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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: 5-140114310-TGGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=140114310&ref=TGGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 140114310,
"ref": "TGGC",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000331327.5",
"consequences": [
{
"aa_ref": "GG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"hgvs_c": "c.144_146delCGG",
"hgvs_p": "p.Gly49del",
"transcript": "NM_005859.5",
"protein_id": "NP_005850.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 322,
"cds_start": 144,
"cds_end": null,
"cds_length": 969,
"cdna_start": 217,
"cdna_end": null,
"cdna_length": 11511,
"mane_select": "ENST00000331327.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GG",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"hgvs_c": "c.144_146delCGG",
"hgvs_p": "p.Gly49del",
"transcript": "ENST00000331327.5",
"protein_id": "ENSP00000332706.3",
"transcript_support_level": 6,
"aa_start": 48,
"aa_end": null,
"aa_length": 322,
"cds_start": 144,
"cds_end": null,
"cds_length": 969,
"cdna_start": 217,
"cdna_end": null,
"cdna_length": 11511,
"mane_select": "NM_005859.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"hgvs_c": "c.144_146delCGG",
"hgvs_p": "p.Gly49del",
"transcript": "ENST00000651386.1",
"protein_id": "ENSP00000499133.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 322,
"cds_start": 144,
"cds_end": null,
"cds_length": 969,
"cdna_start": 690,
"cdna_end": null,
"cdna_length": 1919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "GG",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"hgvs_c": "c.144_146delCGG",
"hgvs_p": "p.Gly49del",
"transcript": "ENST00000505703.2",
"protein_id": "ENSP00000498560.1",
"transcript_support_level": 3,
"aa_start": 48,
"aa_end": null,
"aa_length": 105,
"cds_start": 144,
"cds_end": null,
"cds_length": 319,
"cdna_start": 609,
"cdna_end": null,
"cdna_length": 784,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MALINC1",
"gene_hgnc_id": 49009,
"hgvs_c": "n.312+91_312+93delGCC",
"hgvs_p": null,
"transcript": "ENST00000520928.2",
"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": 1099,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MALINC1",
"gene_hgnc_id": 49009,
"hgvs_c": "n.154+91_154+93delGCC",
"hgvs_p": null,
"transcript": "ENST00000521133.2",
"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": 868,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MALINC1",
"gene_hgnc_id": 49009,
"hgvs_c": "n.255+91_255+93delGCC",
"hgvs_p": null,
"transcript": "ENST00000719579.1",
"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": 1135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"hgvs_c": "c.*51_*53delGGC",
"hgvs_p": null,
"transcript": "ENST00000502351.1",
"protein_id": "ENSP00000498760.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 25,
"cds_start": -4,
"cds_end": null,
"cds_length": 79,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"dbsnp": "rs754074166",
"frequency_reference_population": 0.0013243977,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1479,
"gnomad_exomes_af": 0.0013244,
"gnomad_genomes_af": 0.0000143316,
"gnomad_exomes_ac": 1479,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.671,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP3,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000331327.5",
"gene_symbol": "PURA",
"hgnc_id": 9701,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.144_146delCGG",
"hgvs_p": "p.Gly49del"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000520928.2",
"gene_symbol": "MALINC1",
"hgnc_id": 49009,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.312+91_312+93delGCC",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,PURA-related disorder,PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome|not provided|PURA-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}