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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: 14-77557151-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=77557151&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 77557151,
"ref": "A",
"alt": "G",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_004863.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.851-5T>C",
"hgvs_p": null,
"transcript": "NM_004863.4",
"protein_id": "NP_004854.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 562,
"cds_start": null,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8034,
"mane_select": "ENST00000216484.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004863.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.851-5T>C",
"hgvs_p": null,
"transcript": "ENST00000216484.7",
"protein_id": "ENSP00000216484.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 562,
"cds_start": null,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8034,
"mane_select": "NM_004863.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216484.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.659-5T>C",
"hgvs_p": null,
"transcript": "ENST00000554901.1",
"protein_id": "ENSP00000452189.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 406,
"cds_start": null,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1518,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000554901.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.947-5T>C",
"hgvs_p": null,
"transcript": "ENST00000950640.1",
"protein_id": "ENSP00000620699.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 594,
"cds_start": null,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2120,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950640.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.851-5T>C",
"hgvs_p": null,
"transcript": "ENST00000950639.1",
"protein_id": "ENSP00000620698.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 580,
"cds_start": null,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4923,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950639.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.884-5T>C",
"hgvs_p": null,
"transcript": "ENST00000921639.1",
"protein_id": "ENSP00000591699.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 573,
"cds_start": null,
"cds_end": null,
"cds_length": 1722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1995,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921639.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.656-5T>C",
"hgvs_p": null,
"transcript": "ENST00000865813.1",
"protein_id": "ENSP00000535872.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 497,
"cds_start": null,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1796,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865813.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.851-5T>C",
"hgvs_p": null,
"transcript": "XM_011537384.3",
"protein_id": "XP_011535686.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 470,
"cds_start": null,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1767,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537384.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.171T>C",
"hgvs_p": null,
"transcript": "ENST00000554365.1",
"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": 604,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000554365.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.614-5T>C",
"hgvs_p": null,
"transcript": "ENST00000687688.1",
"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": 7733,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000687688.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.628-5T>C",
"hgvs_p": null,
"transcript": "ENST00000691887.1",
"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": 933,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000691887.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.583-5T>C",
"hgvs_p": null,
"transcript": "ENST00000692906.1",
"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": 7702,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000692906.1"
}
],
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"dbsnp": "rs199867946",
"frequency_reference_population": 0.0002718646,
"hom_count_reference_population": 2,
"allele_count_reference_population": 438,
"gnomad_exomes_af": 0.000276245,
"gnomad_genomes_af": 0.000229891,
"gnomad_exomes_ac": 403,
"gnomad_genomes_ac": 35,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8600000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.00800000037997961,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.86,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.754,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000386585164961458,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004863.4",
"gene_symbol": "SPTLC2",
"hgnc_id": 11278,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.851-5T>C",
"hgvs_p": null
}
],
"clinvar_disease": " hereditary sensory and autonomic, type 1C,Inborn genetic diseases,Neuropathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3 B:1",
"phenotype_combined": "not specified|Neuropathy, hereditary sensory and autonomic, type 1C|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}