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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: 14-77552172-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=77552172&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 77552172,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_004863.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1227G>A",
"hgvs_p": "p.Thr409Thr",
"transcript": "NM_004863.4",
"protein_id": "NP_004854.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 562,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000216484.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004863.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1227G>A",
"hgvs_p": "p.Thr409Thr",
"transcript": "ENST00000216484.7",
"protein_id": "ENSP00000216484.2",
"transcript_support_level": 1,
"aa_start": 409,
"aa_end": null,
"aa_length": 562,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004863.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216484.7"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1035G>A",
"hgvs_p": "p.Thr345Thr",
"transcript": "ENST00000554901.1",
"protein_id": "ENSP00000452189.1",
"transcript_support_level": 1,
"aa_start": 345,
"aa_end": null,
"aa_length": 406,
"cds_start": 1035,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000554901.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1323G>A",
"hgvs_p": "p.Thr441Thr",
"transcript": "ENST00000950640.1",
"protein_id": "ENSP00000620699.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 594,
"cds_start": 1323,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950640.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1227G>A",
"hgvs_p": "p.Thr409Thr",
"transcript": "ENST00000950639.1",
"protein_id": "ENSP00000620698.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 580,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950639.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1260G>A",
"hgvs_p": "p.Thr420Thr",
"transcript": "ENST00000921639.1",
"protein_id": "ENSP00000591699.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 573,
"cds_start": 1260,
"cds_end": null,
"cds_length": 1722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921639.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1032G>A",
"hgvs_p": "p.Thr344Thr",
"transcript": "ENST00000865813.1",
"protein_id": "ENSP00000535872.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 497,
"cds_start": 1032,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865813.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "c.1227G>A",
"hgvs_p": "p.Thr409Thr",
"transcript": "XM_011537384.3",
"protein_id": "XP_011535686.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 470,
"cds_start": 1227,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.552G>A",
"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": null,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.21G>A",
"hgvs_p": null,
"transcript": "ENST00000556607.1",
"protein_id": "ENSP00000451029.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000556607.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.259G>A",
"hgvs_p": null,
"transcript": "ENST00000686627.1",
"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": "ENST00000686627.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.990G>A",
"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": null,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"hgvs_c": "n.959G>A",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000692906.1"
}
],
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"dbsnp": "rs9323646",
"frequency_reference_population": 0.0010054803,
"hom_count_reference_population": 14,
"allele_count_reference_population": 1623,
"gnomad_exomes_af": 0.000573933,
"gnomad_genomes_af": 0.00514733,
"gnomad_exomes_ac": 839,
"gnomad_genomes_ac": 784,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.017999999225139618,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.018,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.602,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004863.4",
"gene_symbol": "SPTLC2",
"hgnc_id": 11278,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1227G>A",
"hgvs_p": "p.Thr409Thr"
}
],
"clinvar_disease": " hereditary sensory and autonomic, type 1C,Inborn genetic diseases,Neuropathy,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:4",
"phenotype_combined": "not specified|Neuropathy, hereditary sensory and autonomic, type 1C|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}