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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: 3-142469458-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=142469458&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 142469458,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001184.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6431A>G",
"hgvs_p": "p.Gln2144Arg",
"transcript": "NM_001184.4",
"protein_id": "NP_001175.2",
"transcript_support_level": null,
"aa_start": 2144,
"aa_end": null,
"aa_length": 2644,
"cds_start": 6431,
"cds_end": null,
"cds_length": 7935,
"cdna_start": 6460,
"cdna_end": null,
"cdna_length": 8158,
"mane_select": "ENST00000350721.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001184.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6431A>G",
"hgvs_p": "p.Gln2144Arg",
"transcript": "ENST00000350721.9",
"protein_id": "ENSP00000343741.4",
"transcript_support_level": 1,
"aa_start": 2144,
"aa_end": null,
"aa_length": 2644,
"cds_start": 6431,
"cds_end": null,
"cds_length": 7935,
"cdna_start": 6460,
"cdna_end": null,
"cdna_length": 8158,
"mane_select": "NM_001184.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000350721.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.1615A>G",
"hgvs_p": null,
"transcript": "ENST00000513291.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 6835,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000513291.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6278A>G",
"hgvs_p": "p.Gln2093Arg",
"transcript": "ENST00000936442.1",
"protein_id": "ENSP00000606501.1",
"transcript_support_level": null,
"aa_start": 2093,
"aa_end": null,
"aa_length": 2593,
"cds_start": 6278,
"cds_end": null,
"cds_length": 7782,
"cdna_start": 6295,
"cdna_end": null,
"cdna_length": 7991,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936442.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6239A>G",
"hgvs_p": "p.Gln2080Arg",
"transcript": "NM_001354579.2",
"protein_id": "NP_001341508.1",
"transcript_support_level": null,
"aa_start": 2080,
"aa_end": null,
"aa_length": 2580,
"cds_start": 6239,
"cds_end": null,
"cds_length": 7743,
"cdna_start": 6268,
"cdna_end": null,
"cdna_length": 7966,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354579.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6239A>G",
"hgvs_p": "p.Gln2080Arg",
"transcript": "ENST00000661310.1",
"protein_id": "ENSP00000499589.1",
"transcript_support_level": null,
"aa_start": 2080,
"aa_end": null,
"aa_length": 2580,
"cds_start": 6239,
"cds_end": null,
"cds_length": 7743,
"cdna_start": 6258,
"cdna_end": null,
"cdna_length": 7838,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000661310.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6431A>G",
"hgvs_p": "p.Gln2144Arg",
"transcript": "ENST00000936443.1",
"protein_id": "ENSP00000606502.1",
"transcript_support_level": null,
"aa_start": 2144,
"aa_end": null,
"aa_length": 2574,
"cds_start": 6431,
"cds_end": null,
"cds_length": 7725,
"cdna_start": 6448,
"cdna_end": null,
"cdna_length": 7934,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936443.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6437A>G",
"hgvs_p": "p.Gln2146Arg",
"transcript": "XM_011512924.2",
"protein_id": "XP_011511226.1",
"transcript_support_level": null,
"aa_start": 2146,
"aa_end": null,
"aa_length": 2646,
"cds_start": 6437,
"cds_end": null,
"cds_length": 7941,
"cdna_start": 6466,
"cdna_end": null,
"cdna_length": 8164,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512924.2"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6437A>G",
"hgvs_p": "p.Gln2146Arg",
"transcript": "XM_047448360.1",
"protein_id": "XP_047304316.1",
"transcript_support_level": null,
"aa_start": 2146,
"aa_end": null,
"aa_length": 2612,
"cds_start": 6437,
"cds_end": null,
"cds_length": 7839,
"cdna_start": 6466,
"cdna_end": null,
"cdna_length": 10365,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448360.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6437A>G",
"hgvs_p": "p.Gln2146Arg",
"transcript": "XM_047448361.1",
"protein_id": "XP_047304317.1",
"transcript_support_level": null,
"aa_start": 2146,
"aa_end": null,
"aa_length": 2598,
"cds_start": 6437,
"cds_end": null,
"cds_length": 7797,
"cdna_start": 6466,
"cdna_end": null,
"cdna_length": 7840,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448361.1"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.6245A>G",
"hgvs_p": "p.Gln2082Arg",
"transcript": "XM_011512925.2",
"protein_id": "XP_011511227.1",
"transcript_support_level": null,
"aa_start": 2082,
"aa_end": null,
"aa_length": 2582,
"cds_start": 6245,
"cds_end": null,
"cds_length": 7749,
"cdna_start": 6274,
"cdna_end": null,
"cdna_length": 7972,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512925.2"
},
{
"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.293-10075A>G",
"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": 1300,
"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": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.1274A>G",
"hgvs_p": null,
"transcript": "ENST00000654170.1",
"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": 2961,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000654170.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.5219A>G",
"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": 7056,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000656590.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.286A>G",
"hgvs_p": null,
"transcript": "ENST00000665483.1",
"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": 5569,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000665483.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.266A>G",
"hgvs_p": null,
"transcript": "ENST00000666447.1",
"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": 4534,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000666447.1"
},
{
"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": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.1895A>G",
"hgvs_p": null,
"transcript": "ENST00000666943.1",
"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": 4763,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000666943.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000244327",
"gene_hgnc_id": null,
"hgvs_c": "n.268+2612A>G",
"hgvs_p": null,
"transcript": "ENST00000460977.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 765,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000460977.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295506",
"gene_hgnc_id": null,
"hgvs_c": "n.143-14908T>C",
"hgvs_p": null,
"transcript": "ENST00000730510.1",
"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": 367,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000730510.1"
}
],
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"dbsnp": "rs387906797",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9397015571594238,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.663,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9328,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.004,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001184.4",
"gene_symbol": "ATR",
"hgnc_id": 882,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.6431A>G",
"hgvs_p": "p.Gln2144Arg"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000460977.1",
"gene_symbol": "ENSG00000244327",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.268+2612A>G",
"hgvs_p": null
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000730510.1",
"gene_symbol": "ENSG00000295506",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.143-14908T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}