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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: 16-55529858-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=55529858&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 3,
"criteria": [
"PM2",
"BP4",
"BP6_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "LPCAT2",
"hgnc_id": 26032,
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -1,
"transcript": "NM_017839.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4,BP6_Moderate",
"acmg_score": -1,
"allele_count_reference_population": 2,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0966,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"chr": "16",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.3570036292076111,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 544,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5313,
"cdna_start": 663,
"cds_end": null,
"cds_length": 1635,
"cds_start": 553,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_017839.5",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262134.10",
"protein_coding": true,
"protein_id": "NP_060309.2",
"strand": true,
"transcript": "NM_017839.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 544,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5313,
"cdna_start": 663,
"cds_end": null,
"cds_length": 1635,
"cds_start": 553,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000262134.10",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017839.5",
"protein_coding": true,
"protein_id": "ENSP00000262134.5",
"strand": true,
"transcript": "ENST00000262134.10",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 551,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3936,
"cdna_start": 741,
"cds_end": null,
"cds_length": 1656,
"cds_start": 553,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000947554.1",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000617613.1",
"strand": true,
"transcript": "ENST00000947554.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 511,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3734,
"cdna_start": 659,
"cds_end": null,
"cds_length": 1536,
"cds_start": 553,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000929287.1",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599346.1",
"strand": true,
"transcript": "ENST00000929287.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 502,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5141,
"cdna_start": 617,
"cds_end": null,
"cds_length": 1509,
"cds_start": 553,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000929286.1",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599345.1",
"strand": true,
"transcript": "ENST00000929286.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 187,
"aa_ref": "V",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 616,
"cdna_start": 126,
"cds_end": null,
"cds_length": 564,
"cds_start": 124,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000564084.1",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.124G>A",
"hgvs_p": "p.Val42Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457496.1",
"strand": true,
"transcript": "ENST00000564084.1",
"transcript_support_level": 3
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 488,
"aa_ref": "V",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5050,
"cdna_start": 400,
"cds_end": null,
"cds_length": 1467,
"cds_start": 385,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047434277.1",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.385G>A",
"hgvs_p": "p.Val129Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290233.1",
"strand": true,
"transcript": "XM_047434277.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 330,
"aa_ref": "V",
"aa_start": 185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1154,
"cdna_start": 663,
"cds_end": null,
"cds_length": 993,
"cds_start": 553,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_005256006.4",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005256063.1",
"strand": true,
"transcript": "XM_005256006.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 274,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4618,
"cdna_start": null,
"cds_end": null,
"cds_length": 825,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011523169.4",
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"hgvs_c": "c.-240G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011521471.1",
"strand": true,
"transcript": "XM_011523169.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs777807704",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013705821,
"gene_hgnc_id": 26032,
"gene_symbol": "LPCAT2",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137058,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.919,
"pos": 55529858,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.377,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_017839.5"
}
]
}