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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: 14-77512309-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=77512309&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SPTLC2",
"hgnc_id": 11278,
"hgvs_c": "c.1664C>T",
"hgvs_p": "p.Thr555Met",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_004863.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 7560,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1598,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.01,
"chr": "14",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " hereditary sensory and autonomic, type 1C,Neuropathy,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:6",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.006336510181427002,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 562,
"aa_ref": "T",
"aa_start": 555,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8034,
"cdna_start": 1722,
"cds_end": null,
"cds_length": 1689,
"cds_start": 1664,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_004863.4",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "c.1664C>T",
"hgvs_p": "p.Thr555Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000216484.7",
"protein_coding": true,
"protein_id": "NP_004854.1",
"strand": false,
"transcript": "NM_004863.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 562,
"aa_ref": "T",
"aa_start": 555,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8034,
"cdna_start": 1722,
"cds_end": null,
"cds_length": 1689,
"cds_start": 1664,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000216484.7",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "c.1664C>T",
"hgvs_p": "p.Thr555Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004863.4",
"protein_coding": true,
"protein_id": "ENSP00000216484.2",
"strand": false,
"transcript": "ENST00000216484.7",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 594,
"aa_ref": "T",
"aa_start": 587,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2120,
"cdna_start": 1830,
"cds_end": null,
"cds_length": 1785,
"cds_start": 1760,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000950640.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "c.1760C>T",
"hgvs_p": "p.Thr587Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620699.1",
"strand": false,
"transcript": "ENST00000950640.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 580,
"aa_ref": "T",
"aa_start": 573,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4923,
"cdna_start": 1811,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1718,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000950639.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "c.1718C>T",
"hgvs_p": "p.Thr573Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620698.1",
"strand": false,
"transcript": "ENST00000950639.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 573,
"aa_ref": "T",
"aa_start": 566,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1995,
"cdna_start": 1703,
"cds_end": null,
"cds_length": 1722,
"cds_start": 1697,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000921639.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "c.1697C>T",
"hgvs_p": "p.Thr566Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591699.1",
"strand": false,
"transcript": "ENST00000921639.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 497,
"aa_ref": "T",
"aa_start": 490,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1796,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 1494,
"cds_start": 1469,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000865813.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "c.1469C>T",
"hgvs_p": "p.Thr490Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535872.1",
"strand": false,
"transcript": "ENST00000865813.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 7002,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000686627.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "n.696C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000686627.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 7733,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000687688.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "n.1427C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000687688.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 7702,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000692906.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "n.1396C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000692906.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 460,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000556607.1",
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"hgvs_c": "n.*369C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000451029.1",
"strand": true,
"transcript": "ENST00000556607.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs138652708",
"effect": "missense_variant",
"frequency_reference_population": 0.004683626,
"gene_hgnc_id": 11278,
"gene_symbol": "SPTLC2",
"gnomad_exomes_ac": 6904,
"gnomad_exomes_af": 0.00472276,
"gnomad_exomes_homalt": 49,
"gnomad_genomes_ac": 656,
"gnomad_genomes_af": 0.00430797,
"gnomad_genomes_homalt": 9,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 58,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Neuropathy, hereditary sensory and autonomic, type 1C|not provided|not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.801,
"pos": 77512309,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.482,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_004863.4"
}
]
}