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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: 9-98060765-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=98060765&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "NANS",
"hgnc_id": 19237,
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -4,
"transcript": "NM_018946.4",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "TRIM14",
"hgnc_id": 16283,
"hgvs_c": "c.*29-24952G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -4,
"transcript": "XM_047424162.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_score": -4,
"allele_count_reference_population": 10,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "9",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8199999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 359,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1179,
"cdna_start": null,
"cds_end": null,
"cds_length": 1080,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_018946.4",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000210444.6",
"protein_coding": true,
"protein_id": "NP_061819.2",
"strand": true,
"transcript": "NM_018946.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 359,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1179,
"cdna_start": null,
"cds_end": null,
"cds_length": 1080,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000210444.6",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018946.4",
"protein_coding": true,
"protein_id": "ENSP00000210444.5",
"strand": true,
"transcript": "ENST00000210444.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 377,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1277,
"cdna_start": null,
"cds_end": null,
"cds_length": 1134,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000924305.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594364.1",
"strand": true,
"transcript": "ENST00000924305.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 358,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1231,
"cdna_start": null,
"cds_end": null,
"cds_length": 1077,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000924304.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-20C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594363.1",
"strand": true,
"transcript": "ENST00000924304.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 356,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1153,
"cdna_start": null,
"cds_end": null,
"cds_length": 1071,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000869791.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539850.1",
"strand": true,
"transcript": "ENST00000869791.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 356,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1234,
"cdna_start": null,
"cds_end": null,
"cds_length": 1071,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000924303.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594362.1",
"strand": true,
"transcript": "ENST00000924303.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 330,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1084,
"cdna_start": null,
"cds_end": null,
"cds_length": 993,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000956796.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626855.1",
"strand": true,
"transcript": "ENST00000956796.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 296,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 981,
"cdna_start": null,
"cds_end": null,
"cds_length": 891,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000869790.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539849.1",
"strand": true,
"transcript": "ENST00000869790.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 292,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 976,
"cdna_start": null,
"cds_end": null,
"cds_length": 879,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000924307.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594366.1",
"strand": true,
"transcript": "ENST00000924307.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 287,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 990,
"cdna_start": null,
"cds_end": null,
"cds_length": 864,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000924306.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.132+3825C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594365.1",
"strand": true,
"transcript": "ENST00000924306.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 274,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 975,
"cdna_start": null,
"cds_end": null,
"cds_length": 825,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000869789.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539848.1",
"strand": true,
"transcript": "ENST00000869789.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 270,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 904,
"cdna_start": null,
"cds_end": null,
"cds_length": 813,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000956797.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.133-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626856.1",
"strand": true,
"transcript": "ENST00000956797.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 442,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1408,
"cdna_start": null,
"cds_end": null,
"cds_length": 1329,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047424162.1",
"gene_hgnc_id": 16283,
"gene_symbol": "TRIM14",
"hgvs_c": "c.*29-24952G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047280118.1",
"strand": false,
"transcript": "XM_047424162.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 649,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000480925.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "n.172-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000480925.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 764,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000495319.1",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "n.174-17C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000495319.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 243,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 998,
"cdna_start": null,
"cds_end": null,
"cds_length": 732,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011518787.3",
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"hgvs_c": "c.-396C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011517089.1",
"strand": true,
"transcript": "XM_011518787.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1413064834",
"effect": "intron_variant",
"frequency_reference_population": 0.000006848208,
"gene_hgnc_id": 19237,
"gene_symbol": "NANS",
"gnomad_exomes_ac": 10,
"gnomad_exomes_af": 0.00000684821,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.171,
"pos": 98060765,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_018946.4"
}
]
}