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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: X-119943275-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=119943275&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 119943275,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_024528.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKAP",
"gene_hgnc_id": 29873,
"hgvs_c": "c.331G>C",
"hgvs_p": "p.Asp111His",
"transcript": "NM_024528.4",
"protein_id": "NP_078804.2",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 415,
"cds_start": 331,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371410.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024528.4"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKAP",
"gene_hgnc_id": 29873,
"hgvs_c": "c.331G>C",
"hgvs_p": "p.Asp111His",
"transcript": "ENST00000371410.5",
"protein_id": "ENSP00000360464.3",
"transcript_support_level": 1,
"aa_start": 111,
"aa_end": null,
"aa_length": 415,
"cds_start": 331,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024528.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371410.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RHOXF1P3",
"gene_hgnc_id": 51612,
"hgvs_c": "c.-1502C>G",
"hgvs_p": null,
"transcript": "ENST00000640298.3",
"protein_id": "ENSP00000515421.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 132,
"cds_start": null,
"cds_end": null,
"cds_length": 399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640298.3"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKAP",
"gene_hgnc_id": 29873,
"hgvs_c": "c.328G>C",
"hgvs_p": "p.Asp110His",
"transcript": "ENST00000652253.1",
"protein_id": "ENSP00000498376.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 413,
"cds_start": 328,
"cds_end": null,
"cds_length": 1242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000652253.1"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKAP",
"gene_hgnc_id": 29873,
"hgvs_c": "c.331G>C",
"hgvs_p": "p.Asp111His",
"transcript": "ENST00000934466.1",
"protein_id": "ENSP00000604525.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 388,
"cds_start": 331,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934466.1"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NKAP",
"gene_hgnc_id": 29873,
"hgvs_c": "c.331G>C",
"hgvs_p": "p.Asp111His",
"transcript": "ENST00000966801.1",
"protein_id": "ENSP00000636860.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 303,
"cds_start": 331,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966801.1"
}
],
"gene_symbol": "NKAP",
"gene_hgnc_id": 29873,
"dbsnp": "rs200925009",
"frequency_reference_population": 0.000040548683,
"hom_count_reference_population": 10,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000364976,
"gnomad_genomes_af": 0.0000800263,
"gnomad_exomes_ac": 40,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04308497905731201,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.092,
"revel_prediction": "Benign",
"alphamissense_score": 0.271,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.846,
"phylop100way_prediction": "Benign",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_024528.4",
"gene_symbol": "NKAP",
"hgnc_id": 29873,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.331G>C",
"hgvs_p": "p.Asp111His"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000640298.3",
"gene_symbol": "RHOXF1P3",
"hgnc_id": 51612,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-1502C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}