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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: 5-140114302-G-GGCGGCA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=140114302&ref=G&alt=GGCGGCA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 140114302,
"ref": "G",
"alt": "GGCGGCA",
"effect": "disruptive_inframe_insertion",
"transcript": "NM_005859.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "SGS",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"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.123_128dupCGGCAG",
"hgvs_p": "p.Ser43_Gly44insGlySer",
"transcript": "NM_005859.5",
"protein_id": "NP_005850.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 322,
"cds_start": 129,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000331327.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005859.5"
},
{
"aa_ref": "S",
"aa_alt": "SGS",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"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.123_128dupCGGCAG",
"hgvs_p": "p.Ser43_Gly44insGlySer",
"transcript": "ENST00000331327.5",
"protein_id": "ENSP00000332706.3",
"transcript_support_level": 6,
"aa_start": 43,
"aa_end": null,
"aa_length": 322,
"cds_start": 129,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005859.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000331327.5"
},
{
"aa_ref": "S",
"aa_alt": "SGS",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"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.123_128dupCGGCAG",
"hgvs_p": "p.Ser43_Gly44insGlySer",
"transcript": "ENST00000651386.1",
"protein_id": "ENSP00000499133.1",
"transcript_support_level": null,
"aa_start": 43,
"aa_end": null,
"aa_length": 322,
"cds_start": 129,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000651386.1"
},
{
"aa_ref": "S",
"aa_alt": "SGS",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"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.123_128dupCGGCAG",
"hgvs_p": "p.Ser43_Gly44insGlySer",
"transcript": "ENST00000505703.2",
"protein_id": "ENSP00000498560.1",
"transcript_support_level": 3,
"aa_start": 43,
"aa_end": null,
"aa_length": 105,
"cds_start": 129,
"cds_end": null,
"cds_length": 319,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505703.2"
},
{
"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+96_312+101dupTGCCGC",
"hgvs_p": null,
"transcript": "ENST00000520928.2",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000520928.2"
},
{
"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+96_154+101dupTGCCGC",
"hgvs_p": null,
"transcript": "ENST00000521133.2",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000521133.2"
},
{
"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+96_255+101dupTGCCGC",
"hgvs_p": null,
"transcript": "ENST00000719579.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000719579.1"
},
{
"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.*42_*43insGCGGCA",
"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": null,
"cds_end": null,
"cds_length": 79,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502351.1"
}
],
"gene_symbol": "PURA",
"gene_hgnc_id": 9701,
"dbsnp": "rs1039658835",
"frequency_reference_population": 0.0001947068,
"hom_count_reference_population": 0,
"allele_count_reference_population": 249,
"gnomad_exomes_af": 0.000213373,
"gnomad_genomes_af": 0.0000535583,
"gnomad_exomes_ac": 241,
"gnomad_genomes_ac": 8,
"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": 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": 5.663,
"phylop100way_prediction": "Uncertain_significance",
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005859.5",
"gene_symbol": "PURA",
"hgnc_id": 9701,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.123_128dupCGGCAG",
"hgvs_p": "p.Ser43_Gly44insGlySer"
},
{
"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+96_312+101dupTGCCGC",
"hgvs_p": null
}
],
"clinvar_disease": "PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "not specified|PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}