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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: 9-98078306-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=98078306&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 98078306,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000210444.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.562T>C",
"hgvs_p": "p.Tyr188His",
"transcript": "NM_018946.4",
"protein_id": "NP_061819.2",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 359,
"cds_start": 562,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 1179,
"mane_select": "ENST00000210444.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.562T>C",
"hgvs_p": "p.Tyr188His",
"transcript": "ENST00000210444.6",
"protein_id": "ENSP00000210444.5",
"transcript_support_level": 1,
"aa_start": 188,
"aa_end": null,
"aa_length": 359,
"cds_start": 562,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 1179,
"mane_select": "NM_018946.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.139T>C",
"hgvs_p": "p.Tyr47His",
"transcript": "ENST00000415280.1",
"protein_id": "ENSP00000404107.1",
"transcript_support_level": 5,
"aa_start": 47,
"aa_end": null,
"aa_length": 139,
"cds_start": 139,
"cds_end": null,
"cds_length": 420,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.214T>C",
"hgvs_p": "p.Tyr72His",
"transcript": "XM_011518787.3",
"protein_id": "XP_011517089.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 243,
"cds_start": 214,
"cds_end": null,
"cds_length": 732,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 998,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.214T>C",
"hgvs_p": "p.Tyr72His",
"transcript": "XM_047423476.1",
"protein_id": "XP_047279432.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 243,
"cds_start": 214,
"cds_end": null,
"cds_length": 732,
"cdna_start": 467,
"cdna_end": null,
"cdna_length": 1007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.187T>C",
"hgvs_p": "p.Tyr63His",
"transcript": "XM_011518788.3",
"protein_id": "XP_011517090.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 234,
"cds_start": 187,
"cds_end": null,
"cds_length": 705,
"cdna_start": 201,
"cdna_end": null,
"cdna_length": 741,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "n.2489T>C",
"hgvs_p": null,
"transcript": "ENST00000461452.1",
"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": 3027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "TRIM14",
"gene_hgnc_id": 16283,
"hgvs_c": "c.*109A>G",
"hgvs_p": null,
"transcript": "XM_017015353.3",
"protein_id": "XP_016870842.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TRIM14",
"gene_hgnc_id": 16283,
"hgvs_c": "c.*29-8619A>G",
"hgvs_p": null,
"transcript": "ENST00000375098.7",
"protein_id": "ENSP00000364239.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TRIM14",
"gene_hgnc_id": 16283,
"hgvs_c": "c.*29-8459A>G",
"hgvs_p": null,
"transcript": "XM_047424160.1",
"protein_id": "XP_047280116.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TRIM14",
"gene_hgnc_id": 16283,
"hgvs_c": "c.*28+9136A>G",
"hgvs_p": null,
"transcript": "XM_047424161.1",
"protein_id": "XP_047280117.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1409,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "TRIM14",
"gene_hgnc_id": 16283,
"hgvs_c": "c.*28+9136A>G",
"hgvs_p": null,
"transcript": "XM_047424162.1",
"protein_id": "XP_047280118.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 442,
"cds_start": -4,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "c.-15T>C",
"hgvs_p": null,
"transcript": "ENST00000427646.1",
"protein_id": "ENSP00000404642.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 115,
"cds_start": -4,
"cds_end": null,
"cds_length": 348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"hgvs_c": "n.*2T>C",
"hgvs_p": null,
"transcript": "ENST00000495319.1",
"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": 764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NANS",
"gene_hgnc_id": 19237,
"dbsnp": "rs878852981",
"frequency_reference_population": 0.000006196478,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000342026,
"gnomad_genomes_af": 0.0000329069,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9828099012374878,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.87,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9984,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.616,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000210444.6",
"gene_symbol": "NANS",
"hgnc_id": 19237,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.562T>C",
"hgvs_p": "p.Tyr188His"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "XM_017015353.3",
"gene_symbol": "TRIM14",
"hgnc_id": 16283,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*109A>G",
"hgvs_p": null
}
],
"clinvar_disease": " Genevieve type,Spondyloepimetaphyseal dysplasia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Spondyloepimetaphyseal dysplasia, Genevieve type",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}