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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: 2-208124338-TCCTC-GTGATCTGCAAGG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=208124338&ref=TCCTC&alt=GTGATCTGCAAGG&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 208124338,
"ref": "TCCTC",
"alt": "GTGATCTGCAAGG",
"effect": "frameshift_variant,missense_variant",
"transcript": "ENST00000264376.5",
"consequences": [
{
"aa_ref": "ED",
"aa_alt": "PCRS?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYGD",
"gene_hgnc_id": 2411,
"hgvs_c": "c.22_26delGAGGAinsCCTTGCAGATCAC",
"hgvs_p": "p.Glu8fs",
"transcript": "NM_006891.4",
"protein_id": "NP_008822.2",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 174,
"cds_start": 22,
"cds_end": null,
"cds_length": 525,
"cdna_start": 77,
"cdna_end": null,
"cdna_length": 642,
"mane_select": "ENST00000264376.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "ED",
"aa_alt": "PCRS?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYGD",
"gene_hgnc_id": 2411,
"hgvs_c": "c.22_26delGAGGAinsCCTTGCAGATCAC",
"hgvs_p": "p.Glu8fs",
"transcript": "ENST00000264376.5",
"protein_id": "ENSP00000264376.4",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 174,
"cds_start": 22,
"cds_end": null,
"cds_length": 525,
"cdna_start": 77,
"cdna_end": null,
"cdna_length": 642,
"mane_select": "NM_006891.4",
"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": "ENSG00000295187",
"gene_hgnc_id": null,
"hgvs_c": "n.100+5113_100+5117delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null,
"transcript": "ENST00000728538.1",
"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": 466,
"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": "ENSG00000295187",
"gene_hgnc_id": null,
"hgvs_c": "n.117+5113_117+5117delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null,
"transcript": "ENST00000728539.1",
"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": 458,
"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": "ENSG00000295187",
"gene_hgnc_id": null,
"hgvs_c": "n.125-1032_125-1028delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null,
"transcript": "ENST00000728540.1",
"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": 503,
"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": "ENSG00000295187",
"gene_hgnc_id": null,
"hgvs_c": "n.118-1032_118-1028delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null,
"transcript": "ENST00000728541.1",
"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": 483,
"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": "LOC100507443",
"gene_hgnc_id": null,
"hgvs_c": "n.97+5113_97+5117delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null,
"transcript": "NR_038437.1",
"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": 437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CRYGD",
"gene_hgnc_id": 2411,
"dbsnp": "rs1553584085",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"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": 6.011,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Strong",
"PM2"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000264376.5",
"gene_symbol": "CRYGD",
"hgnc_id": 2411,
"effects": [
"frameshift_variant",
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.22_26delGAGGAinsCCTTGCAGATCAC",
"hgvs_p": "p.Glu8fs"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NR_038437.1",
"gene_symbol": "LOC100507443",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.97+5113_97+5117delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000728538.1",
"gene_symbol": "ENSG00000295187",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.100+5113_100+5117delTCCTCinsGTGATCTGCAAGG",
"hgvs_p": null
}
],
"clinvar_disease": "Aculeiform cataract",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Aculeiform cataract",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}