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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: 5-82276483-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=82276483&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 82276483,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000296674.13",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "NM_001025.5",
"protein_id": "NP_001016.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 143,
"cds_start": 200,
"cds_end": null,
"cds_length": 432,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 3252,
"mane_select": "ENST00000296674.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "ENST00000296674.13",
"protein_id": "ENSP00000296674.8",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 143,
"cds_start": 200,
"cds_end": null,
"cds_length": 432,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 3252,
"mane_select": "NM_001025.5",
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "n.295G>A",
"hgvs_p": null,
"transcript": "ENST00000504293.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "ENST00000651545.1",
"protein_id": "ENSP00000498621.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 143,
"cds_start": 200,
"cds_end": null,
"cds_length": 432,
"cdna_start": 245,
"cdna_end": null,
"cdna_length": 3142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "ENST00000510210.5",
"protein_id": "ENSP00000427043.1",
"transcript_support_level": 2,
"aa_start": 67,
"aa_end": null,
"aa_length": 134,
"cds_start": 200,
"cds_end": null,
"cds_length": 405,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 1058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "ENST00000512493.5",
"protein_id": "ENSP00000425865.1",
"transcript_support_level": 3,
"aa_start": 67,
"aa_end": null,
"aa_length": 134,
"cds_start": 200,
"cds_end": null,
"cds_length": 405,
"cdna_start": 228,
"cdna_end": null,
"cdna_length": 443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "ENST00000507980.1",
"protein_id": "ENSP00000422071.1",
"transcript_support_level": 2,
"aa_start": 67,
"aa_end": null,
"aa_length": 123,
"cds_start": 200,
"cds_end": null,
"cds_length": 372,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys",
"transcript": "ENST00000510019.5",
"protein_id": "ENSP00000425833.1",
"transcript_support_level": 4,
"aa_start": 67,
"aa_end": null,
"aa_length": 85,
"cds_start": 200,
"cds_end": null,
"cds_length": 258,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 1019,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"hgvs_c": "n.409G>A",
"hgvs_p": null,
"transcript": "ENST00000503605.1",
"protein_id": null,
"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": 595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ATG10",
"gene_hgnc_id": 20315,
"hgvs_c": "n.530C>T",
"hgvs_p": null,
"transcript": "ENST00000514253.2",
"protein_id": null,
"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": 904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG10",
"gene_hgnc_id": 20315,
"hgvs_c": "n.*186C>T",
"hgvs_p": null,
"transcript": "ENST00000508814.5",
"protein_id": null,
"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": 413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RPS23",
"gene_hgnc_id": 10410,
"dbsnp": "rs1060505034",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9579610824584961,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.531,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9968,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.792,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000296674.13",
"gene_symbol": "RPS23",
"hgnc_id": 10410,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Lys"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000514253.2",
"gene_symbol": "ATG10",
"hgnc_id": 20315,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.530C>T",
"hgvs_p": null
}
],
"clinvar_disease": " and developmental delay, trichomegaly,Brachycephaly,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Brachycephaly, trichomegaly, and developmental delay|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}