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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: 19-15179079-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=15179079&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 15179079,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000263388.7",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.3664T>G",
"hgvs_p": "p.Cys1222Gly",
"transcript": "NM_000435.3",
"protein_id": "NP_000426.2",
"transcript_support_level": null,
"aa_start": 1222,
"aa_end": null,
"aa_length": 2321,
"cds_start": 3664,
"cds_end": null,
"cds_length": 6966,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 8680,
"mane_select": "ENST00000263388.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.3664T>G",
"hgvs_p": "p.Cys1222Gly",
"transcript": "ENST00000263388.7",
"protein_id": "ENSP00000263388.1",
"transcript_support_level": 1,
"aa_start": 1222,
"aa_end": null,
"aa_length": 2321,
"cds_start": 3664,
"cds_end": null,
"cds_length": 6966,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 8680,
"mane_select": "NM_000435.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.3505T>G",
"hgvs_p": "p.Cys1169Gly",
"transcript": "ENST00000601011.1",
"protein_id": "ENSP00000473138.1",
"transcript_support_level": 5,
"aa_start": 1169,
"aa_end": null,
"aa_length": 1285,
"cds_start": 3505,
"cds_end": null,
"cds_length": 3858,
"cdna_start": 3505,
"cdna_end": null,
"cdna_length": 3858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "c.3508T>G",
"hgvs_p": "p.Cys1170Gly",
"transcript": "XM_005259924.5",
"protein_id": "XP_005259981.1",
"transcript_support_level": null,
"aa_start": 1170,
"aa_end": null,
"aa_length": 2269,
"cds_start": 3508,
"cds_end": null,
"cds_length": 6810,
"cdna_start": 3598,
"cdna_end": null,
"cdna_length": 8524,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "n.500T>G",
"hgvs_p": null,
"transcript": "ENST00000595045.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 558,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"hgvs_c": "n.142T>G",
"hgvs_p": null,
"transcript": "ENST00000600841.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 748,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6795",
"gene_hgnc_id": 50031,
"hgvs_c": "n.*204T>G",
"hgvs_p": null,
"transcript": "ENST00000620824.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 68,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6795",
"gene_hgnc_id": 50031,
"hgvs_c": "n.*204T>G",
"hgvs_p": null,
"transcript": "NR_106853.1",
"protein_id": null,
"transcript_support_level": null,
"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": 68,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6795",
"gene_hgnc_id": 50031,
"hgvs_c": "n.*204T>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_3247",
"protein_id": null,
"transcript_support_level": null,
"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": 21,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MIR6795",
"gene_hgnc_id": 50031,
"hgvs_c": "n.*243T>G",
"hgvs_p": null,
"transcript": "unassigned_transcript_3248",
"protein_id": null,
"transcript_support_level": null,
"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": 24,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NOTCH3",
"gene_hgnc_id": 7883,
"dbsnp": "rs199638166",
"frequency_reference_population": 0.00017285046,
"hom_count_reference_population": 0,
"allele_count_reference_population": 279,
"gnomad_exomes_af": 0.000179909,
"gnomad_genomes_af": 0.000105085,
"gnomad_exomes_ac": 263,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9082653522491455,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.524,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9193,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.673,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000263388.7",
"gene_symbol": "NOTCH3",
"hgnc_id": 7883,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3664T>G",
"hgvs_p": "p.Cys1222Gly"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NR_106853.1",
"gene_symbol": "MIR6795",
"hgnc_id": 50031,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*204T>G",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal dominant, type 1, with subcortical infarcts and leukoencephalopathy,Cerebral arteriopathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:7 O:1",
"phenotype_combined": "not provided|not specified|Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}