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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: 19-15187220-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=15187220&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 15187220,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000435.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Thr575Thr",
"transcript": "NM_000435.3",
"protein_id": "NP_000426.2",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 2321,
"cds_start": 1725,
"cds_end": null,
"cds_length": 6966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263388.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000435.3"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Thr575Thr",
"transcript": "ENST00000263388.7",
"protein_id": "ENSP00000263388.1",
"transcript_support_level": 1,
"aa_start": 575,
"aa_end": null,
"aa_length": 2321,
"cds_start": 1725,
"cds_end": null,
"cds_length": 6966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000435.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263388.7"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Thr575Thr",
"transcript": "ENST00000931534.1",
"protein_id": "ENSP00000601593.1",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 2366,
"cds_start": 1725,
"cds_end": null,
"cds_length": 7101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931534.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1704G>A",
"hgvs_p": "p.Thr568Thr",
"transcript": "ENST00000931532.1",
"protein_id": "ENSP00000601591.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 2262,
"cds_start": 1704,
"cds_end": null,
"cds_length": 6789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931532.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Thr575Thr",
"transcript": "ENST00000931535.1",
"protein_id": "ENSP00000601594.1",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 2253,
"cds_start": 1725,
"cds_end": null,
"cds_length": 6762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931535.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1722G>A",
"hgvs_p": "p.Thr574Thr",
"transcript": "ENST00000601011.1",
"protein_id": "ENSP00000473138.1",
"transcript_support_level": 5,
"aa_start": 574,
"aa_end": null,
"aa_length": 1285,
"cds_start": 1722,
"cds_end": null,
"cds_length": 3858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000601011.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Thr575Thr",
"transcript": "XM_005259924.5",
"protein_id": "XP_005259981.1",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 2269,
"cds_start": 1725,
"cds_end": null,
"cds_length": 6810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005259924.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.1037-1541G>A",
"hgvs_p": null,
"transcript": "ENST00000931533.1",
"protein_id": "ENSP00000601592.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1964,
"cds_start": null,
"cds_end": null,
"cds_length": 5895,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931533.1"
}
],
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"dbsnp": "rs79926127",
"frequency_reference_population": 0.008773473,
"hom_count_reference_population": 74,
"allele_count_reference_population": 14161,
"gnomad_exomes_af": 0.0089474,
"gnomad_genomes_af": 0.00710421,
"gnomad_exomes_ac": 13079,
"gnomad_genomes_ac": 1082,
"gnomad_exomes_homalt": 71,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5199999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8700000047683716,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -6.822,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.87,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PP3_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000435.3",
"gene_symbol": "NOTCH3",
"hgnc_id": 7883,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Thr575Thr"
}
],
"clinvar_disease": " autosomal dominant, type 1, with subcortical infarcts and leukoencephalopathy,Cerebral arteriopathy,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}