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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: 5-74718856-TAG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=74718856&ref=TAG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 74718856,
"ref": "TAG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "ENST00000261416.12",
"consequences": [
{
"aa_ref": "RV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.1305_1306delAG",
"hgvs_p": "p.Arg435fs",
"transcript": "NM_000521.4",
"protein_id": "NP_000512.2",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 556,
"cds_start": 1305,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1333,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": "ENST00000261416.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RV",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.1305_1306delAG",
"hgvs_p": "p.Arg435fs",
"transcript": "ENST00000261416.12",
"protein_id": "ENSP00000261416.7",
"transcript_support_level": 1,
"aa_start": 435,
"aa_end": null,
"aa_length": 556,
"cds_start": 1305,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1333,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": "NM_000521.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.630_631delAG",
"hgvs_p": "p.Arg210fs",
"transcript": "ENST00000511181.5",
"protein_id": "ENSP00000426285.1",
"transcript_support_level": 1,
"aa_start": 210,
"aa_end": null,
"aa_length": 331,
"cds_start": 630,
"cds_end": null,
"cds_length": 996,
"cdna_start": 1542,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.630_631delAG",
"hgvs_p": "p.Arg210fs",
"transcript": "NM_001292004.2",
"protein_id": "NP_001278933.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 331,
"cds_start": 630,
"cds_end": null,
"cds_length": 996,
"cdna_start": 1542,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "RV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.240_241delAG",
"hgvs_p": "p.Arg80fs",
"transcript": "ENST00000513336.5",
"protein_id": "ENSP00000423713.1",
"transcript_support_level": 3,
"aa_start": 80,
"aa_end": null,
"aa_length": 201,
"cds_start": 240,
"cds_end": null,
"cds_length": 606,
"cdna_start": 241,
"cdna_end": null,
"cdna_length": 720,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.180_181delAG",
"hgvs_p": null,
"transcript": "ENST00000503312.5",
"protein_id": "ENSP00000426384.1",
"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": 756,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.502_503delAG",
"hgvs_p": null,
"transcript": "ENST00000504459.5",
"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": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.74-50_74-49delAG",
"hgvs_p": null,
"transcript": "ENST00000513539.1",
"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": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"dbsnp": "rs779328596",
"frequency_reference_population": 0.0000055762357,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000547272,
"gnomad_genomes_af": 0.00000657047,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"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": -0.494,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000261416.12",
"gene_symbol": "HEXB",
"hgnc_id": 4879,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1305_1306delAG",
"hgvs_p": "p.Arg435fs"
}
],
"clinvar_disease": "Sandhoff disease",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"phenotype_combined": "Sandhoff disease",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}