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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: 5-154713059-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=154713059&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 154713059,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015315.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Pro45Leu",
"transcript": "ENST00000336314.9",
"protein_id": "ENSP00000336721.4",
"transcript_support_level": 1,
"aa_start": 45,
"aa_end": null,
"aa_length": 1019,
"cds_start": 134,
"cds_end": null,
"cds_length": 3060,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336314.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-915C>T",
"hgvs_p": null,
"transcript": "XM_047417040.1",
"protein_id": "XP_047272996.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 988,
"cds_start": null,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417040.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Pro45Leu",
"transcript": "NM_015315.6",
"protein_id": "NP_056130.2",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 1019,
"cds_start": 134,
"cds_end": null,
"cds_length": 3060,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015315.6"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Pro45Leu",
"transcript": "NM_001367717.1",
"protein_id": "NP_001354646.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 993,
"cds_start": 134,
"cds_end": null,
"cds_length": 2982,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367717.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Pro45Leu",
"transcript": "XM_047417042.1",
"protein_id": "XP_047272998.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 986,
"cds_start": 134,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417042.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Pro45Leu",
"transcript": "XM_047417044.1",
"protein_id": "XP_047273000.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 952,
"cds_start": 134,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417044.1"
},
{
"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": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-915C>T",
"hgvs_p": null,
"transcript": "XM_047417040.1",
"protein_id": "XP_047272996.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 988,
"cds_start": null,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417040.1"
},
{
"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": 19,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-180+30022C>T",
"hgvs_p": null,
"transcript": "NM_001367713.1",
"protein_id": "NP_001354642.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 891,
"cds_start": null,
"cds_end": null,
"cds_length": 2676,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367713.1"
},
{
"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": 20,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-297+30022C>T",
"hgvs_p": null,
"transcript": "NM_001367714.1",
"protein_id": "NP_001354643.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 891,
"cds_start": null,
"cds_end": null,
"cds_length": 2676,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367714.1"
},
{
"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": 19,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-180+30022C>T",
"hgvs_p": null,
"transcript": "NM_001367716.1",
"protein_id": "NP_001354645.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 858,
"cds_start": null,
"cds_end": null,
"cds_length": 2577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367716.1"
},
{
"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": 19,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-180+30022C>T",
"hgvs_p": null,
"transcript": "ENST00000687700.1",
"protein_id": "ENSP00000508958.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 858,
"cds_start": null,
"cds_end": null,
"cds_length": 2577,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000687700.1"
},
{
"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": 18,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-180+30022C>T",
"hgvs_p": null,
"transcript": "NM_001367715.1",
"protein_id": "NP_001354644.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 824,
"cds_start": null,
"cds_end": null,
"cds_length": 2475,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001367715.1"
},
{
"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": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-843-4684C>T",
"hgvs_p": null,
"transcript": "XM_047417041.1",
"protein_id": "XP_047272997.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 988,
"cds_start": null,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417041.1"
},
{
"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": 19,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"hgvs_c": "c.-180+30022C>T",
"hgvs_p": null,
"transcript": "XM_047417045.1",
"protein_id": "XP_047273001.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 865,
"cds_start": null,
"cds_end": null,
"cds_length": 2598,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417045.1"
}
],
"gene_symbol": "LARP1",
"gene_hgnc_id": 29531,
"dbsnp": "rs757070815",
"frequency_reference_population": 0.000009293392,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00000752457,
"gnomad_genomes_af": 0.000026286,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08729630708694458,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.1046,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.893,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_015315.6",
"gene_symbol": "LARP1",
"hgnc_id": 29531,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Pro45Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}