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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: 18-3086067-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=3086067&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MYOM1",
"hgnc_id": 7613,
"hgvs_c": "c.4222G>A",
"hgvs_p": "p.Asp1408Asn",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_003803.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 123631,
"alphamissense_prediction": null,
"alphamissense_score": 0.2544,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"chr": "18",
"clinvar_classification": "Benign",
"clinvar_disease": "Cardiovascular phenotype,Hypertrophic cardiomyopathy,MYOM1-related disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.002406388521194458,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 1685,
"aa_ref": "D",
"aa_start": 1408,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5707,
"cdna_start": 4416,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4222,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "NM_003803.4",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4222G>A",
"hgvs_p": "p.Asp1408Asn",
"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": "N",
"aa_end": null,
"aa_length": 1685,
"aa_ref": "D",
"aa_start": 1408,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5707,
"cdna_start": 4416,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4222,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000356443.9",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4222G>A",
"hgvs_p": "p.Asp1408Asn",
"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": "N",
"aa_end": null,
"aa_length": 1589,
"aa_ref": "D",
"aa_start": 1312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5154,
"cdna_start": 4009,
"cds_end": null,
"cds_length": 4770,
"cds_start": 3934,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000261606.11",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.3934G>A",
"hgvs_p": "p.Asp1312Asn",
"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": "N",
"aa_end": null,
"aa_length": 1673,
"aa_ref": "D",
"aa_start": 1396,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5785,
"cdna_start": 4380,
"cds_end": null,
"cds_length": 5022,
"cds_start": 4186,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000941943.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4186G>A",
"hgvs_p": "p.Asp1396Asn",
"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": "N",
"aa_end": null,
"aa_length": 1622,
"aa_ref": "D",
"aa_start": 1345,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5677,
"cdna_start": 4385,
"cds_end": null,
"cds_length": 4869,
"cds_start": 4033,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000941942.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4033G>A",
"hgvs_p": "p.Asp1345Asn",
"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": "N",
"aa_end": null,
"aa_length": 1589,
"aa_ref": "D",
"aa_start": 1312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5419,
"cdna_start": 4128,
"cds_end": null,
"cds_length": 4770,
"cds_start": 3934,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "NM_019856.2",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.3934G>A",
"hgvs_p": "p.Asp1312Asn",
"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": "N",
"aa_end": null,
"aa_length": 1589,
"aa_ref": "D",
"aa_start": 1312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5545,
"cdna_start": 4253,
"cds_end": null,
"cds_length": 4770,
"cds_start": 3934,
"consequences": [
"missense_variant"
],
"exon_count": 37,
"exon_rank": 29,
"exon_rank_end": null,
"feature": "ENST00000941945.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.3934G>A",
"hgvs_p": "p.Asp1312Asn",
"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": "N",
"aa_end": null,
"aa_length": 1179,
"aa_ref": "D",
"aa_start": 902,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4188,
"cdna_start": 2898,
"cds_end": null,
"cds_length": 3540,
"cds_start": 2704,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000941944.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.2704G>A",
"hgvs_p": "p.Asp902Asn",
"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": "N",
"aa_end": null,
"aa_length": 1726,
"aa_ref": "D",
"aa_start": 1449,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5816,
"cdna_start": 4525,
"cds_end": null,
"cds_length": 5181,
"cds_start": 4345,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "XM_047437909.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4345G>A",
"hgvs_p": "p.Asp1449Asn",
"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": "N",
"aa_end": null,
"aa_length": 1714,
"aa_ref": "D",
"aa_start": 1437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5780,
"cdna_start": 4489,
"cds_end": null,
"cds_length": 5145,
"cds_start": 4309,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "XM_017026062.2",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4309G>A",
"hgvs_p": "p.Asp1437Asn",
"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": "N",
"aa_end": null,
"aa_length": 1685,
"aa_ref": "D",
"aa_start": 1408,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6919,
"cdna_start": 5628,
"cds_end": null,
"cds_length": 5058,
"cds_start": 4222,
"consequences": [
"missense_variant"
],
"exon_count": 39,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "XM_047437910.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4222G>A",
"hgvs_p": "p.Asp1408Asn",
"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": "N",
"aa_end": null,
"aa_length": 1630,
"aa_ref": "D",
"aa_start": 1353,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5528,
"cdna_start": 4237,
"cds_end": null,
"cds_length": 4893,
"cds_start": 4057,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "XM_047437911.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "c.4057G>A",
"hgvs_p": "p.Asp1353Asn",
"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": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 684,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000581075.1",
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"hgvs_c": "n.322G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000462039.1",
"strand": false,
"transcript": "ENST00000581075.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs3765623",
"effect": "missense_variant",
"frequency_reference_population": 0.076914035,
"gene_hgnc_id": 7613,
"gene_symbol": "MYOM1",
"gnomad_exomes_ac": 115160,
"gnomad_exomes_af": 0.0791407,
"gnomad_exomes_homalt": 4891,
"gnomad_genomes_ac": 8471,
"gnomad_genomes_af": 0.0556344,
"gnomad_genomes_homalt": 308,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 5199,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Cardiovascular phenotype|Hypertrophic cardiomyopathy|not provided|MYOM1-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.877,
"pos": 3086067,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.206,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_003803.4"
}
]
}