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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: 3-142536128-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=142536128&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 142536128,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001184.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "NM_001184.4",
"protein_id": "NP_001175.2",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2644,
"cds_start": 3799,
"cds_end": null,
"cds_length": 7935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000350721.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001184.4"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "ENST00000350721.9",
"protein_id": "ENSP00000343741.4",
"transcript_support_level": 1,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2644,
"cds_start": 3799,
"cds_end": null,
"cds_length": 7935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001184.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000350721.9"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3646G>A",
"hgvs_p": "p.Val1216Ile",
"transcript": "ENST00000936442.1",
"protein_id": "ENSP00000606501.1",
"transcript_support_level": null,
"aa_start": 1216,
"aa_end": null,
"aa_length": 2593,
"cds_start": 3646,
"cds_end": null,
"cds_length": 7782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936442.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3607G>A",
"hgvs_p": "p.Val1203Ile",
"transcript": "NM_001354579.2",
"protein_id": "NP_001341508.1",
"transcript_support_level": null,
"aa_start": 1203,
"aa_end": null,
"aa_length": 2580,
"cds_start": 3607,
"cds_end": null,
"cds_length": 7743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354579.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3607G>A",
"hgvs_p": "p.Val1203Ile",
"transcript": "ENST00000661310.1",
"protein_id": "ENSP00000499589.1",
"transcript_support_level": null,
"aa_start": 1203,
"aa_end": null,
"aa_length": 2580,
"cds_start": 3607,
"cds_end": null,
"cds_length": 7743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000661310.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "ENST00000936443.1",
"protein_id": "ENSP00000606502.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2574,
"cds_start": 3799,
"cds_end": null,
"cds_length": 7725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936443.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "XM_011512924.2",
"protein_id": "XP_011511226.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2646,
"cds_start": 3799,
"cds_end": null,
"cds_length": 7941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512924.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "XM_047448360.1",
"protein_id": "XP_047304316.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2612,
"cds_start": 3799,
"cds_end": null,
"cds_length": 7839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448360.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "XM_047448361.1",
"protein_id": "XP_047304317.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2598,
"cds_start": 3799,
"cds_end": null,
"cds_length": 7797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448361.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3607G>A",
"hgvs_p": "p.Val1203Ile",
"transcript": "XM_011512925.2",
"protein_id": "XP_011511227.1",
"transcript_support_level": null,
"aa_start": 1203,
"aa_end": null,
"aa_length": 2582,
"cds_start": 3607,
"cds_end": null,
"cds_length": 7749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512925.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "XM_047448362.1",
"protein_id": "XP_047304318.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2082,
"cds_start": 3799,
"cds_end": null,
"cds_length": 6249,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448362.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "XM_047448363.1",
"protein_id": "XP_047304319.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 2080,
"cds_start": 3799,
"cds_end": null,
"cds_length": 6243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448363.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile",
"transcript": "XM_047448364.1",
"protein_id": "XP_047304320.1",
"transcript_support_level": null,
"aa_start": 1267,
"aa_end": null,
"aa_length": 1891,
"cds_start": 3799,
"cds_end": null,
"cds_length": 5676,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448364.1"
},
{
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.292+29993G>A",
"hgvs_p": null,
"transcript": "ENST00000892891.1",
"protein_id": "ENSP00000562950.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 344,
"cds_start": null,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000892891.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.3828G>A",
"hgvs_p": null,
"transcript": "ENST00000653868.1",
"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": "ENST00000653868.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.2587G>A",
"hgvs_p": null,
"transcript": "ENST00000656590.1",
"protein_id": "ENSP00000499225.1",
"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": "ENST00000656590.1"
}
],
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"dbsnp": "rs377689383",
"frequency_reference_population": 0.00007069261,
"hom_count_reference_population": 0,
"allele_count_reference_population": 112,
"gnomad_exomes_af": 0.0000649373,
"gnomad_genomes_af": 0.000124857,
"gnomad_exomes_ac": 93,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.045516520738601685,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.079,
"revel_prediction": "Benign",
"alphamissense_score": 0.0745,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.251,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_001184.4",
"gene_symbol": "ATR",
"hgnc_id": 882,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.3799G>A",
"hgvs_p": "p.Val1267Ile"
}
],
"clinvar_disease": "Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome,Inborn genetic diseases,Seckel syndrome 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "Seckel syndrome 1|Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome;Seckel syndrome 1|not provided|Inborn genetic diseases|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}