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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: 6-63720735-ACGATATTTAC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=63720735&ref=ACGATATTTAC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 63720735,
"ref": "ACGATATTTAC",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "ENST00000503581.6",
"consequences": [
{
"aa_ref": "VNIV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EYS",
"gene_hgnc_id": 21555,
"hgvs_c": "c.9286_9295delGTAAATATCG",
"hgvs_p": "p.Val3096fs",
"transcript": "NM_001142800.2",
"protein_id": "NP_001136272.1",
"transcript_support_level": null,
"aa_start": 3096,
"aa_end": null,
"aa_length": 3144,
"cds_start": 9286,
"cds_end": null,
"cds_length": 9435,
"cdna_start": 9834,
"cdna_end": null,
"cdna_length": 10590,
"mane_select": "ENST00000503581.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VNIV",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EYS",
"gene_hgnc_id": 21555,
"hgvs_c": "c.9286_9295delGTAAATATCG",
"hgvs_p": "p.Val3096fs",
"transcript": "ENST00000503581.6",
"protein_id": "ENSP00000424243.1",
"transcript_support_level": 5,
"aa_start": 3096,
"aa_end": null,
"aa_length": 3144,
"cds_start": 9286,
"cds_end": null,
"cds_length": 9435,
"cdna_start": 9834,
"cdna_end": null,
"cdna_length": 10590,
"mane_select": "NM_001142800.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VNIV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EYS",
"gene_hgnc_id": 21555,
"hgvs_c": "c.9349_9358delGTAAATATCG",
"hgvs_p": "p.Val3117fs",
"transcript": "ENST00000370621.7",
"protein_id": "ENSP00000359655.3",
"transcript_support_level": 1,
"aa_start": 3117,
"aa_end": null,
"aa_length": 3165,
"cds_start": 9349,
"cds_end": null,
"cds_length": 9498,
"cdna_start": 9885,
"cdna_end": null,
"cdna_length": 10485,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "NM_001370348.2",
"protein_id": "NP_001357277.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2039,
"cds_start": -4,
"cds_end": null,
"cds_length": 6120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18797,
"mane_select": "ENST00000262043.8",
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "ENST00000262043.8",
"protein_id": "ENSP00000262043.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2039,
"cds_start": -4,
"cds_end": null,
"cds_length": 6120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18797,
"mane_select": "NM_001370348.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "VNIV",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EYS",
"gene_hgnc_id": 21555,
"hgvs_c": "c.9349_9358delGTAAATATCG",
"hgvs_p": "p.Val3117fs",
"transcript": "NM_001292009.2",
"protein_id": "NP_001278938.1",
"transcript_support_level": null,
"aa_start": 3117,
"aa_end": null,
"aa_length": 3165,
"cds_start": 9349,
"cds_end": null,
"cds_length": 9498,
"cdna_start": 9897,
"cdna_end": null,
"cdna_length": 10653,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "NM_015153.4",
"protein_id": "NP_055968.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2039,
"cds_start": -4,
"cds_end": null,
"cds_length": 6120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18449,
"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": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "NM_001290259.2",
"protein_id": "NP_001277188.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1951,
"cds_start": -4,
"cds_end": null,
"cds_length": 5856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18990,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "NM_001370349.2",
"protein_id": "NP_001357278.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1951,
"cds_start": -4,
"cds_end": null,
"cds_length": 5856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18528,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "NM_001370350.2",
"protein_id": "NP_001357279.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1308,
"cds_start": -4,
"cds_end": null,
"cds_length": 3927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 17014,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "XM_011535648.4",
"protein_id": "XP_011533950.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2048,
"cds_start": -4,
"cds_end": null,
"cds_length": 6147,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 19141,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "XM_047418528.1",
"protein_id": "XP_047274484.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1951,
"cds_start": -4,
"cds_end": null,
"cds_length": 5856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 19011,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "XM_047418529.1",
"protein_id": "XP_047274485.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1951,
"cds_start": -4,
"cds_end": null,
"cds_length": 5856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18714,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null,
"transcript": "XM_047418530.1",
"protein_id": "XP_047274486.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1951,
"cds_start": -4,
"cds_end": null,
"cds_length": 5856,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 18642,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PHF3",
"gene_hgnc_id": 8921,
"hgvs_c": "c.361+9375_361+9384delGATATTTACC",
"hgvs_p": null,
"transcript": "ENST00000505138.1",
"protein_id": "ENSP00000421417.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EYS",
"gene_hgnc_id": 21555,
"dbsnp": "rs770748359",
"frequency_reference_population": 0.00010455984,
"hom_count_reference_population": 1,
"allele_count_reference_population": 162,
"gnomad_exomes_af": 0.00010234,
"gnomad_genomes_af": 0.000124964,
"gnomad_exomes_ac": 143,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.106,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000503581.6",
"gene_symbol": "EYS",
"hgnc_id": 21555,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.9286_9295delGTAAATATCG",
"hgvs_p": "p.Val3096fs"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000262043.8",
"gene_symbol": "PHF3",
"hgnc_id": 8921,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*7029_*7038delGATATTTACC",
"hgvs_p": null
}
],
"clinvar_disease": "EYS-related disorder,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 25,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10 LP:1",
"phenotype_combined": "Retinitis pigmentosa 25|not provided|Retinitis pigmentosa|Retinal dystrophy|EYS-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}