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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: 3-197701842-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=197701842&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RUBCN",
"hgnc_id": 28991,
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_001346873.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_score": -9,
"allele_count_reference_population": 1125,
"alphamissense_prediction": null,
"alphamissense_score": 0.103,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.27,
"chr": "3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Autosomal recessive spinocerebellar ataxia 15,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.006392627954483032,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 972,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9255,
"cdna_start": 778,
"cds_end": null,
"cds_length": 2919,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_014687.4",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000296343.10",
"protein_coding": true,
"protein_id": "NP_055502.1",
"strand": false,
"transcript": "NM_014687.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 972,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9255,
"cdna_start": 778,
"cds_end": null,
"cds_length": 2919,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000296343.10",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014687.4",
"protein_coding": true,
"protein_id": "ENSP00000296343.5",
"strand": false,
"transcript": "ENST00000296343.10",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 435,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": 782,
"cds_end": null,
"cds_length": 1308,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000449205.1",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000390962.1",
"strand": false,
"transcript": "ENST00000449205.1",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1011,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9372,
"cdna_start": 778,
"cds_end": null,
"cds_length": 3036,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001346873.2",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001333802.1",
"strand": false,
"transcript": "NM_001346873.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1011,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3218,
"cdna_start": 775,
"cds_end": null,
"cds_length": 3036,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000707076.1",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516727.1",
"strand": false,
"transcript": "ENST00000707076.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 997,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6821,
"cdna_start": 801,
"cds_end": null,
"cds_length": 2994,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000854678.1",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524737.1",
"strand": false,
"transcript": "ENST00000854678.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 971,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6143,
"cdna_start": 782,
"cds_end": null,
"cds_length": 2916,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000935231.1",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605290.1",
"strand": false,
"transcript": "ENST00000935231.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 933,
"aa_ref": "P",
"aa_start": 176,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3801,
"cdna_start": 528,
"cds_end": null,
"cds_length": 2802,
"cds_start": 527,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000413360.5",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.527C>T",
"hgvs_p": "p.Pro176Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000405115.1",
"strand": false,
"transcript": "ENST00000413360.5",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 927,
"aa_ref": "P",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9602,
"cdna_start": 1080,
"cds_end": null,
"cds_length": 2784,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001145642.5",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.413C>T",
"hgvs_p": "p.Pro138Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001139114.1",
"strand": false,
"transcript": "NM_001145642.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 927,
"aa_ref": "P",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6955,
"cdna_start": 959,
"cds_end": null,
"cds_length": 2784,
"cds_start": 413,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000273582.9",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.413C>T",
"hgvs_p": "p.Pro138Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000273582.5",
"strand": false,
"transcript": "ENST00000273582.9",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1012,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9375,
"cdna_start": 778,
"cds_end": null,
"cds_length": 3039,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_006713827.4",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713890.1",
"strand": false,
"transcript": "XM_006713827.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 997,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9330,
"cdna_start": 778,
"cds_end": null,
"cds_length": 2994,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_006713828.4",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713891.1",
"strand": false,
"transcript": "XM_006713828.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 991,
"aa_ref": "P",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9801,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 2976,
"cds_start": 530,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047449268.1",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Pro177Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047305224.1",
"strand": false,
"transcript": "XM_047449268.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 987,
"aa_ref": "P",
"aa_start": 198,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9300,
"cdna_start": 778,
"cds_end": null,
"cds_length": 2964,
"cds_start": 593,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_005269374.4",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Pro198Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005269431.1",
"strand": false,
"transcript": "XM_005269374.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 845,
"aa_ref": "P",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9523,
"cdna_start": 926,
"cds_end": null,
"cds_length": 2538,
"cds_start": 92,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_006713831.5",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.92C>T",
"hgvs_p": "p.Pro31Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006713894.1",
"strand": false,
"transcript": "XM_006713831.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 830,
"aa_ref": "P",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9176,
"cdna_start": 624,
"cds_end": null,
"cds_length": 2493,
"cds_start": 92,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017007543.2",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.92C>T",
"hgvs_p": "p.Pro31Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016863032.1",
"strand": false,
"transcript": "XM_017007543.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 939,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000467303.5",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "n.833C>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": "ENST00000467303.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 679,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2665,
"cdna_start": null,
"cds_end": null,
"cds_length": 2040,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000415452.5",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.-134C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000409618.1",
"strand": true,
"transcript": "ENST00000415452.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 23,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 615,
"cdna_start": null,
"cds_end": null,
"cds_length": 74,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000474214.2",
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"hgvs_c": "c.*18C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000485041.1",
"strand": true,
"transcript": "ENST00000474214.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs145980033",
"effect": "missense_variant",
"frequency_reference_population": 0.0006969837,
"gene_hgnc_id": 28991,
"gene_symbol": "RUBCN",
"gnomad_exomes_ac": 539,
"gnomad_exomes_af": 0.000368707,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_ac": 586,
"gnomad_genomes_af": 0.00384939,
"gnomad_genomes_homalt": 6,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 11,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Autosomal recessive spinocerebellar ataxia 15|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.833,
"pos": 197701842,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.097,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001346873.2"
}
]
}