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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: 19-15187273-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=15187273&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM1",
"PM2",
"PM5",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NOTCH3",
"hgnc_id": 7883,
"hgvs_c": "c.1672C>A",
"hgvs_p": "p.Arg558Ser",
"inheritance_mode": "AD,AR",
"pathogenic_score": 6,
"score": 5,
"transcript": "NM_000435.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,PM5,BP4",
"acmg_score": 5,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.1297,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2895793616771698,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2321,
"aa_ref": "R",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8680,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 6966,
"cds_start": 1672,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_000435.3",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1672C>A",
"hgvs_p": "p.Arg558Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263388.7",
"protein_coding": true,
"protein_id": "NP_000426.2",
"strand": false,
"transcript": "NM_000435.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2321,
"aa_ref": "R",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8680,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 6966,
"cds_start": 1672,
"consequences": [
"missense_variant"
],
"exon_count": 33,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000263388.7",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1672C>A",
"hgvs_p": "p.Arg558Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000435.3",
"protein_coding": true,
"protein_id": "ENSP00000263388.1",
"strand": false,
"transcript": "ENST00000263388.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2366,
"aa_ref": "R",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8221,
"cdna_start": 1763,
"cds_end": null,
"cds_length": 7101,
"cds_start": 1672,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000931534.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1672C>A",
"hgvs_p": "p.Arg558Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601593.1",
"strand": false,
"transcript": "ENST00000931534.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2262,
"aa_ref": "R",
"aa_start": 551,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7910,
"cdna_start": 1742,
"cds_end": null,
"cds_length": 6789,
"cds_start": 1651,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000931532.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1651C>A",
"hgvs_p": "p.Arg551Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601591.1",
"strand": false,
"transcript": "ENST00000931532.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2253,
"aa_ref": "R",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7879,
"cdna_start": 1763,
"cds_end": null,
"cds_length": 6762,
"cds_start": 1672,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000931535.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1672C>A",
"hgvs_p": "p.Arg558Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601594.1",
"strand": false,
"transcript": "ENST00000931535.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1285,
"aa_ref": "R",
"aa_start": 557,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3858,
"cdna_start": 1669,
"cds_end": null,
"cds_length": 3858,
"cds_start": 1669,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000601011.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1669C>A",
"hgvs_p": "p.Arg557Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000473138.1",
"strand": false,
"transcript": "ENST00000601011.1",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2269,
"aa_ref": "R",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8524,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 6810,
"cds_start": 1672,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_005259924.5",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1672C>A",
"hgvs_p": "p.Arg558Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259981.1",
"strand": false,
"transcript": "XM_005259924.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1964,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7015,
"cdna_start": null,
"cds_end": null,
"cds_length": 5895,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931533.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.1037-1594C>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601592.1",
"strand": false,
"transcript": "ENST00000931533.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs75068032",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.253,
"pos": 15187273,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.269,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_000435.3"
}
]
}