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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: 21-42485804-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=42485804&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "RSPH1",
"hgnc_id": 12371,
"hgvs_c": "c.366G>A",
"hgvs_p": "p.Arg122Arg",
"inheritance_mode": "AR,AD",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_080860.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "21",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.20999999344348907,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 309,
"aa_ref": "R",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1300,
"cdna_start": 404,
"cds_end": null,
"cds_length": 930,
"cds_start": 366,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_080860.4",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.366G>A",
"hgvs_p": "p.Arg122Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000291536.8",
"protein_coding": true,
"protein_id": "NP_543136.1",
"strand": false,
"transcript": "NM_080860.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 309,
"aa_ref": "R",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1300,
"cdna_start": 404,
"cds_end": null,
"cds_length": 930,
"cds_start": 366,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000291536.8",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.366G>A",
"hgvs_p": "p.Arg122Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_080860.4",
"protein_coding": true,
"protein_id": "ENSP00000291536.3",
"strand": false,
"transcript": "ENST00000291536.8",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 285,
"aa_ref": "R",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1316,
"cdna_start": 492,
"cds_end": null,
"cds_length": 858,
"cds_start": 366,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000856519.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.366G>A",
"hgvs_p": "p.Arg122Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526578.1",
"strand": false,
"transcript": "ENST00000856519.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 271,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1186,
"cdna_start": 290,
"cds_end": null,
"cds_length": 816,
"cds_start": 252,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001286506.2",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.252G>A",
"hgvs_p": "p.Arg84Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001273435.1",
"strand": false,
"transcript": "NM_001286506.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 271,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 937,
"cdna_start": 252,
"cds_end": null,
"cds_length": 816,
"cds_start": 252,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000398352.3",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.252G>A",
"hgvs_p": "p.Arg84Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000381395.3",
"strand": false,
"transcript": "ENST00000398352.3",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 240,
"aa_ref": "R",
"aa_start": 53,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1198,
"cdna_start": 302,
"cds_end": null,
"cds_length": 723,
"cds_start": 159,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000856518.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.159G>A",
"hgvs_p": "p.Arg53Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526577.1",
"strand": false,
"transcript": "ENST00000856518.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 285,
"aa_ref": "R",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1228,
"cdna_start": 404,
"cds_end": null,
"cds_length": 858,
"cds_start": 366,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011529786.2",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.366G>A",
"hgvs_p": "p.Arg122Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011528088.1",
"strand": false,
"transcript": "XM_011529786.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 240,
"aa_ref": "R",
"aa_start": 53,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1093,
"cdna_start": 197,
"cds_end": null,
"cds_length": 723,
"cds_start": 159,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_005261208.3",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.159G>A",
"hgvs_p": "p.Arg53Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005261265.1",
"strand": false,
"transcript": "XM_005261208.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 158,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 832,
"cdna_start": null,
"cds_end": null,
"cds_length": 477,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000936949.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.274+6954G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000607008.1",
"strand": false,
"transcript": "ENST00000936949.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 136,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 923,
"cdna_start": null,
"cds_end": null,
"cds_length": 411,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000856517.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.55-8360G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526576.1",
"strand": false,
"transcript": "ENST00000856517.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 115,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 751,
"cdna_start": null,
"cds_end": null,
"cds_length": 348,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000856520.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.145+567G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526579.1",
"strand": false,
"transcript": "ENST00000856520.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 89,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 647,
"cdna_start": null,
"cds_end": null,
"cds_length": 270,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000856521.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "c.68-9757G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526580.1",
"strand": false,
"transcript": "ENST00000856521.1",
"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": 2880,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000493019.1",
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"hgvs_c": "n.992G>A",
"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": "ENST00000493019.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.965582998456544,
"dbsnp": "rs797045148",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 6.84061e-7,
"gene_hgnc_id": 12371,
"gene_symbol": "RSPH1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84061e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.106,
"pos": 42485804,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.7239999771118164,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.19,
"transcript": "NM_080860.4"
}
]
}