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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: 14-77552173-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=77552173&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 77552173,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000216484.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.1226C>T",
"hgvs_p": "p.Thr409Met",
"transcript": "NM_004863.4",
"protein_id": "NP_004854.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 562,
"cds_start": 1226,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 1284,
"cdna_end": null,
"cdna_length": 8034,
"mane_select": "ENST00000216484.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.1226C>T",
"hgvs_p": "p.Thr409Met",
"transcript": "ENST00000216484.7",
"protein_id": "ENSP00000216484.2",
"transcript_support_level": 1,
"aa_start": 409,
"aa_end": null,
"aa_length": 562,
"cds_start": 1226,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 1284,
"cdna_end": null,
"cdna_length": 8034,
"mane_select": "NM_004863.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.1034C>T",
"hgvs_p": "p.Thr345Met",
"transcript": "ENST00000554901.1",
"protein_id": "ENSP00000452189.1",
"transcript_support_level": 1,
"aa_start": 345,
"aa_end": null,
"aa_length": 406,
"cds_start": 1034,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1035,
"cdna_end": null,
"cdna_length": 1518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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.1226C>T",
"hgvs_p": "p.Thr409Met",
"transcript": "XM_011537384.3",
"protein_id": "XP_011535686.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 470,
"cds_start": 1226,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1284,
"cdna_end": null,
"cdna_length": 1767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.551C>T",
"hgvs_p": null,
"transcript": "ENST00000554365.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.20C>T",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.258C>T",
"hgvs_p": null,
"transcript": "ENST00000686627.1",
"protein_id": null,
"transcript_support_level": null,
"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": 7002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.989C>T",
"hgvs_p": null,
"transcript": "ENST00000687688.1",
"protein_id": null,
"transcript_support_level": null,
"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": 7733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.958C>T",
"hgvs_p": null,
"transcript": "ENST00000692906.1",
"protein_id": null,
"transcript_support_level": null,
"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": 7702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPTLC2",
"gene_hgnc_id": 11278,
"dbsnp": "rs368357970",
"frequency_reference_population": 0.000017967248,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000177857,
"gnomad_genomes_af": 0.0000197112,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7289363145828247,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.673,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1498,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.147,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.07,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000216484.7",
"gene_symbol": "SPTLC2",
"hgnc_id": 11278,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1226C>T",
"hgvs_p": "p.Thr409Met"
}
],
"clinvar_disease": " hereditary sensory and autonomic, type 1C,Neuropathy,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|Neuropathy, hereditary sensory and autonomic, type 1C",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}