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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: 6-7393228-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=7393228&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 7393228,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_031480.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "NM_031480.3",
"protein_id": "NP_113668.2",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 568,
"cds_start": 201,
"cds_end": null,
"cds_length": 1707,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379834.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_031480.3"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000379834.7",
"protein_id": "ENSP00000369162.2",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 568,
"cds_start": 201,
"cds_end": null,
"cds_length": 1707,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_031480.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379834.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "n.201T>A",
"hgvs_p": null,
"transcript": "ENST00000475351.5",
"protein_id": "ENSP00000418263.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000475351.5"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000967571.1",
"protein_id": "ENSP00000637630.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 599,
"cds_start": 201,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967571.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.291T>A",
"hgvs_p": "p.Asp97Glu",
"transcript": "ENST00000911539.1",
"protein_id": "ENSP00000581598.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 598,
"cds_start": 291,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911539.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000875537.1",
"protein_id": "ENSP00000545596.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 573,
"cds_start": 201,
"cds_end": null,
"cds_length": 1722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875537.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000875536.1",
"protein_id": "ENSP00000545595.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 568,
"cds_start": 201,
"cds_end": null,
"cds_length": 1707,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875536.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000967569.1",
"protein_id": "ENSP00000637628.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 550,
"cds_start": 201,
"cds_end": null,
"cds_length": 1653,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967569.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000967570.1",
"protein_id": "ENSP00000637629.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 537,
"cds_start": 201,
"cds_end": null,
"cds_length": 1614,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967570.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu",
"transcript": "ENST00000911540.1",
"protein_id": "ENSP00000581599.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 517,
"cds_start": 201,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911540.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.237T>A",
"hgvs_p": "p.Asp79Glu",
"transcript": "XM_011514933.4",
"protein_id": "XP_011513235.2",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 580,
"cds_start": 237,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011514933.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"hgvs_c": "c.-144T>A",
"hgvs_p": null,
"transcript": "NM_001348194.2",
"protein_id": "NP_001335123.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 464,
"cds_start": null,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348194.2"
}
],
"gene_symbol": "RIOK1",
"gene_hgnc_id": 18656,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03996586799621582,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.032,
"revel_prediction": "Benign",
"alphamissense_score": 0.0853,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.894,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_031480.3",
"gene_symbol": "RIOK1",
"hgnc_id": 18656,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.201T>A",
"hgvs_p": "p.Asp67Glu"
}
],
"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
}