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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: 1-68439568-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=68439568&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 68439568,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000262340.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "c.718G>T",
"hgvs_p": "p.Val240Phe",
"transcript": "NM_000329.3",
"protein_id": "NP_000320.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 533,
"cds_start": 718,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 2605,
"mane_select": "ENST00000262340.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "c.718G>T",
"hgvs_p": "p.Val240Phe",
"transcript": "ENST00000262340.6",
"protein_id": "ENSP00000262340.5",
"transcript_support_level": 1,
"aa_start": 240,
"aa_end": null,
"aa_length": 533,
"cds_start": 718,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 2605,
"mane_select": "NM_000329.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "c.610G>T",
"hgvs_p": "p.Val204Phe",
"transcript": "NM_001406853.1",
"protein_id": "NP_001393782.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 497,
"cds_start": 610,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 2497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "c.442G>T",
"hgvs_p": "p.Val148Phe",
"transcript": "NM_001406856.1",
"protein_id": "NP_001393785.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 441,
"cds_start": 442,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 2454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "c.442G>T",
"hgvs_p": "p.Val148Phe",
"transcript": "NM_001406857.1",
"protein_id": "NP_001393786.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 441,
"cds_start": 442,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 684,
"cdna_end": null,
"cdna_length": 2522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "c.718G>T",
"hgvs_p": "p.Val240Phe",
"transcript": "NM_001406859.1",
"protein_id": "NP_001393788.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 404,
"cds_start": 718,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 1787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "n.*623G>T",
"hgvs_p": null,
"transcript": "ENST00000713936.1",
"protein_id": "ENSP00000519233.1",
"transcript_support_level": null,
"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": 3920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "n.718G>T",
"hgvs_p": null,
"transcript": "ENST00000713937.1",
"protein_id": "ENSP00000519234.1",
"transcript_support_level": null,
"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": 4141,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "n.*438G>T",
"hgvs_p": null,
"transcript": "ENST00000713939.1",
"protein_id": "ENSP00000519236.1",
"transcript_support_level": null,
"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": 2097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "n.*623G>T",
"hgvs_p": null,
"transcript": "ENST00000713936.1",
"protein_id": "ENSP00000519233.1",
"transcript_support_level": null,
"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": 3920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "n.*438G>T",
"hgvs_p": null,
"transcript": "ENST00000713939.1",
"protein_id": "ENSP00000519236.1",
"transcript_support_level": null,
"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": 2097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"hgvs_c": "n.644-245G>T",
"hgvs_p": null,
"transcript": "ENST00000713938.1",
"protein_id": "ENSP00000519235.1",
"transcript_support_level": null,
"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": 2306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124904198",
"gene_hgnc_id": null,
"hgvs_c": "n.72-8964C>A",
"hgvs_p": null,
"transcript": "XR_007066164.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RPE65",
"gene_hgnc_id": 10294,
"dbsnp": "rs192907397",
"frequency_reference_population": 0.000034700963,
"hom_count_reference_population": 0,
"allele_count_reference_population": 56,
"gnomad_exomes_af": 0.0000321581,
"gnomad_genomes_af": 0.0000591102,
"gnomad_exomes_ac": 47,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6491665244102478,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.459,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6378,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.689,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PP2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000262340.6",
"gene_symbol": "RPE65",
"hgnc_id": 10294,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.718G>T",
"hgvs_p": "p.Val240Phe"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_007066164.1",
"gene_symbol": "LOC124904198",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.72-8964C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Leber congenital amaurosis,Leber congenital amaurosis 2,Retinitis pigmentosa 20,Retinitis pigmentosa 87 with choroidal involvement",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:4",
"phenotype_combined": "Retinitis pigmentosa 20;Leber congenital amaurosis 2|Leber congenital amaurosis|Retinitis pigmentosa 20;Leber congenital amaurosis 2;Retinitis pigmentosa 87 with choroidal involvement|Retinitis pigmentosa 20",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}