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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: 12-53066438-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=53066438&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 53066438,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_032840.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1070G>C",
"hgvs_p": "p.Arg357Pro",
"transcript": "NM_032840.3",
"protein_id": "NP_116229.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 442,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000301463.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032840.3"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1070G>C",
"hgvs_p": "p.Arg357Pro",
"transcript": "ENST00000301463.9",
"protein_id": "ENSP00000301463.4",
"transcript_support_level": 1,
"aa_start": 357,
"aa_end": null,
"aa_length": 442,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032840.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000301463.9"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1181G>C",
"hgvs_p": "p.Arg394Pro",
"transcript": "ENST00000547837.5",
"protein_id": "ENSP00000449452.1",
"transcript_support_level": 5,
"aa_start": 394,
"aa_end": null,
"aa_length": 479,
"cds_start": 1181,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000547837.5"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1106G>C",
"hgvs_p": "p.Arg369Pro",
"transcript": "ENST00000970163.1",
"protein_id": "ENSP00000640222.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 454,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970163.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1070G>C",
"hgvs_p": "p.Arg357Pro",
"transcript": "ENST00000851413.1",
"protein_id": "ENSP00000521472.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 441,
"cds_start": 1070,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851413.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1064G>C",
"hgvs_p": "p.Arg355Pro",
"transcript": "ENST00000851415.1",
"protein_id": "ENSP00000521474.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 440,
"cds_start": 1064,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851415.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.1043G>C",
"hgvs_p": "p.Arg348Pro",
"transcript": "ENST00000970160.1",
"protein_id": "ENSP00000640219.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 433,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970160.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.950G>C",
"hgvs_p": "p.Arg317Pro",
"transcript": "ENST00000851414.1",
"protein_id": "ENSP00000521473.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 402,
"cds_start": 950,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851414.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.923G>C",
"hgvs_p": "p.Arg308Pro",
"transcript": "ENST00000970162.1",
"protein_id": "ENSP00000640221.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 393,
"cds_start": 923,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970162.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.884G>C",
"hgvs_p": "p.Arg295Pro",
"transcript": "ENST00000851412.1",
"protein_id": "ENSP00000521471.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 380,
"cds_start": 884,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000851412.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.869G>C",
"hgvs_p": "p.Arg290Pro",
"transcript": "ENST00000970161.1",
"protein_id": "ENSP00000640220.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 375,
"cds_start": 869,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970161.1"
},
{
"aa_ref": "R",
"aa_alt": "P",
"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": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "c.764G>C",
"hgvs_p": "p.Arg255Pro",
"transcript": "ENST00000939794.1",
"protein_id": "ENSP00000609853.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 340,
"cds_start": 764,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939794.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "n.-80G>C",
"hgvs_p": null,
"transcript": "ENST00000547257.1",
"protein_id": "ENSP00000448845.1",
"transcript_support_level": 5,
"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": "ENST00000547257.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"hgvs_c": "n.*522G>C",
"hgvs_p": null,
"transcript": "ENST00000537540.1",
"protein_id": "ENSP00000446156.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000537540.1"
}
],
"gene_symbol": "SPRYD3",
"gene_hgnc_id": 25920,
"dbsnp": "rs372927015",
"frequency_reference_population": 0.0000068153063,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000478835,
"gnomad_genomes_af": 0.0000262926,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24956634640693665,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.117,
"revel_prediction": "Benign",
"alphamissense_score": 0.1226,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.48,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_032840.3",
"gene_symbol": "SPRYD3",
"hgnc_id": 25920,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1070G>C",
"hgvs_p": "p.Arg357Pro"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}