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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: 20-45001251-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=45001251&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "STK4",
"hgnc_id": 11408,
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Asp349Asn",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_006282.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": 0.0743,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.56,
"chr": "20",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Combined immunodeficiency due to STK4 deficiency",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.1577286720275879,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 487,
"aa_ref": "D",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6366,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 1464,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_006282.5",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Asp349Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372806.8",
"protein_coding": true,
"protein_id": "NP_006273.1",
"strand": true,
"transcript": "NM_006282.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 487,
"aa_ref": "D",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6366,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 1464,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000372806.8",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Asp349Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006282.5",
"protein_coding": true,
"protein_id": "ENSP00000361892.3",
"strand": true,
"transcript": "ENST00000372806.8",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 432,
"aa_ref": "D",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10380,
"cdna_start": 923,
"cds_end": null,
"cds_length": 1299,
"cds_start": 880,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000499879.8",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.880G>A",
"hgvs_p": "p.Asp294Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443514.1",
"strand": true,
"transcript": "ENST00000499879.8",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 462,
"aa_ref": "D",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6461,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 1389,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001352385.2",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Asp349Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001339314.1",
"strand": true,
"transcript": "NM_001352385.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 462,
"aa_ref": "D",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2038,
"cdna_start": 1092,
"cds_end": null,
"cds_length": 1389,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000372801.5",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Asp349Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000361887.1",
"strand": true,
"transcript": "ENST00000372801.5",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 441,
"aa_ref": "D",
"aa_start": 303,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6184,
"cdna_start": 982,
"cds_end": null,
"cds_length": 1326,
"cds_start": 907,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000925605.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Asp303Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595664.1",
"strand": true,
"transcript": "ENST00000925605.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 411,
"aa_ref": "D",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6286,
"cdna_start": 1074,
"cds_end": null,
"cds_length": 1236,
"cds_start": 817,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000474717.3",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.817G>A",
"hgvs_p": "p.Asp273Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479564.2",
"strand": true,
"transcript": "ENST00000474717.3",
"transcript_support_level": 3
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 474,
"aa_ref": "D",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10455,
"cdna_start": 5191,
"cds_end": null,
"cds_length": 1425,
"cds_start": 1006,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005260532.5",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005260589.1",
"strand": true,
"transcript": "XM_005260532.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 474,
"aa_ref": "D",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11830,
"cdna_start": 6566,
"cds_end": null,
"cds_length": 1425,
"cds_start": 1006,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_017028031.3",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016883520.1",
"strand": true,
"transcript": "XM_017028031.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 474,
"aa_ref": "D",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11812,
"cdna_start": 6548,
"cds_end": null,
"cds_length": 1425,
"cds_start": 1006,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047440425.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296381.1",
"strand": true,
"transcript": "XM_047440425.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 458,
"aa_ref": "D",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6311,
"cdna_start": 1047,
"cds_end": null,
"cds_length": 1377,
"cds_start": 958,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047440426.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.958G>A",
"hgvs_p": "p.Asp320Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296382.1",
"strand": true,
"transcript": "XM_047440426.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 411,
"aa_ref": "D",
"aa_start": 273,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10519,
"cdna_start": 5255,
"cds_end": null,
"cds_length": 1236,
"cds_start": 817,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011529018.4",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.817G>A",
"hgvs_p": "p.Asp273Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011527320.1",
"strand": true,
"transcript": "XM_011529018.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 388,
"aa_ref": "D",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1324,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 1167,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_017028033.2",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Asp349Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016883522.1",
"strand": true,
"transcript": "XM_017028033.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2115,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000698221.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "n.*97G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513614.1",
"strand": true,
"transcript": "ENST00000698221.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2010,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000698222.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "n.*1006G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513615.1",
"strand": true,
"transcript": "ENST00000698222.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2260,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000698225.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "n.1245G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000698225.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2115,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000698221.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "n.*97G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513614.1",
"strand": true,
"transcript": "ENST00000698221.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2010,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000698222.1",
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"hgvs_c": "n.*1006G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513615.1",
"strand": true,
"transcript": "ENST00000698222.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs930004106",
"effect": "missense_variant",
"frequency_reference_population": 0.0000037172417,
"gene_hgnc_id": 11408,
"gene_symbol": "STK4",
"gnomad_exomes_ac": 4,
"gnomad_exomes_af": 0.0000027362,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131389,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Combined immunodeficiency due to STK4 deficiency",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.074,
"pos": 45001251,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.102,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006282.5"
}
]
}