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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: 12-55721847-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=55721847&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 55721847,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000257895.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157Trp",
"transcript": "NM_002905.5",
"protein_id": "NP_002896.2",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 318,
"cds_start": 469,
"cds_end": null,
"cds_length": 957,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 1274,
"mane_select": "ENST00000257895.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157Trp",
"transcript": "ENST00000257895.10",
"protein_id": "ENSP00000257895.6",
"transcript_support_level": 1,
"aa_start": 157,
"aa_end": null,
"aa_length": 318,
"cds_start": 469,
"cds_end": null,
"cds_length": 957,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 1274,
"mane_select": "NM_002905.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157Trp",
"transcript": "ENST00000548082.1",
"protein_id": "ENSP00000447128.1",
"transcript_support_level": 1,
"aa_start": 157,
"aa_end": null,
"aa_length": 318,
"cds_start": 469,
"cds_end": null,
"cds_length": 957,
"cdna_start": 611,
"cdna_end": null,
"cdna_length": 1259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"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": "ENSG00000258311",
"gene_hgnc_id": null,
"hgvs_c": "c.*141C>T",
"hgvs_p": null,
"transcript": "ENST00000550412.5",
"protein_id": "ENSP00000447650.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": -4,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3382,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157Trp",
"transcript": "NM_001199771.3",
"protein_id": "NP_001186700.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 318,
"cds_start": 469,
"cds_end": null,
"cds_length": 957,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 1279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "c.178C>T",
"hgvs_p": "p.Arg60Trp",
"transcript": "ENST00000547072.5",
"protein_id": "ENSP00000449927.1",
"transcript_support_level": 5,
"aa_start": 60,
"aa_end": null,
"aa_length": 221,
"cds_start": 178,
"cds_end": null,
"cds_length": 666,
"cdna_start": 505,
"cdna_end": null,
"cdna_length": 1054,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258311",
"gene_hgnc_id": null,
"hgvs_c": "n.*141C>T",
"hgvs_p": null,
"transcript": "ENST00000257899.3",
"protein_id": "ENSP00000257899.3",
"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": 745,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "n.479C>T",
"hgvs_p": null,
"transcript": "ENST00000548486.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 971,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "n.608C>T",
"hgvs_p": null,
"transcript": "ENST00000550608.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1419,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258311",
"gene_hgnc_id": null,
"hgvs_c": "n.*272C>T",
"hgvs_p": null,
"transcript": "ENST00000551946.5",
"protein_id": "ENSP00000450201.1",
"transcript_support_level": 2,
"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": 1024,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "n.479C>T",
"hgvs_p": null,
"transcript": "ENST00000553187.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 625,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S1-RDH5",
"gene_hgnc_id": null,
"hgvs_c": "n.528C>T",
"hgvs_p": null,
"transcript": "NR_037658.1",
"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": 1213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258311",
"gene_hgnc_id": null,
"hgvs_c": "n.*141C>T",
"hgvs_p": null,
"transcript": "ENST00000257899.3",
"protein_id": "ENSP00000257899.3",
"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": 745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258311",
"gene_hgnc_id": null,
"hgvs_c": "n.*272C>T",
"hgvs_p": null,
"transcript": "ENST00000551946.5",
"protein_id": "ENSP00000450201.1",
"transcript_support_level": 2,
"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": 1024,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "n.298+353C>T",
"hgvs_p": null,
"transcript": "ENST00000548123.1",
"protein_id": "ENSP00000447513.1",
"transcript_support_level": 3,
"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": 581,
"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": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "n.406-348C>T",
"hgvs_p": null,
"transcript": "ENST00000553160.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 522,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "c.*11C>T",
"hgvs_p": null,
"transcript": "ENST00000552930.5",
"protein_id": "ENSP00000448014.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 54,
"cds_start": -4,
"cds_end": null,
"cds_length": 167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 527,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258311",
"gene_hgnc_id": null,
"hgvs_c": "c.*141C>T",
"hgvs_p": null,
"transcript": "ENST00000549424.1",
"protein_id": "ENSP00000447621.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 44,
"cds_start": -4,
"cds_end": null,
"cds_length": 135,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"hgvs_c": "n.*19C>T",
"hgvs_p": null,
"transcript": "ENST00000547301.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RDH5",
"gene_hgnc_id": 9940,
"dbsnp": "rs104894374",
"frequency_reference_population": 0.000019827698,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000177871,
"gnomad_genomes_af": 0.0000394296,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9773889780044556,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.797,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6763,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.46,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.719,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000257895.10",
"gene_symbol": "RDH5",
"hgnc_id": 9940,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,SD,AD",
"hgvs_c": "c.469C>T",
"hgvs_p": "p.Arg157Trp"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000550412.5",
"gene_symbol": "ENSG00000258311",
"hgnc_id": null,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*141C>T",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_037658.1",
"gene_symbol": "BLOC1S1-RDH5",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.528C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive,Fundus albipunctatus,Pigmentary retinal dystrophy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Fundus albipunctatus, autosomal recessive|not provided|Pigmentary retinal dystrophy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}