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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: 21-43793384-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=43793384&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 43793384,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003683.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "NM_003683.6",
"protein_id": "NP_003674.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 461,
"cds_start": 340,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000497547.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003683.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000497547.2",
"protein_id": "ENSP00000417464.1",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 461,
"cds_start": 340,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003683.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000497547.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "n.454C>T",
"hgvs_p": null,
"transcript": "ENST00000467112.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000467112.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000856885.1",
"protein_id": "ENSP00000526944.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 472,
"cds_start": 340,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856885.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000856887.1",
"protein_id": "ENSP00000526946.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 459,
"cds_start": 340,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856887.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000917587.1",
"protein_id": "ENSP00000587646.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 456,
"cds_start": 340,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917587.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000856884.1",
"protein_id": "ENSP00000526943.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 444,
"cds_start": 340,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856884.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000917588.1",
"protein_id": "ENSP00000587647.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 439,
"cds_start": 340,
"cds_end": null,
"cds_length": 1320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917588.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "ENST00000917589.1",
"protein_id": "ENSP00000587648.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 423,
"cds_start": 340,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917589.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "XM_017028485.3",
"protein_id": "XP_016883974.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 415,
"cds_start": 340,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017028485.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.217-1805C>T",
"hgvs_p": null,
"transcript": "ENST00000917586.1",
"protein_id": "ENSP00000587645.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 413,
"cds_start": null,
"cds_end": null,
"cds_length": 1242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917586.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "c.162+2006C>T",
"hgvs_p": null,
"transcript": "ENST00000856886.1",
"protein_id": "ENSP00000526945.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 340,
"cds_start": null,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000856886.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "n.390C>T",
"hgvs_p": null,
"transcript": "ENST00000475534.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000475534.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "n.*243C>T",
"hgvs_p": null,
"transcript": "ENST00000483896.5",
"protein_id": "ENSP00000426898.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000483896.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "n.982C>T",
"hgvs_p": null,
"transcript": "ENST00000492638.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000492638.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"hgvs_c": "n.*243C>T",
"hgvs_p": null,
"transcript": "ENST00000483896.5",
"protein_id": "ENSP00000426898.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000483896.5"
}
],
"gene_symbol": "RRP1",
"gene_hgnc_id": 18785,
"dbsnp": "rs763767114",
"frequency_reference_population": 0.000018592844,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000198453,
"gnomad_genomes_af": 0.00000656953,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9821521043777466,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.903,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8087,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.942,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_003683.6",
"gene_symbol": "RRP1",
"hgnc_id": 18785,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys"
}
],
"clinvar_disease": "Breast ductal adenocarcinoma",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Breast ductal adenocarcinoma",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}