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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: 4-76741016-T-TGGG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=76741016&ref=T&alt=TGGG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 76741016,
"ref": "T",
"alt": "TGGG",
"effect": "disruptive_inframe_insertion",
"transcript": "NM_020859.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "GA",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"hgvs_c": "c.2846_2848dupGGG",
"hgvs_p": "p.Gly949dup",
"transcript": "NM_020859.4",
"protein_id": "NP_065910.3",
"transcript_support_level": null,
"aa_start": 950,
"aa_end": null,
"aa_length": 1996,
"cds_start": 2849,
"cds_end": null,
"cds_length": 5991,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296043.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020859.4"
},
{
"aa_ref": "A",
"aa_alt": "GA",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"hgvs_c": "c.2846_2848dupGGG",
"hgvs_p": "p.Gly949dup",
"transcript": "ENST00000296043.7",
"protein_id": "ENSP00000296043.6",
"transcript_support_level": 1,
"aa_start": 950,
"aa_end": null,
"aa_length": 1996,
"cds_start": 2849,
"cds_end": null,
"cds_length": 5991,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020859.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296043.7"
},
{
"aa_ref": "A",
"aa_alt": "GA",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"hgvs_c": "c.2849_2851dupGGG",
"hgvs_p": "p.Gly950dup",
"transcript": "ENST00000912766.1",
"protein_id": "ENSP00000582825.1",
"transcript_support_level": null,
"aa_start": 951,
"aa_end": null,
"aa_length": 1997,
"cds_start": 2852,
"cds_end": null,
"cds_length": 5994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912766.1"
},
{
"aa_ref": "A",
"aa_alt": "GA",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"hgvs_c": "c.2603_2605dupGGG",
"hgvs_p": "p.Gly868dup",
"transcript": "ENST00000646790.1",
"protein_id": "ENSP00000494970.1",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 1915,
"cds_start": 2606,
"cds_end": null,
"cds_length": 5748,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646790.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"hgvs_c": "n.2655_2657dupGGG",
"hgvs_p": null,
"transcript": "ENST00000486758.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000486758.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"hgvs_c": "n.415-7998_415-7996dupGGG",
"hgvs_p": null,
"transcript": "ENST00000469923.5",
"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": "ENST00000469923.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.371-30625_371-30623dupCCC",
"hgvs_p": null,
"transcript": "ENST00000660459.1",
"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": "ENST00000660459.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.517+1789_517+1791dupCCC",
"hgvs_p": null,
"transcript": "ENST00000666924.2",
"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": "ENST00000666924.2"
},
{
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.441+1789_441+1791dupCCC",
"hgvs_p": null,
"transcript": "ENST00000747876.1",
"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": "ENST00000747876.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.465+1789_465+1791dupCCC",
"hgvs_p": null,
"transcript": "ENST00000747877.1",
"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": "ENST00000747877.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.471+1789_471+1791dupCCC",
"hgvs_p": null,
"transcript": "ENST00000747878.1",
"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": "ENST00000747878.1"
},
{
"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": 3,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.1044+1789_1044+1791dupCCC",
"hgvs_p": null,
"transcript": "NR_187404.1",
"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": "NR_187404.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHROOM3-AS1",
"gene_hgnc_id": 41265,
"hgvs_c": "n.500+1789_500+1791dupCCC",
"hgvs_p": null,
"transcript": "NR_187405.1",
"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": "NR_187405.1"
}
],
"gene_symbol": "SHROOM3",
"gene_hgnc_id": 30422,
"dbsnp": "rs863225433",
"frequency_reference_population": 7.4966005e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.4966e-7,
"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": -0.164,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM4_Supporting",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PM4_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020859.4",
"gene_symbol": "SHROOM3",
"hgnc_id": 30422,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2846_2848dupGGG",
"hgvs_p": "p.Gly949dup"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NR_187404.1",
"gene_symbol": "SHROOM3-AS1",
"hgnc_id": 41265,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1044+1789_1044+1791dupCCC",
"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
}