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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: 8-102232231-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=102232231&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 102232231,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000251810.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"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.122G>C",
"hgvs_p": "p.Arg41Pro",
"transcript": "NM_015713.5",
"protein_id": "NP_056528.2",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 351,
"cds_start": 122,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 4774,
"mane_select": "ENST00000251810.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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.122G>C",
"hgvs_p": "p.Arg41Pro",
"transcript": "ENST00000251810.8",
"protein_id": "ENSP00000251810.3",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 351,
"cds_start": 122,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 209,
"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.49-6197G>C",
"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+6596G>C",
"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+6596G>C",
"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": "P",
"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.338G>C",
"hgvs_p": "p.Arg113Pro",
"transcript": "NM_001172477.1",
"protein_id": "NP_001165948.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 423,
"cds_start": 338,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 4913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"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.290G>C",
"hgvs_p": "p.Arg97Pro",
"transcript": "ENST00000522368.5",
"protein_id": "ENSP00000428115.1",
"transcript_support_level": 2,
"aa_start": 97,
"aa_end": null,
"aa_length": 407,
"cds_start": 290,
"cds_end": null,
"cds_length": 1224,
"cdna_start": 291,
"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.431G>C",
"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.122G>C",
"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.*45G>C",
"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.*45G>C",
"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.49-6197G>C",
"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": "rs200273673",
"frequency_reference_population": 0.0000018589019,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000136827,
"gnomad_genomes_af": 0.0000065722,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.98566734790802,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.967,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9322,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.61,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.834,
"phylop100way_prediction": "Pathogenic",
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000251810.8",
"gene_symbol": "RRM2B",
"hgnc_id": 17296,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.122G>C",
"hgvs_p": "p.Arg41Pro"
}
],
"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,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1 O:1",
"phenotype_combined": "RRM2B-related mitochondrial disease|not provided|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": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}