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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: 9-136504896-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136504896&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 136504896,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017617.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4795G>A",
"hgvs_p": "p.Val1599Met",
"transcript": "NM_017617.5",
"protein_id": "NP_060087.3",
"transcript_support_level": null,
"aa_start": 1599,
"aa_end": null,
"aa_length": 2555,
"cds_start": 4795,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000651671.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017617.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4795G>A",
"hgvs_p": "p.Val1599Met",
"transcript": "ENST00000651671.1",
"protein_id": "ENSP00000498587.1",
"transcript_support_level": null,
"aa_start": 1599,
"aa_end": null,
"aa_length": 2555,
"cds_start": 4795,
"cds_end": null,
"cds_length": 7668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017617.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000651671.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4684G>A",
"hgvs_p": "p.Val1562Met",
"transcript": "ENST00000927794.1",
"protein_id": "ENSP00000597853.1",
"transcript_support_level": null,
"aa_start": 1562,
"aa_end": null,
"aa_length": 2518,
"cds_start": 4684,
"cds_end": null,
"cds_length": 7557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927794.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4681G>A",
"hgvs_p": "p.Val1561Met",
"transcript": "ENST00000680133.1",
"protein_id": "ENSP00000505319.1",
"transcript_support_level": null,
"aa_start": 1561,
"aa_end": null,
"aa_length": 2517,
"cds_start": 4681,
"cds_end": null,
"cds_length": 7554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680133.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4681G>A",
"hgvs_p": "p.Val1561Met",
"transcript": "ENST00000680668.1",
"protein_id": "ENSP00000506336.1",
"transcript_support_level": null,
"aa_start": 1561,
"aa_end": null,
"aa_length": 2517,
"cds_start": 4681,
"cds_end": null,
"cds_length": 7554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680668.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4675G>A",
"hgvs_p": "p.Val1559Met",
"transcript": "ENST00000680218.1",
"protein_id": "ENSP00000505339.1",
"transcript_support_level": null,
"aa_start": 1559,
"aa_end": null,
"aa_length": 2515,
"cds_start": 4675,
"cds_end": null,
"cds_length": 7548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680218.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Val798Met",
"transcript": "ENST00000680778.1",
"protein_id": "ENSP00000506033.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 1754,
"cds_start": 2392,
"cds_end": null,
"cds_length": 5265,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680778.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "c.4072G>A",
"hgvs_p": "p.Val1358Met",
"transcript": "XM_011518717.3",
"protein_id": "XP_011517019.2",
"transcript_support_level": null,
"aa_start": 1358,
"aa_end": null,
"aa_length": 2314,
"cds_start": 4072,
"cds_end": null,
"cds_length": 6945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518717.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.2602G>A",
"hgvs_p": null,
"transcript": "ENST00000645828.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000645828.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.4795G>A",
"hgvs_p": null,
"transcript": "ENST00000679595.1",
"protein_id": "ENSP00000506241.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000679595.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.*2195G>A",
"hgvs_p": null,
"transcript": "ENST00000680924.1",
"protein_id": "ENSP00000506031.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000680924.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.*2404G>A",
"hgvs_p": null,
"transcript": "ENST00000681135.1",
"protein_id": "ENSP00000506636.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681135.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.1608G>A",
"hgvs_p": null,
"transcript": "ENST00000681298.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000681298.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.*4031G>A",
"hgvs_p": null,
"transcript": "ENST00000681454.1",
"protein_id": "ENSP00000505763.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681454.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.*2195G>A",
"hgvs_p": null,
"transcript": "ENST00000680924.1",
"protein_id": "ENSP00000506031.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000680924.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.*2404G>A",
"hgvs_p": null,
"transcript": "ENST00000681135.1",
"protein_id": "ENSP00000506636.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681135.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"hgvs_c": "n.*4031G>A",
"hgvs_p": null,
"transcript": "ENST00000681454.1",
"protein_id": "ENSP00000505763.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681454.1"
}
],
"gene_symbol": "NOTCH1",
"gene_hgnc_id": 7881,
"dbsnp": "rs543770603",
"frequency_reference_population": 0.000021458902,
"hom_count_reference_population": 1,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000160603,
"gnomad_genomes_af": 0.0000722173,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4534040689468384,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.43,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1184,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.262,
"phylop100way_prediction": "Benign",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_017617.5",
"gene_symbol": "NOTCH1",
"hgnc_id": 7881,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4795G>A",
"hgvs_p": "p.Val1599Met"
}
],
"clinvar_disease": "Adams-Oliver syndrome 5,Aortic valve disease 1,Familial thoracic aortic aneurysm and aortic dissection,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 B:1",
"phenotype_combined": "Adams-Oliver syndrome 5|not specified|Aortic valve disease 1|Aortic valve disease 1;Adams-Oliver syndrome 5|Familial thoracic aortic aneurysm and aortic dissection",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}