "ENST00000504568.5",
"protein_id": "ENSP00000424847.1",
"transcript_support_level": 3,
"aa_start": 167,
"aa_end": null,
"aa_length": 193,
"cds_start": 501,
"cds_end": null,
"cds_length": 584,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.543T>C",
"hgvs_p": "p.Asn181Asn",
"transcript": "XM_047415650.1",
"protein_id": "XP_047271606.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 632,
"cds_start": 543,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 2099,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.603T>C",
"hgvs_p": null,
"transcript": "ENST00000509948.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 796,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.360T>C",
"hgvs_p": null,
"transcript": "ENST00000514192.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 697,
"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": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.443T>C",
"hgvs_p": null,
"transcript": "ENST00000514698.5",
"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": 2185,
"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": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.599T>C",
"hgvs_p": null,
"transcript": "ENST00000652070.1",
"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": 2130,
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.631T>C",
"hgvs_p": null,
"transcript": "NR_110313.1",
"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": 2218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"dbsnp": "rs6815946",
"frequency_reference_population": 0.16344617,
"hom_count_reference_population": 23253,
"allele_count_reference_population": 263639,
"gnomad_exomes_af": 0.162418,
"gnomad_genomes_af": 0.173319,
"gnomad_exomes_ac": 237274,
"gnomad_genomes_ac": 26365,
"gnomad_exomes_homalt": 20855,
"gnomad_genomes_homalt": 2398,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10999999940395355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.11,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.186,
"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": "BA1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000514224.2",
"gene_symbol": "IDUA",
"hgnc_id": 5391,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.543T>C",
"hgvs_p": "p.Asn181Asn"
}
],
"clinvar_disease": " MPS-I-H/S, MPS-I-S,Hurler syndrome,Mucopolysaccharidosis,Mucopolysaccharidosis type 1,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "B:10",
"phenotype_combined": "not specified|Mucopolysaccharidosis type 1|Mucopolysaccharidosis, MPS-I-S|Hurler syndrome|not provided|Mucopolysaccharidosis, MPS-I-H/S",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}