← Back to variant description
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: 1-113093204-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=113093204&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Moderate"
],
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"gene_symbol": "LRIG2",
"hgnc_id": 20889,
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_014813.3",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "ENSG00000303525",
"hgnc_id": null,
"hgvs_c": "n.*127T>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "ENST00000795269.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Moderate",
"acmg_score": 6,
"allele_count_reference_population": 16,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"chr": "1",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.3400000035762787,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1065,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11566,
"cdna_start": null,
"cds_end": null,
"cds_length": 3198,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_014813.3",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000361127.6",
"protein_coding": true,
"protein_id": "NP_055628.1",
"strand": true,
"transcript": "NM_014813.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1065,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 11566,
"cdna_start": null,
"cds_end": null,
"cds_length": 3198,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000361127.6",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014813.3",
"protein_coding": true,
"protein_id": "ENSP00000355396.4",
"strand": true,
"transcript": "ENST00000361127.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1083,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4582,
"cdna_start": null,
"cds_end": null,
"cds_length": 3252,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000922864.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592923.1",
"strand": true,
"transcript": "ENST00000922864.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1043,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4445,
"cdna_start": null,
"cds_end": null,
"cds_length": 3132,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000890456.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.240-2A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560515.1",
"strand": true,
"transcript": "ENST00000890456.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1012,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4345,
"cdna_start": null,
"cds_end": null,
"cds_length": 3039,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000922865.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592924.1",
"strand": true,
"transcript": "ENST00000922865.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 968,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4179,
"cdna_start": null,
"cds_end": null,
"cds_length": 2907,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000969894.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639953.1",
"strand": true,
"transcript": "ENST00000969894.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 962,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11678,
"cdna_start": null,
"cds_end": null,
"cds_length": 2889,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001312686.2",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.-4-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001299615.1",
"strand": true,
"transcript": "NM_001312686.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4201,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000890455.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560514.1",
"strand": true,
"transcript": "ENST00000890455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 674,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3297,
"cdna_start": null,
"cds_end": null,
"cds_length": 2025,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000969895.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639954.1",
"strand": true,
"transcript": "ENST00000969895.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 991,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16400,
"cdna_start": null,
"cds_end": null,
"cds_length": 2976,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047435521.1",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.84-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047291477.1",
"strand": true,
"transcript": "XM_047435521.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 962,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11342,
"cdna_start": null,
"cds_end": null,
"cds_length": 2889,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024451227.2",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.-4-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024306995.1",
"strand": true,
"transcript": "XM_024451227.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11245,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005271369.3",
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"hgvs_c": "c.306-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005271426.1",
"strand": true,
"transcript": "XM_005271369.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 595,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000795269.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000303525",
"hgvs_c": "n.*127T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000795269.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbsnp": "rs1364461144",
"effect": "splice_acceptor_variant,intron_variant",
"frequency_reference_population": 0.000011205345,
"gene_hgnc_id": 20889,
"gene_symbol": "LRIG2",
"gnomad_exomes_ac": 16,
"gnomad_exomes_af": 0.0000112053,
"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": "Likely pathogenic",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.792,
"pos": 113093204,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9279999732971191,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.97,
"transcript": "NM_014813.3"
}
]
}