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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: 9-123371419-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=123371419&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 123371419,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000373631.8",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2277G>A",
"hgvs_p": "p.Trp759*",
"transcript": "NM_173689.7",
"protein_id": "NP_775960.4",
"transcript_support_level": null,
"aa_start": 759,
"aa_end": null,
"aa_length": 1285,
"cds_start": 2277,
"cds_end": null,
"cds_length": 3858,
"cdna_start": 2341,
"cdna_end": null,
"cdna_length": 5613,
"mane_select": "ENST00000373631.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2277G>A",
"hgvs_p": "p.Trp759*",
"transcript": "ENST00000373631.8",
"protein_id": "ENSP00000362734.3",
"transcript_support_level": 1,
"aa_start": 759,
"aa_end": null,
"aa_length": 1285,
"cds_start": 2277,
"cds_end": null,
"cds_length": 3858,
"cdna_start": 2341,
"cdna_end": null,
"cdna_length": 5613,
"mane_select": "NM_173689.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2277G>A",
"hgvs_p": "p.Trp759*",
"transcript": "ENST00000359999.7",
"protein_id": "ENSP00000353092.3",
"transcript_support_level": 2,
"aa_start": 759,
"aa_end": null,
"aa_length": 1176,
"cds_start": 2277,
"cds_end": null,
"cds_length": 3531,
"cdna_start": 2368,
"cdna_end": null,
"cdna_length": 3659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2277G>A",
"hgvs_p": "p.Trp759*",
"transcript": "XM_011518556.4",
"protein_id": "XP_011516858.1",
"transcript_support_level": null,
"aa_start": 759,
"aa_end": null,
"aa_length": 1276,
"cds_start": 2277,
"cds_end": null,
"cds_length": 3831,
"cdna_start": 2341,
"cdna_end": null,
"cdna_length": 5586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2163G>A",
"hgvs_p": "p.Trp721*",
"transcript": "XM_047423244.1",
"protein_id": "XP_047279200.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 1247,
"cds_start": 2163,
"cds_end": null,
"cds_length": 3744,
"cdna_start": 2227,
"cdna_end": null,
"cdna_length": 5499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2163G>A",
"hgvs_p": "p.Trp721*",
"transcript": "XM_047423245.1",
"protein_id": "XP_047279201.1",
"transcript_support_level": null,
"aa_start": 721,
"aa_end": null,
"aa_length": 1238,
"cds_start": 2163,
"cds_end": null,
"cds_length": 3717,
"cdna_start": 2227,
"cdna_end": null,
"cdna_length": 5472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2082G>A",
"hgvs_p": "p.Trp694*",
"transcript": "XM_011518557.4",
"protein_id": "XP_011516859.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 1220,
"cds_start": 2082,
"cds_end": null,
"cds_length": 3663,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 5614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.2082G>A",
"hgvs_p": "p.Trp694*",
"transcript": "XM_011518558.4",
"protein_id": "XP_011516860.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 1220,
"cds_start": 2082,
"cds_end": null,
"cds_length": 3663,
"cdna_start": 2733,
"cdna_end": null,
"cdna_length": 6005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "c.1281G>A",
"hgvs_p": "p.Trp427*",
"transcript": "XM_005251934.4",
"protein_id": "XP_005251991.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 953,
"cds_start": 1281,
"cds_end": null,
"cds_length": 2862,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 4663,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "n.1281G>A",
"hgvs_p": null,
"transcript": "ENST00000460253.1",
"protein_id": "ENSP00000435279.1",
"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": 3947,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"hgvs_c": "n.1391G>A",
"hgvs_p": null,
"transcript": "NR_104603.2",
"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": 3949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CRB2",
"gene_hgnc_id": 18688,
"dbsnp": "rs375072557",
"frequency_reference_population": 0.00007566924,
"hom_count_reference_population": 0,
"allele_count_reference_population": 122,
"gnomad_exomes_af": 0.0000821867,
"gnomad_genomes_af": 0.0000131415,
"gnomad_exomes_ac": 120,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5400000214576721,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.865,
"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": 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": "ENST00000373631.8",
"gene_symbol": "CRB2",
"hgnc_id": 18688,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2277G>A",
"hgvs_p": "p.Trp759*"
}
],
"clinvar_disease": "Ventriculomegaly-cystic kidney disease,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Ventriculomegaly-cystic kidney disease|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}