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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: 9-127695053-TTGATGATGATGATGATGATGATGATGA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=127695053&ref=TTGATGATGATGATGATGATGATGATGA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 127695053,
"ref": "TTGATGATGATGATGATGATGATGATGA",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000335223.5",
"consequences": [
{
"aa_ref": "HHHHHHHHHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTRH1",
"gene_hgnc_id": 27039,
"hgvs_c": "c.267_293delTCATCATCATCATCATCATCATCATCA",
"hgvs_p": "p.His89_His97del",
"transcript": "ENST00000335223.5",
"protein_id": "ENSP00000493136.1",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 159,
"cds_start": 267,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335223.5"
},
{
"aa_ref": "IIIIIIIIIN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTRH1",
"gene_hgnc_id": 27039,
"hgvs_c": "c.524_550delTCATCATCATCATCATCATCATCATCA",
"hgvs_p": "p.Ile175_Ile183del",
"transcript": "XM_047422774.1",
"protein_id": "XP_047278730.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 185,
"cds_start": 524,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047422774.1"
},
{
"aa_ref": "IIIIIIIIIN",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTRH1",
"gene_hgnc_id": 27039,
"hgvs_c": "c.368_394delTCATCATCATCATCATCATCATCATCA",
"hgvs_p": "p.Ile123_Ile131del",
"transcript": "XM_047422775.1",
"protein_id": "XP_047278731.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 133,
"cds_start": 368,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047422775.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STXBP1",
"gene_hgnc_id": 11444,
"hgvs_c": "c.*52_*78delATGATGATGATGATGATGATGATGATG",
"hgvs_p": null,
"transcript": "NM_001374314.1",
"protein_id": "NP_001361243.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 574,
"cds_start": null,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374314.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STXBP1",
"gene_hgnc_id": 11444,
"hgvs_c": "c.*52_*78delATGATGATGATGATGATGATGATGATG",
"hgvs_p": null,
"transcript": "ENST00000636962.2",
"protein_id": "ENSP00000489762.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 574,
"cds_start": null,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000636962.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STXBP1",
"gene_hgnc_id": 11444,
"hgvs_c": "n.*52_*78delATGATGATGATGATGATGATGATGATG",
"hgvs_p": null,
"transcript": "ENST00000635950.2",
"protein_id": "ENSP00000490903.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000635950.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STXBP1",
"gene_hgnc_id": 11444,
"hgvs_c": "n.*52_*78delATGATGATGATGATGATGATGATGATG",
"hgvs_p": null,
"transcript": "ENST00000635950.2",
"protein_id": "ENSP00000490903.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000635950.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTRH1",
"gene_hgnc_id": 27039,
"hgvs_c": "c.-121_-95delTCATCATCATCATCATCATCATCATCA",
"hgvs_p": null,
"transcript": "ENST00000641641.1",
"protein_id": "ENSP00000492921.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 35,
"cds_start": null,
"cds_end": null,
"cds_length": 108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641641.1"
}
],
"gene_symbol": "PTRH1",
"gene_hgnc_id": 27039,
"dbsnp": "rs57076743",
"frequency_reference_population": 0.00000190804,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0.00000190804,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.093,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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": "BP3",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP3"
],
"verdict": "Likely_benign",
"transcript": "ENST00000335223.5",
"gene_symbol": "PTRH1",
"hgnc_id": 27039,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.267_293delTCATCATCATCATCATCATCATCATCA",
"hgvs_p": "p.His89_His97del"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_001374314.1",
"gene_symbol": "STXBP1",
"hgnc_id": 11444,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.*52_*78delATGATGATGATGATGATGATGATGATG",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}