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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: 3-158646851-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=158646851&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 158646851,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000486715.6",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "NM_024996.7",
"protein_id": "NP_079272.4",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 751,
"cds_start": 476,
"cds_end": null,
"cds_length": 2256,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": "ENST00000486715.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "ENST00000486715.6",
"protein_id": "ENSP00000419038.1",
"transcript_support_level": 1,
"aa_start": 159,
"aa_end": null,
"aa_length": 751,
"cds_start": 476,
"cds_end": null,
"cds_length": 2256,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": "NM_024996.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "NM_001308164.2",
"protein_id": "NP_001295093.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 770,
"cds_start": 476,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 6535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "ENST00000264263.9",
"protein_id": "ENSP00000264263.5",
"transcript_support_level": 5,
"aa_start": 159,
"aa_end": null,
"aa_length": 770,
"cds_start": 476,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 514,
"cdna_end": null,
"cdna_length": 3453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "NM_001374355.1",
"protein_id": "NP_001361284.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 724,
"cds_start": 476,
"cds_end": null,
"cds_length": 2175,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 3388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "NM_001374356.1",
"protein_id": "NP_001361285.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 712,
"cds_start": 476,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 3352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.251A>G",
"hgvs_p": "p.Asn84Ser",
"transcript": "NM_001374357.1",
"protein_id": "NP_001361286.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 676,
"cds_start": 251,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 750,
"cdna_end": null,
"cdna_length": 3635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "NM_001308166.2",
"protein_id": "NP_001295095.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 591,
"cds_start": 476,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 2148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser",
"transcript": "ENST00000478576.5",
"protein_id": "ENSP00000418755.1",
"transcript_support_level": 2,
"aa_start": 159,
"aa_end": null,
"aa_length": 591,
"cds_start": 476,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 583,
"cdna_end": null,
"cdna_length": 2147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.476A>G",
"hgvs_p": null,
"transcript": "ENST00000478254.5",
"protein_id": "ENSP00000417225.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.584A>G",
"hgvs_p": null,
"transcript": "NR_164499.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.584A>G",
"hgvs_p": null,
"transcript": "NR_164500.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.584A>G",
"hgvs_p": null,
"transcript": "NR_164502.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.234+1070A>G",
"hgvs_p": null,
"transcript": "NM_001374358.1",
"protein_id": "NP_001361287.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 598,
"cds_start": -4,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.5+1070A>G",
"hgvs_p": null,
"transcript": "NM_001374359.1",
"protein_id": "NP_001361288.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 562,
"cds_start": -4,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.5+1070A>G",
"hgvs_p": null,
"transcript": "NM_001374360.1",
"protein_id": "NP_001361289.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 544,
"cds_start": -4,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.5+1070A>G",
"hgvs_p": null,
"transcript": "NM_001374361.1",
"protein_id": "NP_001361290.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 523,
"cds_start": -4,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LXN",
"gene_hgnc_id": 13347,
"hgvs_c": "c.361-642T>C",
"hgvs_p": null,
"transcript": "ENST00000482640.5",
"protein_id": "ENSP00000419373.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": -4,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.342+1070A>G",
"hgvs_p": null,
"transcript": "NR_164501.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.-37A>G",
"hgvs_p": null,
"transcript": "ENST00000478251.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.*70A>G",
"hgvs_p": null,
"transcript": "ENST00000464732.1",
"protein_id": "ENSP00000417532.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 59,
"cds_start": -4,
"cds_end": null,
"cds_length": 181,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"dbsnp": "rs34297061",
"frequency_reference_population": 0.0024007037,
"hom_count_reference_population": 92,
"allele_count_reference_population": 3875,
"gnomad_exomes_af": 0.00137495,
"gnomad_genomes_af": 0.0122504,
"gnomad_exomes_ac": 2010,
"gnomad_genomes_ac": 1865,
"gnomad_exomes_homalt": 55,
"gnomad_genomes_homalt": 37,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0111846923828125,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.18,
"revel_prediction": "Benign",
"alphamissense_score": 0.0847,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.871,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000486715.6",
"gene_symbol": "GFM1",
"hgnc_id": 13780,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.476A>G",
"hgvs_p": "p.Asn159Ser"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000482640.5",
"gene_symbol": "LXN",
"hgnc_id": 13347,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.361-642T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not provided|not specified|Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}