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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: 8-102232232-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=102232232&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 102232232,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000251810.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.121C>T",
"hgvs_p": "p.Arg41Trp",
"transcript": "NM_015713.5",
"protein_id": "NP_056528.2",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 351,
"cds_start": 121,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 208,
"cdna_end": null,
"cdna_length": 4774,
"mane_select": "ENST00000251810.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.121C>T",
"hgvs_p": "p.Arg41Trp",
"transcript": "ENST00000251810.8",
"protein_id": "ENSP00000251810.3",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 351,
"cds_start": 121,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 208,
"cdna_end": null,
"cdna_length": 4774,
"mane_select": "NM_015713.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.49-6198C>T",
"hgvs_p": null,
"transcript": "ENST00000395912.6",
"protein_id": "ENSP00000379248.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.48+6595C>T",
"hgvs_p": null,
"transcript": "ENST00000519317.5",
"protein_id": "ENSP00000430641.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 139,
"cds_start": -4,
"cds_end": null,
"cds_length": 420,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.48+6595C>T",
"hgvs_p": null,
"transcript": "ENST00000519962.5",
"protein_id": "ENSP00000429140.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 66,
"cds_start": -4,
"cds_end": null,
"cds_length": 201,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.337C>T",
"hgvs_p": "p.Arg113Trp",
"transcript": "NM_001172477.1",
"protein_id": "NP_001165948.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 423,
"cds_start": 337,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 4913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.289C>T",
"hgvs_p": "p.Arg97Trp",
"transcript": "ENST00000522368.5",
"protein_id": "ENSP00000428115.1",
"transcript_support_level": 2,
"aa_start": 97,
"aa_end": null,
"aa_length": 407,
"cds_start": 289,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 1613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "n.430C>T",
"hgvs_p": null,
"transcript": "ENST00000517517.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "n.121C>T",
"hgvs_p": null,
"transcript": "ENST00000522394.1",
"protein_id": "ENSP00000429578.1",
"transcript_support_level": 2,
"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": 389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "n.*44C>T",
"hgvs_p": null,
"transcript": "ENST00000523957.1",
"protein_id": "ENSP00000427830.1",
"transcript_support_level": 5,
"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": 603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "n.*44C>T",
"hgvs_p": null,
"transcript": "ENST00000523957.1",
"protein_id": "ENSP00000427830.1",
"transcript_support_level": 5,
"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": 603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"hgvs_c": "c.49-6198C>T",
"hgvs_p": null,
"transcript": "NM_001172478.2",
"protein_id": "NP_001165949.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 299,
"cds_start": -4,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RRM2B",
"gene_hgnc_id": 17296,
"dbsnp": "rs515726181",
"frequency_reference_population": 0.0000013682904,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136829,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9888217449188232,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.925,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7899,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.523,
"phylop100way_prediction": "Uncertain_significance",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000251810.8",
"gene_symbol": "RRM2B",
"hgnc_id": 17296,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.121C>T",
"hgvs_p": "p.Arg41Trp"
}
],
"clinvar_disease": " and Fanconi-type renal dysfunction, autosomal dominant 5, sensorineural deafness,Mitochondrial DNA depletion syndrome 8a,Progressive external ophthalmoplegia with mitochondrial DNA deletions,RRM2B-related mitochondrial disease,Rod-cone dystrophy",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1 O:1",
"phenotype_combined": "RRM2B-related mitochondrial disease|Mitochondrial DNA depletion syndrome 8a|Mitochondrial DNA depletion syndrome 8a;Rod-cone dystrophy, sensorineural deafness, and Fanconi-type renal dysfunction;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 5",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}