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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: 16-67942514-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=67942514&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 67942514,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000264005.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "c.597C>T",
"hgvs_p": "p.Val199Val",
"transcript": "NM_000229.2",
"protein_id": "NP_000220.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 440,
"cds_start": 597,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 1496,
"mane_select": "ENST00000264005.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "c.597C>T",
"hgvs_p": "p.Val199Val",
"transcript": "ENST00000264005.10",
"protein_id": "ENSP00000264005.5",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 440,
"cds_start": 597,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 1496,
"mane_select": "NM_000229.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "c.381C>T",
"hgvs_p": "p.Val127Val",
"transcript": "ENST00000570980.1",
"protein_id": "ENSP00000464651.1",
"transcript_support_level": 2,
"aa_start": 127,
"aa_end": null,
"aa_length": 254,
"cds_start": 381,
"cds_end": null,
"cds_length": 765,
"cdna_start": 856,
"cdna_end": null,
"cdna_length": 1240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "c.63C>T",
"hgvs_p": "p.Val21Val",
"transcript": "ENST00000576450.1",
"protein_id": "ENSP00000458141.1",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 79,
"cds_start": 63,
"cds_end": null,
"cds_length": 240,
"cdna_start": 64,
"cdna_end": null,
"cdna_length": 359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "n.240C>T",
"hgvs_p": null,
"transcript": "ENST00000573538.5",
"protein_id": "ENSP00000463220.1",
"transcript_support_level": 3,
"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": 1083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "n.211C>T",
"hgvs_p": null,
"transcript": "ENST00000573846.1",
"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": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "n.458C>T",
"hgvs_p": null,
"transcript": "ENST00000575277.1",
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "n.*292C>T",
"hgvs_p": null,
"transcript": "ENST00000575467.5",
"protein_id": "ENSP00000460653.1",
"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": 842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "n.*292C>T",
"hgvs_p": null,
"transcript": "ENST00000575467.5",
"protein_id": "ENSP00000460653.1",
"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": 842,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "c.154+347C>T",
"hgvs_p": null,
"transcript": "ENST00000570369.5",
"protein_id": "ENSP00000459014.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 106,
"cds_start": -4,
"cds_end": null,
"cds_length": 321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "LCAT",
"gene_hgnc_id": 6522,
"hgvs_c": "c.-56C>T",
"hgvs_p": null,
"transcript": "ENST00000570396.1",
"protein_id": "ENSP00000459291.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 186,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LCAT",
"gene_hgnc_id": 6522,
"dbsnp": "rs5922",
"frequency_reference_population": 0.000059488768,
"hom_count_reference_population": 1,
"allele_count_reference_population": 96,
"gnomad_exomes_af": 0.0000321603,
"gnomad_genomes_af": 0.000321687,
"gnomad_exomes_ac": 47,
"gnomad_genomes_ac": 49,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.604,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000264005.10",
"gene_symbol": "LCAT",
"hgnc_id": 6522,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.597C>T",
"hgvs_p": "p.Val199Val"
}
],
"clinvar_disease": "Cardiovascular phenotype,LCAT deficiency,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "LCAT deficiency|not provided|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}