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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: 3-158649090-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=158649090&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 158649090,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000486715.6",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "NM_024996.7",
"protein_id": "NP_079272.4",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 751,
"cds_start": 622,
"cds_end": null,
"cds_length": 2256,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": "ENST00000486715.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "ENST00000486715.6",
"protein_id": "ENSP00000419038.1",
"transcript_support_level": 1,
"aa_start": 208,
"aa_end": null,
"aa_length": 751,
"cds_start": 622,
"cds_end": null,
"cds_length": 2256,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": "NM_024996.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "NM_001308164.2",
"protein_id": "NP_001295093.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 770,
"cds_start": 622,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 6535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "ENST00000264263.9",
"protein_id": "ENSP00000264263.5",
"transcript_support_level": 5,
"aa_start": 208,
"aa_end": null,
"aa_length": 770,
"cds_start": 622,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 660,
"cdna_end": null,
"cdna_length": 3453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "NM_001374355.1",
"protein_id": "NP_001361284.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 724,
"cds_start": 622,
"cds_end": null,
"cds_length": 2175,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 3388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Glu133Lys",
"transcript": "NM_001374357.1",
"protein_id": "NP_001361286.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 676,
"cds_start": 397,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 896,
"cdna_end": null,
"cdna_length": 3635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "NM_001308166.2",
"protein_id": "NP_001295095.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 591,
"cds_start": 622,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 2148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys",
"transcript": "ENST00000478576.5",
"protein_id": "ENSP00000418755.1",
"transcript_support_level": 2,
"aa_start": 208,
"aa_end": null,
"aa_length": 591,
"cds_start": 622,
"cds_end": null,
"cds_length": 1776,
"cdna_start": 729,
"cdna_end": null,
"cdna_length": 2147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.55G>A",
"hgvs_p": "p.Glu19Lys",
"transcript": "NM_001374359.1",
"protein_id": "NP_001361288.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 562,
"cds_start": 55,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 392,
"cdna_end": null,
"cdna_length": 3131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.55G>A",
"hgvs_p": "p.Glu19Lys",
"transcript": "NM_001374360.1",
"protein_id": "NP_001361289.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 544,
"cds_start": 55,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 392,
"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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.110G>A",
"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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.622G>A",
"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": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.730G>A",
"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": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.730G>A",
"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": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.572+2143G>A",
"hgvs_p": null,
"transcript": "NM_001374356.1",
"protein_id": "NP_001361285.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 712,
"cds_start": -4,
"cds_end": null,
"cds_length": 2139,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3352,
"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.235-3010G>A",
"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": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.6-3006G>A",
"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.361-2881C>T",
"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.343-3006G>A",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.680+2143G>A",
"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
}
],
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"dbsnp": "rs191462023",
"frequency_reference_population": 0.00007907209,
"hom_count_reference_population": 0,
"allele_count_reference_population": 125,
"gnomad_exomes_af": 0.000072801,
"gnomad_genomes_af": 0.0001379,
"gnomad_exomes_ac": 104,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.057215481996536255,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.739,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5123,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.232,
"phylop100way_prediction": "Pathogenic",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000486715.6",
"gene_symbol": "GFM1",
"hgnc_id": 13780,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.622G>A",
"hgvs_p": "p.Glu208Lys"
},
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000482640.5",
"gene_symbol": "LXN",
"hgnc_id": 13347,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.361-2881C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "not provided|Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}