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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: 9-110800771-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=110800771&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 110800771,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000374448.9",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2393A>G",
"hgvs_p": "p.Tyr798Cys",
"transcript": "NM_005592.4",
"protein_id": "NP_005583.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 869,
"cds_start": 2393,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 8294,
"mane_select": "ENST00000374448.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2393A>G",
"hgvs_p": "p.Tyr798Cys",
"transcript": "ENST00000374448.9",
"protein_id": "ENSP00000363571.4",
"transcript_support_level": 5,
"aa_start": 798,
"aa_end": null,
"aa_length": 869,
"cds_start": 2393,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 8294,
"mane_select": "NM_005592.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2369A>G",
"hgvs_p": "p.Tyr790Cys",
"transcript": "ENST00000416899.7",
"protein_id": "ENSP00000393608.3",
"transcript_support_level": 5,
"aa_start": 790,
"aa_end": null,
"aa_length": 861,
"cds_start": 2369,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2495,
"cdna_end": null,
"cdna_length": 3344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2135A>G",
"hgvs_p": "p.Tyr712Cys",
"transcript": "NM_001166280.2",
"protein_id": "NP_001159752.1",
"transcript_support_level": null,
"aa_start": 712,
"aa_end": null,
"aa_length": 783,
"cds_start": 2135,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2249,
"cdna_end": null,
"cdna_length": 8036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2135A>G",
"hgvs_p": "p.Tyr712Cys",
"transcript": "ENST00000189978.10",
"protein_id": "ENSP00000189978.6",
"transcript_support_level": 5,
"aa_start": 712,
"aa_end": null,
"aa_length": 783,
"cds_start": 2135,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 2181,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2105A>G",
"hgvs_p": "p.Tyr702Cys",
"transcript": "NM_001166281.2",
"protein_id": "NP_001159753.1",
"transcript_support_level": null,
"aa_start": 702,
"aa_end": null,
"aa_length": 773,
"cds_start": 2105,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 2219,
"cdna_end": null,
"cdna_length": 8006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1133A>G",
"hgvs_p": "p.Tyr378Cys",
"transcript": "NM_001369398.1",
"protein_id": "NP_001356327.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 449,
"cds_start": 1133,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1775,
"cdna_end": null,
"cdna_length": 7562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2423A>G",
"hgvs_p": "p.Tyr808Cys",
"transcript": "XM_005251994.4",
"protein_id": "XP_005252051.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 879,
"cds_start": 2423,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 2537,
"cdna_end": null,
"cdna_length": 8324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2399A>G",
"hgvs_p": "p.Tyr800Cys",
"transcript": "XM_005251995.4",
"protein_id": "XP_005252052.1",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 871,
"cds_start": 2399,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 2513,
"cdna_end": null,
"cdna_length": 8300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2369A>G",
"hgvs_p": "p.Tyr790Cys",
"transcript": "XM_005251996.4",
"protein_id": "XP_005252053.1",
"transcript_support_level": null,
"aa_start": 790,
"aa_end": null,
"aa_length": 861,
"cds_start": 2369,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 2483,
"cdna_end": null,
"cdna_length": 8270,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.2159A>G",
"hgvs_p": "p.Tyr720Cys",
"transcript": "XM_017014734.2",
"protein_id": "XP_016870223.1",
"transcript_support_level": null,
"aa_start": 720,
"aa_end": null,
"aa_length": 791,
"cds_start": 2159,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 2273,
"cdna_end": null,
"cdna_length": 8060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1157A>G",
"hgvs_p": "p.Tyr386Cys",
"transcript": "XM_011518708.3",
"protein_id": "XP_011517010.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 457,
"cds_start": 1157,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 7059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"dbsnp": "rs188840021",
"frequency_reference_population": 0.00011585949,
"hom_count_reference_population": 0,
"allele_count_reference_population": 187,
"gnomad_exomes_af": 0.0000820953,
"gnomad_genomes_af": 0.000439898,
"gnomad_exomes_ac": 120,
"gnomad_genomes_ac": 67,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3029518723487854,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.42,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4194,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.052,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000374448.9",
"gene_symbol": "MUSK",
"hgnc_id": 7525,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2393A>G",
"hgvs_p": "p.Tyr798Cys"
}
],
"clinvar_disease": "Congenital myasthenic syndrome 9,Fetal akinesia deformation sequence 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "Congenital myasthenic syndrome 9|not provided|Fetal akinesia deformation sequence 1;Congenital myasthenic syndrome 9|Fetal akinesia deformation sequence 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}