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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: 6-83909009-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=83909009&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 83909009,
"ref": "G",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_016230.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYB5R4",
"gene_hgnc_id": 20147,
"hgvs_c": "c.331G>T",
"hgvs_p": "p.Val111Phe",
"transcript": "NM_016230.4",
"protein_id": "NP_057314.2",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 521,
"cds_start": 331,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 425,
"cdna_end": null,
"cdna_length": 9205,
"mane_select": "ENST00000369681.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYB5R4",
"gene_hgnc_id": 20147,
"hgvs_c": "c.331G>T",
"hgvs_p": "p.Val111Phe",
"transcript": "ENST00000369681.10",
"protein_id": "ENSP00000358695.3",
"transcript_support_level": 1,
"aa_start": 111,
"aa_end": null,
"aa_length": 521,
"cds_start": 331,
"cds_end": null,
"cds_length": 1566,
"cdna_start": 425,
"cdna_end": null,
"cdna_length": 9205,
"mane_select": "NM_016230.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIPPLY2-CYB5R4",
"gene_hgnc_id": null,
"hgvs_c": "c.229G>T",
"hgvs_p": "p.Val77Phe",
"transcript": "NM_001400774.1",
"protein_id": "NP_001387703.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 487,
"cds_start": 229,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 9270,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYB5R4",
"gene_hgnc_id": 20147,
"hgvs_c": "c.229G>T",
"hgvs_p": "p.Val77Phe",
"transcript": "ENST00000369679.4",
"protein_id": "ENSP00000358693.4",
"transcript_support_level": 3,
"aa_start": 77,
"aa_end": null,
"aa_length": 109,
"cds_start": 229,
"cds_end": null,
"cds_length": 330,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIPPLY2-CYB5R4",
"gene_hgnc_id": null,
"hgvs_c": "n.490G>T",
"hgvs_p": null,
"transcript": "NR_174603.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIPPLY2-CYB5R4",
"gene_hgnc_id": null,
"hgvs_c": "n.552G>T",
"hgvs_p": null,
"transcript": "NR_174604.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9332,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RIPPLY2-CYB5R4",
"gene_hgnc_id": null,
"hgvs_c": "n.711G>T",
"hgvs_p": null,
"transcript": "NR_174605.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYB5R4",
"gene_hgnc_id": 20147,
"dbsnp": "rs2099464270",
"frequency_reference_population": 0.000007530667,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000753067,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8958616852760315,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9480000138282776,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.564,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3909,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.028,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.998647310410916,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016230.4",
"gene_symbol": "CYB5R4",
"hgnc_id": 20147,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.331G>T",
"hgvs_p": "p.Val111Phe"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001400774.1",
"gene_symbol": "RIPPLY2-CYB5R4",
"hgnc_id": null,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.229G>T",
"hgvs_p": "p.Val77Phe"
}
],
"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
}