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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: 17-40184257-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=40184257&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 40184257,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016339.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Arg215Trp",
"transcript": "NM_016339.6",
"protein_id": "NP_057423.2",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 662,
"cds_start": 643,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000620260.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016339.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Arg215Trp",
"transcript": "ENST00000620260.6",
"protein_id": "ENSP00000479735.1",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 662,
"cds_start": 643,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016339.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620260.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.190C>T",
"hgvs_p": "p.Arg64Trp",
"transcript": "ENST00000456989.6",
"protein_id": "ENSP00000394530.2",
"transcript_support_level": 1,
"aa_start": 64,
"aa_end": null,
"aa_length": 511,
"cds_start": 190,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000456989.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Arg58Trp",
"transcript": "ENST00000544503.5",
"protein_id": "ENSP00000438631.1",
"transcript_support_level": 2,
"aa_start": 58,
"aa_end": null,
"aa_length": 505,
"cds_start": 172,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544503.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"transcript": "ENST00000264644.10",
"protein_id": "ENSP00000264644.5",
"transcript_support_level": 5,
"aa_start": 9,
"aa_end": null,
"aa_length": 456,
"cds_start": 25,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264644.10"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"transcript": "ENST00000543876.5",
"protein_id": "ENSP00000440226.1",
"transcript_support_level": 4,
"aa_start": 9,
"aa_end": null,
"aa_length": 148,
"cds_start": 25,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000543876.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"transcript": "ENST00000538981.1",
"protein_id": "ENSP00000441059.1",
"transcript_support_level": 2,
"aa_start": 9,
"aa_end": null,
"aa_length": 100,
"cds_start": 25,
"cds_end": null,
"cds_length": 304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538981.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "ENST00000541245.1",
"protein_id": "ENSP00000444646.1",
"transcript_support_level": 3,
"aa_start": 46,
"aa_end": null,
"aa_length": 61,
"cds_start": 136,
"cds_end": null,
"cds_length": 187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541245.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"transcript": "ENST00000538884.1",
"protein_id": "ENSP00000440006.1",
"transcript_support_level": 4,
"aa_start": 9,
"aa_end": null,
"aa_length": 19,
"cds_start": 25,
"cds_end": null,
"cds_length": 62,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538884.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.190C>T",
"hgvs_p": "p.Arg64Trp",
"transcript": "NM_001303533.2",
"protein_id": "NP_001290462.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 511,
"cds_start": 190,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303533.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.172C>T",
"hgvs_p": "p.Arg58Trp",
"transcript": "NM_001303534.3",
"protein_id": "NP_001290463.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 505,
"cds_start": 172,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303534.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Arg215Trp",
"transcript": "XM_047436203.1",
"protein_id": "XP_047292159.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 662,
"cds_start": 643,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436203.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.136C>T",
"hgvs_p": "p.Arg46Trp",
"transcript": "XM_047436204.1",
"protein_id": "XP_047292160.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 493,
"cds_start": 136,
"cds_end": null,
"cds_length": 1482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436204.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"hgvs_c": "c.25C>T",
"hgvs_p": "p.Arg9Trp",
"transcript": "XM_047436205.1",
"protein_id": "XP_047292161.1",
"transcript_support_level": null,
"aa_start": 9,
"aa_end": null,
"aa_length": 456,
"cds_start": 25,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436205.1"
}
],
"gene_symbol": "RAPGEFL1",
"gene_hgnc_id": 17428,
"dbsnp": "rs765143011",
"frequency_reference_population": 0.00003284931,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000328458,
"gnomad_genomes_af": 0.0000328826,
"gnomad_exomes_ac": 48,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.26755595207214355,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.221,
"revel_prediction": "Benign",
"alphamissense_score": 0.1824,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.559,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016339.6",
"gene_symbol": "RAPGEFL1",
"hgnc_id": 17428,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Arg215Trp"
}
],
"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
}