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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: 18-3067417-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=3067417&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MYOM1",
"hgnc_id": 7613,
"hgvs_c": "c.4903G>A",
"hgvs_p": "p.Gly1635Ser",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_003803.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_score": -9,
"allele_count_reference_population": 1408,
"alphamissense_prediction": null,
"alphamissense_score": 0.1633,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "18",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Hypertrophic cardiomyopathy,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.053989946842193604,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1685,
"aa_ref": "G",
"aa_start": 1635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5707,
"cdna_start": 5097,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4903,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "NM_003803.4",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4903G>A",
"hgvs_p": "p.Gly1635Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000356443.9",
"protein_coding": true,
"protein_id": "NP_003794.3",
"strand": false,
"transcript": "NM_003803.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1685,
"aa_ref": "G",
"aa_start": 1635,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5707,
"cdna_start": 5097,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4903,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "ENST00000356443.9",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4903G>A",
"hgvs_p": "p.Gly1635Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003803.4",
"protein_coding": true,
"protein_id": "ENSP00000348821.4",
"strand": false,
"transcript": "ENST00000356443.9",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1589,
"aa_ref": "G",
"aa_start": 1539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5154,
"cdna_start": 4690,
"cds_end": null,
"cds_length": 4770,
"cds_start": 4615,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000261606.11",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4615G>A",
"hgvs_p": "p.Gly1539Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000261606.7",
"strand": false,
"transcript": "ENST00000261606.11",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1673,
"aa_ref": "G",
"aa_start": 1623,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5785,
"cdna_start": 5061,
"cds_end": null,
"cds_length": 5022,
"cds_start": 4867,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "ENST00000941943.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4867G>A",
"hgvs_p": "p.Gly1623Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612002.1",
"strand": false,
"transcript": "ENST00000941943.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1622,
"aa_ref": "G",
"aa_start": 1572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5677,
"cdna_start": 5066,
"cds_end": null,
"cds_length": 4869,
"cds_start": 4714,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000941942.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4714G>A",
"hgvs_p": "p.Gly1572Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612001.1",
"strand": false,
"transcript": "ENST00000941942.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1589,
"aa_ref": "G",
"aa_start": 1539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5419,
"cdna_start": 4809,
"cds_end": null,
"cds_length": 4770,
"cds_start": 4615,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "NM_019856.2",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4615G>A",
"hgvs_p": "p.Gly1539Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_062830.1",
"strand": false,
"transcript": "NM_019856.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1589,
"aa_ref": "G",
"aa_start": 1539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5545,
"cdna_start": 4934,
"cds_end": null,
"cds_length": 4770,
"cds_start": 4615,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000941945.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4615G>A",
"hgvs_p": "p.Gly1539Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612004.1",
"strand": false,
"transcript": "ENST00000941945.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1179,
"aa_ref": "G",
"aa_start": 1129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4188,
"cdna_start": 3579,
"cds_end": null,
"cds_length": 3540,
"cds_start": 3385,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000941944.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.3385G>A",
"hgvs_p": "p.Gly1129Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612003.1",
"strand": false,
"transcript": "ENST00000941944.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1726,
"aa_ref": "G",
"aa_start": 1676,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5816,
"cdna_start": 5206,
"cds_end": null,
"cds_length": 5181,
"cds_start": 5026,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "XM_047437909.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.5026G>A",
"hgvs_p": "p.Gly1676Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293865.1",
"strand": false,
"transcript": "XM_047437909.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1714,
"aa_ref": "G",
"aa_start": 1664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5780,
"cdna_start": 5170,
"cds_end": null,
"cds_length": 5145,
"cds_start": 4990,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "XM_017026062.2",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4990G>A",
"hgvs_p": "p.Gly1664Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016881551.2",
"strand": false,
"transcript": "XM_017026062.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1685,
"aa_ref": "G",
"aa_start": 1635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6919,
"cdna_start": 6309,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4903,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "XM_047437910.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4903G>A",
"hgvs_p": "p.Gly1635Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293866.1",
"strand": false,
"transcript": "XM_047437910.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1630,
"aa_ref": "G",
"aa_start": 1580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5528,
"cdna_start": 4918,
"cds_end": null,
"cds_length": 4893,
"cds_start": 4738,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 38,
"exon_rank_end": null,
"feature": "XM_047437911.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4738G>A",
"hgvs_p": "p.Gly1580Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293867.1",
"strand": false,
"transcript": "XM_047437911.1",
"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": 545,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000581804.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "n.393G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000581804.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200773357",
"effect": "missense_variant",
"frequency_reference_population": 0.0008725841,
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"gnomad_exomes_ac": 1318,
"gnomad_exomes_af": 0.000901971,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 90,
"gnomad_genomes_af": 0.000590729,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Hypertrophic cardiomyopathy|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.8,
"pos": 3067417,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.128,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003803.4"
}
]
}