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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: 18-3116391-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=3116391&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 3116391,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000356443.9",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.3243G>T",
"hgvs_p": "p.Lys1081Asn",
"transcript": "NM_003803.4",
"protein_id": "NP_003794.3",
"transcript_support_level": null,
"aa_start": 1081,
"aa_end": null,
"aa_length": 1685,
"cds_start": 3243,
"cds_end": null,
"cds_length": 5058,
"cdna_start": 3437,
"cdna_end": null,
"cdna_length": 5707,
"mane_select": "ENST00000356443.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.3243G>T",
"hgvs_p": "p.Lys1081Asn",
"transcript": "ENST00000356443.9",
"protein_id": "ENSP00000348821.4",
"transcript_support_level": 1,
"aa_start": 1081,
"aa_end": null,
"aa_length": 1685,
"cds_start": 3243,
"cds_end": null,
"cds_length": 5058,
"cdna_start": 3437,
"cdna_end": null,
"cdna_length": 5707,
"mane_select": "NM_003803.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.2955G>T",
"hgvs_p": "p.Lys985Asn",
"transcript": "ENST00000261606.11",
"protein_id": "ENSP00000261606.7",
"transcript_support_level": 1,
"aa_start": 985,
"aa_end": null,
"aa_length": 1589,
"cds_start": 2955,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 3030,
"cdna_end": null,
"cdna_length": 5154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.2955G>T",
"hgvs_p": "p.Lys985Asn",
"transcript": "NM_019856.2",
"protein_id": "NP_062830.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 1589,
"cds_start": 2955,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 3149,
"cdna_end": null,
"cdna_length": 5419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.3366G>T",
"hgvs_p": "p.Lys1122Asn",
"transcript": "XM_047437909.1",
"protein_id": "XP_047293865.1",
"transcript_support_level": null,
"aa_start": 1122,
"aa_end": null,
"aa_length": 1726,
"cds_start": 3366,
"cds_end": null,
"cds_length": 5181,
"cdna_start": 3546,
"cdna_end": null,
"cdna_length": 5816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.3330G>T",
"hgvs_p": "p.Lys1110Asn",
"transcript": "XM_017026062.2",
"protein_id": "XP_016881551.2",
"transcript_support_level": null,
"aa_start": 1110,
"aa_end": null,
"aa_length": 1714,
"cds_start": 3330,
"cds_end": null,
"cds_length": 5145,
"cdna_start": 3510,
"cdna_end": null,
"cdna_length": 5780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.3243G>T",
"hgvs_p": "p.Lys1081Asn",
"transcript": "XM_047437910.1",
"protein_id": "XP_047293866.1",
"transcript_support_level": null,
"aa_start": 1081,
"aa_end": null,
"aa_length": 1685,
"cds_start": 3243,
"cds_end": null,
"cds_length": 5058,
"cdna_start": 4649,
"cdna_end": null,
"cdna_length": 6919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"hgvs_c": "c.3078G>T",
"hgvs_p": "p.Lys1026Asn",
"transcript": "XM_047437911.1",
"protein_id": "XP_047293867.1",
"transcript_support_level": null,
"aa_start": 1026,
"aa_end": null,
"aa_length": 1630,
"cds_start": 3078,
"cds_end": null,
"cds_length": 4893,
"cdna_start": 3258,
"cdna_end": null,
"cdna_length": 5528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYOM1",
"gene_hgnc_id": 7613,
"dbsnp": "rs1060504726",
"frequency_reference_population": 6.843484e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84348e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.030531316995620728,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.027,
"revel_prediction": "Benign",
"alphamissense_score": 0.4924,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.041,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000356443.9",
"gene_symbol": "MYOM1",
"hgnc_id": 7613,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3243G>T",
"hgvs_p": "p.Lys1081Asn"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}