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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: 2-215344828-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=215344828&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 215344828,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000236959.14",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1277A>G",
"hgvs_p": "p.Lys426Arg",
"transcript": "NM_004044.7",
"protein_id": "NP_004035.2",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 592,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 1972,
"mane_select": "ENST00000236959.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1277A>G",
"hgvs_p": "p.Lys426Arg",
"transcript": "ENST00000236959.14",
"protein_id": "ENSP00000236959.9",
"transcript_support_level": 1,
"aa_start": 426,
"aa_end": null,
"aa_length": 592,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 1972,
"mane_select": "NM_004044.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1274A>G",
"hgvs_p": "p.Lys425Arg",
"transcript": "ENST00000435675.5",
"protein_id": "ENSP00000415935.1",
"transcript_support_level": 2,
"aa_start": 425,
"aa_end": null,
"aa_length": 591,
"cds_start": 1274,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 1665,
"cdna_end": null,
"cdna_length": 2275,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.281A>G",
"hgvs_p": "p.Lys94Arg",
"transcript": "ENST00000426233.1",
"protein_id": "ENSP00000401936.1",
"transcript_support_level": 2,
"aa_start": 94,
"aa_end": null,
"aa_length": 230,
"cds_start": 281,
"cds_end": null,
"cds_length": 693,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1277A>G",
"hgvs_p": "p.Lys426Arg",
"transcript": "XM_047444489.1",
"protein_id": "XP_047300445.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 597,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 7818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1277A>G",
"hgvs_p": "p.Lys426Arg",
"transcript": "XM_047444490.1",
"protein_id": "XP_047300446.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 595,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 3488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1277A>G",
"hgvs_p": "p.Lys426Arg",
"transcript": "XM_017004187.3",
"protein_id": "XP_016859676.1",
"transcript_support_level": null,
"aa_start": 426,
"aa_end": null,
"aa_length": 557,
"cds_start": 1277,
"cds_end": null,
"cds_length": 1674,
"cdna_start": 1361,
"cdna_end": null,
"cdna_length": 3360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "c.1100A>G",
"hgvs_p": "p.Lys367Arg",
"transcript": "XM_047444491.1",
"protein_id": "XP_047300447.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 538,
"cds_start": 1100,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 1352,
"cdna_end": null,
"cdna_length": 7809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.*1374A>G",
"hgvs_p": null,
"transcript": "ENST00000443953.5",
"protein_id": "ENSP00000406792.1",
"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": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.357A>G",
"hgvs_p": null,
"transcript": "ENST00000446622.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.88A>G",
"hgvs_p": null,
"transcript": "ENST00000459796.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.189A>G",
"hgvs_p": null,
"transcript": "ENST00000467388.1",
"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": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.192A>G",
"hgvs_p": null,
"transcript": "ENST00000479093.5",
"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": 772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.1361A>G",
"hgvs_p": null,
"transcript": "XR_007075418.1",
"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": 3820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.1361A>G",
"hgvs_p": null,
"transcript": "XR_007075419.1",
"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": 7998,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"hgvs_c": "n.*1374A>G",
"hgvs_p": null,
"transcript": "ENST00000443953.5",
"protein_id": "ENSP00000406792.1",
"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": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATIC",
"gene_hgnc_id": 794,
"dbsnp": "rs121434478",
"frequency_reference_population": 0.000020447085,
"hom_count_reference_population": 0,
"allele_count_reference_population": 33,
"gnomad_exomes_af": 0.0000205214,
"gnomad_genomes_af": 0.0000197322,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9196053743362427,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.886,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3217,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.287,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.04,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000236959.14",
"gene_symbol": "ATIC",
"hgnc_id": 794,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1277A>G",
"hgvs_p": "p.Lys426Arg"
}
],
"clinvar_disease": "AICA-ribosiduria,See cases,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "AICA-ribosiduria|not provided|See cases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}