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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: 9-97675530-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=97675530&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 97675530,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000380.4",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.His244Arg",
"transcript": "NM_000380.4",
"protein_id": "NP_000371.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 273,
"cds_start": 731,
"cds_end": null,
"cds_length": 822,
"cdna_start": 779,
"cdna_end": null,
"cdna_length": 1400,
"mane_select": "ENST00000375128.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.His244Arg",
"transcript": "ENST00000375128.5",
"protein_id": "ENSP00000364270.5",
"transcript_support_level": 1,
"aa_start": 244,
"aa_end": null,
"aa_length": 273,
"cds_start": 731,
"cds_end": null,
"cds_length": 822,
"cdna_start": 779,
"cdna_end": null,
"cdna_length": 1400,
"mane_select": "NM_000380.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.605A>G",
"hgvs_p": "p.His202Arg",
"transcript": "NM_001354975.2",
"protein_id": "NP_001341904.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 231,
"cds_start": 605,
"cds_end": null,
"cds_length": 696,
"cdna_start": 1802,
"cdna_end": null,
"cdna_length": 2423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.731A>G",
"hgvs_p": "p.His244Arg",
"transcript": "XM_006717278.2",
"protein_id": "XP_006717341.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 262,
"cds_start": 731,
"cds_end": null,
"cds_length": 789,
"cdna_start": 779,
"cdna_end": null,
"cdna_length": 1147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.*167A>G",
"hgvs_p": null,
"transcript": "ENST00000462523.5",
"protein_id": "ENSP00000433006.1",
"transcript_support_level": 5,
"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": 1584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.243A>G",
"hgvs_p": null,
"transcript": "ENST00000485042.1",
"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": 706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.1010A>G",
"hgvs_p": null,
"transcript": "NR_027302.2",
"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": 1631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.507A>G",
"hgvs_p": null,
"transcript": "NR_149091.2",
"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": 1128,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.673A>G",
"hgvs_p": null,
"transcript": "NR_149092.2",
"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": 1294,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.1199A>G",
"hgvs_p": null,
"transcript": "NR_149093.2",
"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": 1820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.1093A>G",
"hgvs_p": null,
"transcript": "NR_149094.2",
"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": 1714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.*167A>G",
"hgvs_p": null,
"transcript": "ENST00000462523.5",
"protein_id": "ENSP00000433006.1",
"transcript_support_level": 5,
"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": 1584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"dbsnp": "rs144725456",
"frequency_reference_population": 0.000113387956,
"hom_count_reference_population": 0,
"allele_count_reference_population": 183,
"gnomad_exomes_af": 0.000117665,
"gnomad_genomes_af": 0.0000722952,
"gnomad_exomes_ac": 172,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9720085859298706,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.87,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9318,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.072,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000380.4",
"gene_symbol": "XPA",
"hgnc_id": 12814,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.731A>G",
"hgvs_p": "p.His244Arg"
}
],
"clinvar_disease": "Xeroderma pigmentosum,Xeroderma pigmentosum group A,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 LP:1 US:1",
"phenotype_combined": "Xeroderma pigmentosum group A|not provided|Xeroderma pigmentosum",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}