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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: 19-6368560-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6368560&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 6368560,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000245816.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.684C>T",
"hgvs_p": "p.Arg228Arg",
"transcript": "NM_006012.4",
"protein_id": "NP_006003.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 277,
"cds_start": 684,
"cds_end": null,
"cds_length": 834,
"cdna_start": 728,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": "ENST00000245816.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.684C>T",
"hgvs_p": "p.Arg228Arg",
"transcript": "ENST00000245816.11",
"protein_id": "ENSP00000245816.3",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 277,
"cds_start": 684,
"cds_end": null,
"cds_length": 834,
"cdna_start": 728,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": "NM_006012.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.95C>T",
"hgvs_p": "p.Ala32Val",
"transcript": "ENST00000646643.1",
"protein_id": "ENSP00000494298.1",
"transcript_support_level": null,
"aa_start": 32,
"aa_end": null,
"aa_length": 33,
"cds_start": 95,
"cds_end": null,
"cds_length": 102,
"cdna_start": 95,
"cdna_end": null,
"cdna_length": 441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.684C>T",
"hgvs_p": "p.Arg228Arg",
"transcript": "ENST00000715787.1",
"protein_id": "ENSP00000520519.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 277,
"cds_start": 684,
"cds_end": null,
"cds_length": 834,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 2514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Arg141Arg",
"transcript": "ENST00000596149.5",
"protein_id": "ENSP00000472227.1",
"transcript_support_level": 2,
"aa_start": 141,
"aa_end": null,
"aa_length": 190,
"cds_start": 423,
"cds_end": null,
"cds_length": 573,
"cdna_start": 551,
"cdna_end": null,
"cdna_length": 745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.780C>T",
"hgvs_p": "p.Arg260Arg",
"transcript": "XM_047439486.1",
"protein_id": "XP_047295442.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 309,
"cds_start": 780,
"cds_end": null,
"cds_length": 930,
"cdna_start": 824,
"cdna_end": null,
"cdna_length": 2506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "n.1199C>T",
"hgvs_p": null,
"transcript": "ENST00000596070.1",
"protein_id": null,
"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": 1346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.*64C>T",
"hgvs_p": null,
"transcript": "ENST00000596605.2",
"protein_id": "ENSP00000469124.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 70,
"cds_start": -4,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"hgvs_c": "c.*64C>T",
"hgvs_p": null,
"transcript": "ENST00000597326.6",
"protein_id": "ENSP00000470098.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 142,
"cds_start": -4,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLPP",
"gene_hgnc_id": 2084,
"dbsnp": "rs876657442",
"frequency_reference_population": 0.0000020522193,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205222,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12521761655807495,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.527,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000245816.11",
"gene_symbol": "CLPP",
"hgnc_id": 2084,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.684C>T",
"hgvs_p": "p.Arg228Arg"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}