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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: 19-15179104-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=15179104&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "NOTCH3",
"hgnc_id": 7883,
"hgvs_c": "c.3639C>G",
"hgvs_p": "p.Ala1213Ala",
"inheritance_mode": "AD,AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_000435.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "MIR6795",
"hgnc_id": 50031,
"hgvs_c": "n.*179C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NR_106853.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4099999964237213,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 2321,
"aa_ref": "A",
"aa_start": 1213,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8680,
"cdna_start": 3729,
"cds_end": null,
"cds_length": 6966,
"cds_start": 3639,
"consequences": [
"synonymous_variant"
],
"exon_count": 33,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_000435.3",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3639C>G",
"hgvs_p": "p.Ala1213Ala",
"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": "A",
"aa_end": null,
"aa_length": 2321,
"aa_ref": "A",
"aa_start": 1213,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8680,
"cdna_start": 3729,
"cds_end": null,
"cds_length": 6966,
"cds_start": 3639,
"consequences": [
"synonymous_variant"
],
"exon_count": 33,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000263388.7",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3639C>G",
"hgvs_p": "p.Ala1213Ala",
"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": "A",
"aa_end": null,
"aa_length": 2366,
"aa_ref": "A",
"aa_start": 1258,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8221,
"cdna_start": 3865,
"cds_end": null,
"cds_length": 7101,
"cds_start": 3774,
"consequences": [
"synonymous_variant"
],
"exon_count": 34,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000931534.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3774C>G",
"hgvs_p": "p.Ala1258Ala",
"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": "A",
"aa_end": null,
"aa_length": 2262,
"aa_ref": "A",
"aa_start": 1154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7910,
"cdna_start": 3553,
"cds_end": null,
"cds_length": 6789,
"cds_start": 3462,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000931532.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3462C>G",
"hgvs_p": "p.Ala1154Ala",
"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": "A",
"aa_end": null,
"aa_length": 2253,
"aa_ref": "A",
"aa_start": 1145,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7879,
"cdna_start": 3526,
"cds_end": null,
"cds_length": 6762,
"cds_start": 3435,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000931535.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3435C>G",
"hgvs_p": "p.Ala1145Ala",
"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": "A",
"aa_end": null,
"aa_length": 1964,
"aa_ref": "A",
"aa_start": 856,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7015,
"cdna_start": 2659,
"cds_end": null,
"cds_length": 5895,
"cds_start": 2568,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000931533.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.2568C>G",
"hgvs_p": "p.Ala856Ala",
"intron_rank": null,
"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
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1285,
"aa_ref": "A",
"aa_start": 1160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3858,
"cdna_start": 3480,
"cds_end": null,
"cds_length": 3858,
"cds_start": 3480,
"consequences": [
"synonymous_variant"
],
"exon_count": 23,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000601011.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3480C>G",
"hgvs_p": "p.Ala1160Ala",
"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": "A",
"aa_end": null,
"aa_length": 2269,
"aa_ref": "A",
"aa_start": 1161,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8524,
"cdna_start": 3573,
"cds_end": null,
"cds_length": 6810,
"cds_start": 3483,
"consequences": [
"synonymous_variant"
],
"exon_count": 32,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "XM_005259924.5",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "c.3483C>G",
"hgvs_p": "p.Ala1161Ala",
"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": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 558,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000595045.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "n.475C>G",
"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": "ENST00000595045.1",
"transcript_support_level": 2
},
{
"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": 748,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000600841.1",
"gene_hgnc_id": 7883,
"gene_symbol": "NOTCH3",
"hgvs_c": "n.117C>G",
"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": "ENST00000600841.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "miRNA",
"canonical": false,
"cdna_end": null,
"cdna_length": 68,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000620824.1",
"gene_hgnc_id": 50031,
"gene_symbol": "MIR6795",
"hgvs_c": "n.*179C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000620824.1",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 68,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_106853.1",
"gene_hgnc_id": 50031,
"gene_symbol": "MIR6795",
"hgvs_c": "n.*179C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_106853.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "miRNA",
"canonical": null,
"cdna_end": null,
"cdna_length": 21,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "unassigned_transcript_3247",
"gene_hgnc_id": 50031,
"gene_symbol": "MIR6795",
"hgvs_c": "n.*179C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "unassigned_transcript_3247",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "miRNA",
"canonical": null,
"cdna_end": null,
"cdna_length": 24,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "unassigned_transcript_3248",
"gene_hgnc_id": 50031,
"gene_symbol": "MIR6795",
"hgvs_c": "n.*218C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "unassigned_transcript_3248",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs374239471",
"effect": "synonymous_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": 2.013,
"pos": 15179104,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.25999999046325684,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.26,
"transcript": "NM_000435.3"
}
]
}