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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: 2-11677686-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=11677686&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 11677686,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001261428.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.39G>C",
"hgvs_p": "p.Glu13Asp",
"transcript": "NM_001261428.3",
"protein_id": "NP_001248357.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 975,
"cds_start": 39,
"cds_end": null,
"cds_length": 2928,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001261428.3"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.39G>C",
"hgvs_p": "p.Glu13Asp",
"transcript": "ENST00000449576.6",
"protein_id": "ENSP00000397908.2",
"transcript_support_level": 2,
"aa_start": 13,
"aa_end": null,
"aa_length": 975,
"cds_start": 39,
"cds_end": null,
"cds_length": 2928,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449576.6"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.39G>C",
"hgvs_p": "p.Glu13Asp",
"transcript": "NM_001349207.2",
"protein_id": "NP_001336136.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 956,
"cds_start": 39,
"cds_end": null,
"cds_length": 2871,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349207.2"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.39G>C",
"hgvs_p": "p.Glu13Asp",
"transcript": "NM_001349208.2",
"protein_id": "NP_001336137.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 939,
"cds_start": 39,
"cds_end": null,
"cds_length": 2820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001349208.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.-109G>C",
"hgvs_p": null,
"transcript": "ENST00000852426.1",
"protein_id": "ENSP00000522485.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 925,
"cds_start": null,
"cds_end": null,
"cds_length": 2778,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852426.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.-109G>C",
"hgvs_p": null,
"transcript": "ENST00000961822.1",
"protein_id": "ENSP00000631881.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 890,
"cds_start": null,
"cds_end": null,
"cds_length": 2673,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961822.1"
},
{
"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": 21,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"hgvs_c": "c.-67+73G>C",
"hgvs_p": null,
"transcript": "ENST00000961823.1",
"protein_id": "ENSP00000631882.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 890,
"cds_start": null,
"cds_end": null,
"cds_length": 2673,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961823.1"
}
],
"gene_symbol": "LPIN1",
"gene_hgnc_id": 13345,
"dbsnp": "rs4669769",
"frequency_reference_population": 0.6347727,
"hom_count_reference_population": 315062,
"allele_count_reference_population": 974578,
"gnomad_exomes_af": 0.643644,
"gnomad_genomes_af": 0.554138,
"gnomad_exomes_ac": 890257,
"gnomad_genomes_ac": 84321,
"gnomad_exomes_homalt": 290103,
"gnomad_genomes_homalt": 24959,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000023455743303202325,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.195,
"revel_prediction": "Benign",
"alphamissense_score": 0.0825,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.349,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001261428.3",
"gene_symbol": "LPIN1",
"hgnc_id": 13345,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.39G>C",
"hgvs_p": "p.Glu13Asp"
}
],
"clinvar_disease": " acute recurrent, autosomal recessive,Myoglobinuria,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|not provided|Myoglobinuria, acute recurrent, autosomal recessive",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}