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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: 3-158690243-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=158690243&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 158690243,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000486715.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1990G>A",
"hgvs_p": "p.Val664Ile",
"transcript": "NM_024996.7",
"protein_id": "NP_079272.4",
"transcript_support_level": null,
"aa_start": 664,
"aa_end": null,
"aa_length": 751,
"cds_start": 1990,
"cds_end": null,
"cds_length": 2256,
"cdna_start": 2098,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": "ENST00000486715.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1990G>A",
"hgvs_p": "p.Val664Ile",
"transcript": "ENST00000486715.6",
"protein_id": "ENSP00000419038.1",
"transcript_support_level": 1,
"aa_start": 664,
"aa_end": null,
"aa_length": 751,
"cds_start": 1990,
"cds_end": null,
"cds_length": 2256,
"cdna_start": 2098,
"cdna_end": null,
"cdna_length": 6478,
"mane_select": "NM_024996.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.2047G>A",
"hgvs_p": "p.Val683Ile",
"transcript": "NM_001308164.2",
"protein_id": "NP_001295093.1",
"transcript_support_level": null,
"aa_start": 683,
"aa_end": null,
"aa_length": 770,
"cds_start": 2047,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 6535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.2047G>A",
"hgvs_p": "p.Val683Ile",
"transcript": "ENST00000264263.9",
"protein_id": "ENSP00000264263.5",
"transcript_support_level": 5,
"aa_start": 683,
"aa_end": null,
"aa_length": 770,
"cds_start": 2047,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 2085,
"cdna_end": null,
"cdna_length": 3453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1909G>A",
"hgvs_p": "p.Val637Ile",
"transcript": "NM_001374355.1",
"protein_id": "NP_001361284.1",
"transcript_support_level": null,
"aa_start": 637,
"aa_end": null,
"aa_length": 724,
"cds_start": 1909,
"cds_end": null,
"cds_length": 2175,
"cdna_start": 2017,
"cdna_end": null,
"cdna_length": 3388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1873G>A",
"hgvs_p": "p.Val625Ile",
"transcript": "NM_001374356.1",
"protein_id": "NP_001361285.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 712,
"cds_start": 1873,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 1981,
"cdna_end": null,
"cdna_length": 3352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1765G>A",
"hgvs_p": "p.Val589Ile",
"transcript": "NM_001374357.1",
"protein_id": "NP_001361286.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 676,
"cds_start": 1765,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 2264,
"cdna_end": null,
"cdna_length": 3635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1531G>A",
"hgvs_p": "p.Val511Ile",
"transcript": "NM_001374358.1",
"protein_id": "NP_001361287.1",
"transcript_support_level": null,
"aa_start": 511,
"aa_end": null,
"aa_length": 598,
"cds_start": 1531,
"cds_end": null,
"cds_length": 1797,
"cdna_start": 1639,
"cdna_end": null,
"cdna_length": 3010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1423G>A",
"hgvs_p": "p.Val475Ile",
"transcript": "NM_001374359.1",
"protein_id": "NP_001361288.1",
"transcript_support_level": null,
"aa_start": 475,
"aa_end": null,
"aa_length": 562,
"cds_start": 1423,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 1760,
"cdna_end": null,
"cdna_length": 3131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1423G>A",
"hgvs_p": "p.Val475Ile",
"transcript": "NM_001374360.1",
"protein_id": "NP_001361289.1",
"transcript_support_level": null,
"aa_start": 475,
"aa_end": null,
"aa_length": 544,
"cds_start": 1423,
"cds_end": null,
"cds_length": 1635,
"cdna_start": 1760,
"cdna_end": null,
"cdna_length": 3077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.1306G>A",
"hgvs_p": "p.Val436Ile",
"transcript": "NM_001374361.1",
"protein_id": "NP_001361290.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 523,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 1643,
"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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.396G>A",
"hgvs_p": null,
"transcript": "ENST00000477721.1",
"protein_id": null,
"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": 739,
"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": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.*630G>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": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.2013G>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": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.1953G>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": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.1498G>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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.1977G>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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "n.*630G>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": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"hgvs_c": "c.38-896G>A",
"hgvs_p": null,
"transcript": "ENST00000472383.1",
"protein_id": "ENSP00000420272.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 16,
"cds_start": -4,
"cds_end": null,
"cds_length": 51,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GFM1",
"gene_hgnc_id": 13780,
"dbsnp": "rs62288347",
"frequency_reference_population": 0.017465396,
"hom_count_reference_population": 331,
"allele_count_reference_population": 28183,
"gnomad_exomes_af": 0.0177642,
"gnomad_genomes_af": 0.0145943,
"gnomad_exomes_ac": 25963,
"gnomad_genomes_ac": 2220,
"gnomad_exomes_homalt": 305,
"gnomad_genomes_homalt": 26,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004495680332183838,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.181,
"revel_prediction": "Benign",
"alphamissense_score": 0.0971,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.637,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.07,
"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.1990G>A",
"hgvs_p": "p.Val664Ile"
}
],
"clinvar_disease": "Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "not specified|Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}