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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: 3-185508849-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=185508849&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 185508849,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_139248.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Leu433Leu",
"transcript": "NM_139248.3",
"protein_id": "NP_640341.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 451,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000296252.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_139248.3"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Leu433Leu",
"transcript": "ENST00000296252.9",
"protein_id": "ENSP00000296252.4",
"transcript_support_level": 1,
"aa_start": 433,
"aa_end": null,
"aa_length": 451,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_139248.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000296252.9"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1195C>T",
"hgvs_p": "p.Leu399Leu",
"transcript": "ENST00000424591.6",
"protein_id": "ENSP00000396384.2",
"transcript_support_level": 1,
"aa_start": 399,
"aa_end": null,
"aa_length": 417,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424591.6"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1318C>T",
"hgvs_p": "p.Leu440Leu",
"transcript": "ENST00000953488.1",
"protein_id": "ENSP00000623547.1",
"transcript_support_level": null,
"aa_start": 440,
"aa_end": null,
"aa_length": 458,
"cds_start": 1318,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953488.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1243C>T",
"hgvs_p": "p.Leu415Leu",
"transcript": "ENST00000897637.1",
"protein_id": "ENSP00000567696.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 433,
"cds_start": 1243,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897637.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1228C>T",
"hgvs_p": "p.Leu410Leu",
"transcript": "ENST00000897638.1",
"protein_id": "ENSP00000567697.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 428,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897638.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1207C>T",
"hgvs_p": "p.Leu403Leu",
"transcript": "NM_001438651.1",
"protein_id": "NP_001425580.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 421,
"cds_start": 1207,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438651.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1207C>T",
"hgvs_p": "p.Leu403Leu",
"transcript": "ENST00000897634.1",
"protein_id": "ENSP00000567693.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 421,
"cds_start": 1207,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897634.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1201C>T",
"hgvs_p": "p.Leu401Leu",
"transcript": "ENST00000953491.1",
"protein_id": "ENSP00000623550.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 419,
"cds_start": 1201,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953491.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1195C>T",
"hgvs_p": "p.Leu399Leu",
"transcript": "NM_001438029.1",
"protein_id": "NP_001424958.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 417,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438029.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1168C>T",
"hgvs_p": "p.Leu390Leu",
"transcript": "NM_001438652.1",
"protein_id": "NP_001425581.1",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 408,
"cds_start": 1168,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438652.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1153C>T",
"hgvs_p": "p.Leu385Leu",
"transcript": "ENST00000897636.1",
"protein_id": "ENSP00000567695.1",
"transcript_support_level": null,
"aa_start": 385,
"aa_end": null,
"aa_length": 403,
"cds_start": 1153,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897636.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1141C>T",
"hgvs_p": "p.Leu381Leu",
"transcript": "ENST00000953490.1",
"protein_id": "ENSP00000623549.1",
"transcript_support_level": null,
"aa_start": 381,
"aa_end": null,
"aa_length": 399,
"cds_start": 1141,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953490.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1123C>T",
"hgvs_p": "p.Leu375Leu",
"transcript": "ENST00000897635.1",
"protein_id": "ENSP00000567694.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 393,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897635.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Leu347Leu",
"transcript": "ENST00000953489.1",
"protein_id": "ENSP00000623548.1",
"transcript_support_level": null,
"aa_start": 347,
"aa_end": null,
"aa_length": 365,
"cds_start": 1039,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953489.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"hgvs_c": "c.*8C>T",
"hgvs_p": null,
"transcript": "ENST00000435679.1",
"protein_id": "ENSP00000390228.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 72,
"cds_start": null,
"cds_end": null,
"cds_length": 219,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000435679.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM41A-DT",
"gene_hgnc_id": 58335,
"hgvs_c": "n.118+9311G>A",
"hgvs_p": null,
"transcript": "ENST00000838616.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000838616.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000309120",
"gene_hgnc_id": null,
"hgvs_c": "n.144-2999G>A",
"hgvs_p": null,
"transcript": "ENST00000838819.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000838819.1"
}
],
"gene_symbol": "LIPH",
"gene_hgnc_id": 18483,
"dbsnp": "rs371600390",
"frequency_reference_population": 0.000020451444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 33,
"gnomad_exomes_af": 0.0000191584,
"gnomad_genomes_af": 0.0000328779,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.468,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_139248.3",
"gene_symbol": "LIPH",
"hgnc_id": 18483,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Leu433Leu"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000838616.1",
"gene_symbol": "TMEM41A-DT",
"hgnc_id": 58335,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.118+9311G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000838819.1",
"gene_symbol": "ENSG00000309120",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.144-2999G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}