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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: 3-51830652-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=51830652&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "IQCF3",
"hgnc_id": 31816,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001085479.3",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000285749",
"hgnc_id": null,
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000456080.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 43,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.1193,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.24429365992546082,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 570,
"cdna_start": 366,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001393887.1",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000440739.4",
"protein_coding": true,
"protein_id": "NP_001380816.1",
"strand": true,
"transcript": "NM_001393887.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 570,
"cdna_start": 366,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000440739.4",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001393887.1",
"protein_coding": true,
"protein_id": "ENSP00000402012.2",
"strand": true,
"transcript": "ENST00000440739.4",
"transcript_support_level": 2
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1299,
"cdna_start": 1095,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000437810.7",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000409373.2",
"strand": true,
"transcript": "ENST00000437810.7",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1241,
"cdna_start": 1062,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000446775.5",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000401767.1",
"strand": true,
"transcript": "ENST00000446775.5",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1685,
"cdna_start": 1481,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000456080.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285749",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000415609.1",
"strand": true,
"transcript": "ENST00000456080.5",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 93,
"aa_ref": "P",
"aa_start": 69,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 450,
"cdna_start": 246,
"cds_end": null,
"cds_length": 282,
"cds_start": 206,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000444293.5",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.206C>T",
"hgvs_p": "p.Pro69Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402530.1",
"strand": true,
"transcript": "ENST00000444293.5",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1299,
"cdna_start": 1095,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001085479.3",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001078948.1",
"strand": true,
"transcript": "NM_001085479.3",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 154,
"aa_ref": "R",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1266,
"cdna_start": 1062,
"cds_end": null,
"cds_length": 465,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001207023.2",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "c.316C>T",
"hgvs_p": "p.Arg106Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001193952.1",
"strand": true,
"transcript": "NM_001207023.2",
"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": 478,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000462079.1",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "n.274C>T",
"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": "ENST00000462079.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 561,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000660642.1",
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"hgvs_c": "n.66+940C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499445.1",
"strand": true,
"transcript": "ENST00000660642.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 68,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3136,
"cdna_start": null,
"cds_end": null,
"cds_length": 209,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650142.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285749",
"hgvs_c": "c.*107C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496952.1",
"strand": true,
"transcript": "ENST00000650142.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs368763541",
"effect": "missense_variant",
"frequency_reference_population": 0.000026643238,
"gene_hgnc_id": 31816,
"gene_symbol": "IQCF3",
"gnomad_exomes_ac": 39,
"gnomad_exomes_af": 0.0000266812,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262791,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.682,
"pos": 51830652,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.327,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_001085479.3"
}
]
}