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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: 8-102238554-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=102238554&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"PP3_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "RRM2B",
"hgnc_id": 17296,
"hgvs_c": "c.264+5G>T",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": -14,
"transcript": "NM_001172477.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PP3_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_score": -14,
"allele_count_reference_population": 2454,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.79,
"chr": "8",
"clinvar_classification": "Benign/Likely benign",
"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 disorder,Rod-cone dystrophy,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7900000214576721,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 351,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4774,
"cdna_start": null,
"cds_end": null,
"cds_length": 1056,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_015713.5",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000251810.8",
"protein_coding": true,
"protein_id": "NP_056528.2",
"strand": false,
"transcript": "NM_015713.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 351,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4774,
"cdna_start": null,
"cds_end": null,
"cds_length": 1056,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000251810.8",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015713.5",
"protein_coding": true,
"protein_id": "ENSP00000251810.3",
"strand": false,
"transcript": "ENST00000251810.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 299,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 900,
"cdna_start": null,
"cds_end": null,
"cds_length": 900,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000395912.6",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379248.2",
"strand": false,
"transcript": "ENST00000395912.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 139,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 420,
"cdna_start": null,
"cds_end": null,
"cds_length": 420,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000519317.5",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000430641.1",
"strand": false,
"transcript": "ENST00000519317.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 66,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 201,
"cdna_start": null,
"cds_end": null,
"cds_length": 201,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000519962.5",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000429140.1",
"strand": false,
"transcript": "ENST00000519962.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 423,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4913,
"cdna_start": null,
"cds_end": null,
"cds_length": 1272,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001172477.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.264+5G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001165948.1",
"strand": false,
"transcript": "NM_001172477.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 407,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1613,
"cdna_start": null,
"cds_end": null,
"cds_length": 1224,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000522368.5",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.216+5G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428115.1",
"strand": false,
"transcript": "ENST00000522368.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 351,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3731,
"cdna_start": null,
"cds_end": null,
"cds_length": 1056,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000930764.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600823.1",
"strand": false,
"transcript": "ENST00000930764.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 350,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2183,
"cdna_start": null,
"cds_end": null,
"cds_length": 1053,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000854932.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524991.1",
"strand": false,
"transcript": "ENST00000854932.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 348,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4743,
"cdna_start": null,
"cds_end": null,
"cds_length": 1047,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000930763.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600822.1",
"strand": false,
"transcript": "ENST00000930763.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 299,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4618,
"cdna_start": null,
"cds_end": null,
"cds_length": 900,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001172478.2",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001165949.1",
"strand": false,
"transcript": "NM_001172478.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 278,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4405,
"cdna_start": null,
"cds_end": null,
"cds_length": 837,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000941786.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611845.1",
"strand": false,
"transcript": "ENST00000941786.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 178,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3062,
"cdna_start": null,
"cds_end": null,
"cds_length": 537,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000930765.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "c.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600824.1",
"strand": false,
"transcript": "ENST00000930765.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 573,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000517517.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "n.244G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000517517.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 389,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000522394.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "n.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000429578.1",
"strand": false,
"transcript": "ENST00000522394.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 603,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000523957.1",
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"hgvs_c": "n.48+273G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000427830.1",
"strand": false,
"transcript": "ENST00000523957.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999737934356059,
"dbsnp": "rs149523343",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": 0.0016229472,
"gene_hgnc_id": 17296,
"gene_symbol": "RRM2B",
"gnomad_exomes_ac": 1163,
"gnomad_exomes_af": 0.000855298,
"gnomad_exomes_homalt": 23,
"gnomad_genomes_ac": 1291,
"gnomad_genomes_af": 0.00847647,
"gnomad_genomes_homalt": 15,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 38,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not provided|Mitochondrial DNA depletion syndrome 8a;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 5;Rod-cone dystrophy, sensorineural deafness, and Fanconi-type renal dysfunction|RRM2B-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.27,
"pos": 102238554,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9240000247955322,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001172477.1"
}
]
}