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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: 14-67729209-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=67729209&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 67729209,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000551171.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH12",
"gene_hgnc_id": 19977,
"hgvs_c": "c.677A>G",
"hgvs_p": "p.Tyr226Cys",
"transcript": "NM_152443.3",
"protein_id": "NP_689656.2",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 316,
"cds_start": 677,
"cds_end": null,
"cds_length": 951,
"cdna_start": 1001,
"cdna_end": null,
"cdna_length": 1878,
"mane_select": "ENST00000551171.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH12",
"gene_hgnc_id": 19977,
"hgvs_c": "c.677A>G",
"hgvs_p": "p.Tyr226Cys",
"transcript": "ENST00000551171.6",
"protein_id": "ENSP00000449079.1",
"transcript_support_level": 1,
"aa_start": 226,
"aa_end": null,
"aa_length": 316,
"cds_start": 677,
"cds_end": null,
"cds_length": 951,
"cdna_start": 1001,
"cdna_end": null,
"cdna_length": 1878,
"mane_select": "NM_152443.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH12",
"gene_hgnc_id": 19977,
"hgvs_c": "c.677A>G",
"hgvs_p": "p.Tyr226Cys",
"transcript": "ENST00000267502.3",
"protein_id": "ENSP00000267502.3",
"transcript_support_level": 5,
"aa_start": 226,
"aa_end": null,
"aa_length": 316,
"cds_start": 677,
"cds_end": null,
"cds_length": 951,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 1833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH12",
"gene_hgnc_id": 19977,
"hgvs_c": "c.677A>G",
"hgvs_p": "p.Tyr226Cys",
"transcript": "XM_047430965.1",
"protein_id": "XP_047286921.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 316,
"cds_start": 677,
"cds_end": null,
"cds_length": 951,
"cdna_start": 1035,
"cdna_end": null,
"cdna_length": 1912,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RDH12",
"gene_hgnc_id": 19977,
"hgvs_c": "n.46A>G",
"hgvs_p": null,
"transcript": "ENST00000552873.1",
"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": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.*533T>C",
"hgvs_p": null,
"transcript": "XM_047431173.1",
"protein_id": "XP_047287129.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2497,
"cds_start": -4,
"cds_end": null,
"cds_length": 7494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "n.3288+2T>C",
"hgvs_p": null,
"transcript": "ENST00000394455.6",
"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": 4134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "GPHN",
"gene_hgnc_id": 15465,
"hgvs_c": "c.1313-5986A>G",
"hgvs_p": null,
"transcript": "XM_047430879.1",
"protein_id": "XP_047286835.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 485,
"cds_start": -4,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RDH12",
"gene_hgnc_id": 19977,
"dbsnp": "rs28940313",
"frequency_reference_population": 0.0000012403254,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.84756e-7,
"gnomad_genomes_af": 0.00000657436,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9805769920349121,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.844,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4037,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.207,
"phylop100way_prediction": "Uncertain_significance",
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000551171.6",
"gene_symbol": "RDH12",
"hgnc_id": 19977,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.677A>G",
"hgvs_p": "p.Tyr226Cys"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000394455.6",
"gene_symbol": "ZFYVE26",
"hgnc_id": 20761,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.3288+2T>C",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XM_047430879.1",
"gene_symbol": "GPHN",
"hgnc_id": 15465,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1313-5986A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Leber congenital amaurosis 13,Retinal dystrophy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:1",
"phenotype_combined": "Leber congenital amaurosis 13|Retinal dystrophy|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}