← Back to variant description
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: 3-142496391-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=142496391&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 19,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "ATR",
"hgnc_id": 882,
"hgvs_c": "c.5868C>T",
"hgvs_p": "p.Tyr1956Tyr",
"inheritance_mode": "AD,Unknown,AR",
"pathogenic_score": 0,
"score": -19,
"transcript": "NM_001184.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -19,
"allele_count_reference_population": 14938,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"chr": "3",
"clinvar_classification": "Benign",
"clinvar_disease": "Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome,Seckel syndrome 1,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:9",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4399999976158142,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2644,
"aa_ref": "Y",
"aa_start": 1956,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8158,
"cdna_start": 5897,
"cds_end": null,
"cds_length": 7935,
"cds_start": 5868,
"consequences": [
"synonymous_variant"
],
"exon_count": 47,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NM_001184.4",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5868C>T",
"hgvs_p": "p.Tyr1956Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000350721.9",
"protein_coding": true,
"protein_id": "NP_001175.2",
"strand": false,
"transcript": "NM_001184.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2644,
"aa_ref": "Y",
"aa_start": 1956,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8158,
"cdna_start": 5897,
"cds_end": null,
"cds_length": 7935,
"cds_start": 5868,
"consequences": [
"synonymous_variant"
],
"exon_count": 47,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000350721.9",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5868C>T",
"hgvs_p": "p.Tyr1956Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001184.4",
"protein_coding": true,
"protein_id": "ENSP00000343741.4",
"strand": false,
"transcript": "ENST00000350721.9",
"transcript_support_level": 1
},
{
"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": 6835,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000513291.2",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "n.1052C>T",
"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": "ENST00000513291.2",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2593,
"aa_ref": "Y",
"aa_start": 1905,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7991,
"cdna_start": 5732,
"cds_end": null,
"cds_length": 7782,
"cds_start": 5715,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000936442.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5715C>T",
"hgvs_p": "p.Tyr1905Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606501.1",
"strand": false,
"transcript": "ENST00000936442.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2580,
"aa_ref": "Y",
"aa_start": 1892,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7966,
"cdna_start": 5705,
"cds_end": null,
"cds_length": 7743,
"cds_start": 5676,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_001354579.2",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5676C>T",
"hgvs_p": "p.Tyr1892Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001341508.1",
"strand": false,
"transcript": "NM_001354579.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2580,
"aa_ref": "Y",
"aa_start": 1892,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7838,
"cdna_start": 5695,
"cds_end": null,
"cds_length": 7743,
"cds_start": 5676,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000661310.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5676C>T",
"hgvs_p": "p.Tyr1892Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000499589.1",
"strand": false,
"transcript": "ENST00000661310.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2574,
"aa_ref": "Y",
"aa_start": 1956,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7934,
"cdna_start": 5885,
"cds_end": null,
"cds_length": 7725,
"cds_start": 5868,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000936443.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5868C>T",
"hgvs_p": "p.Tyr1956Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606502.1",
"strand": false,
"transcript": "ENST00000936443.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2646,
"aa_ref": "Y",
"aa_start": 1958,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8164,
"cdna_start": 5903,
"cds_end": null,
"cds_length": 7941,
"cds_start": 5874,
"consequences": [
"synonymous_variant"
],
"exon_count": 47,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_011512924.2",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5874C>T",
"hgvs_p": "p.Tyr1958Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011511226.1",
"strand": false,
"transcript": "XM_011512924.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2612,
"aa_ref": "Y",
"aa_start": 1958,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10365,
"cdna_start": 5903,
"cds_end": null,
"cds_length": 7839,
"cds_start": 5874,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047448360.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5874C>T",
"hgvs_p": "p.Tyr1958Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304316.1",
"strand": false,
"transcript": "XM_047448360.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2598,
"aa_ref": "Y",
"aa_start": 1958,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7840,
"cdna_start": 5903,
"cds_end": null,
"cds_length": 7797,
"cds_start": 5874,
"consequences": [
"synonymous_variant"
],
"exon_count": 47,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047448361.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5874C>T",
"hgvs_p": "p.Tyr1958Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304317.1",
"strand": false,
"transcript": "XM_047448361.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2582,
"aa_ref": "Y",
"aa_start": 1894,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7972,
"cdna_start": 5711,
"cds_end": null,
"cds_length": 7749,
"cds_start": 5682,
"consequences": [
"synonymous_variant"
],
"exon_count": 46,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "XM_011512925.2",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5682C>T",
"hgvs_p": "p.Tyr1894Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011511227.1",
"strand": false,
"transcript": "XM_011512925.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2082,
"aa_ref": "Y",
"aa_start": 1958,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6349,
"cdna_start": 5903,
"cds_end": null,
"cds_length": 6249,
"cds_start": 5874,
"consequences": [
"synonymous_variant"
],
"exon_count": 37,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047448362.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5874C>T",
"hgvs_p": "p.Tyr1958Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304318.1",
"strand": false,
"transcript": "XM_047448362.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 2080,
"aa_ref": "Y",
"aa_start": 1956,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6349,
"cdna_start": 5897,
"cds_end": null,
"cds_length": 6243,
"cds_start": 5868,
"consequences": [
"synonymous_variant"
],
"exon_count": 37,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047448363.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.5868C>T",
"hgvs_p": "p.Tyr1956Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304319.1",
"strand": false,
"transcript": "XM_047448363.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1891,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5807,
"cdna_start": null,
"cds_end": null,
"cds_length": 5676,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 34,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "XM_047448364.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.*77C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304320.1",
"strand": false,
"transcript": "XM_047448364.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 344,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1300,
"cdna_start": null,
"cds_end": null,
"cds_length": 1035,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000892891.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "c.293-37008C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562950.1",
"strand": false,
"transcript": "ENST00000892891.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 552,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000514393.5",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "n.551C>T",
"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": "ENST00000514393.5",
"transcript_support_level": 4
},
{
"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": 8096,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 35,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000653868.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "n.5897C>T",
"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": "ENST00000653868.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 7056,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 44,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000656590.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "n.4656C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499225.1",
"strand": false,
"transcript": "ENST00000656590.1",
"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": 4763,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000666943.1",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "n.1332C>T",
"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": "ENST00000666943.1",
"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": 837,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000507620.2",
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"hgvs_c": "n.*6C>T",
"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": "ENST00000507620.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs112018640",
"effect": "synonymous_variant",
"frequency_reference_population": 0.009643305,
"gene_hgnc_id": 882,
"gene_symbol": "ATR",
"gnomad_exomes_ac": 13505,
"gnomad_exomes_af": 0.00955902,
"gnomad_exomes_homalt": 268,
"gnomad_genomes_ac": 1433,
"gnomad_genomes_af": 0.0105173,
"gnomad_genomes_homalt": 21,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 289,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Seckel syndrome 1|not provided|Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.817,
"pos": 142496391,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001184.4"
}
]
}