CNV Annotation
Available parameters and response documentation is available here
GET /lookup/cnv/chr1:122:5235:DEL/1019
{
"pos": 122,
"chromosome": "chr1",
"length": 5113,
"type": "deletion",
"end": 5235,
"publication_counts": [
{
"type": "region",
"id": "1019:chr1:122..5235",
"count": 0
}
],
"regions": {
"tcag_dgv": {
"version": "30-Jun-2021",
"items": [
{
"dgvregionjson": {
"accession": "nsv482937",
"observations": {
"observed_gains": 0,
"observed_losses": 1,
"samplesize": 39
},
"pubmedids": null,
"sv_type": "loss"
},
"absolute_positon": 0,
"chromo": "chr1",
"length": 2300000,
"position": 1
}
]
}
},
"coding_gene_id": [],
"coding_genes": null,
"exon": null,
"gene_symbol": null,
"gene_id": null,
"genes": [],
"transcripts": [],
"camouflaged_regions": [],
"sv_acmg_annotation": {
"verdict": {
"saphetor_class": "Benign",
"saphetor_score": -1.0,
"verdict": "Benign",
"approx_score": -1.6
},
"classifications": [
{
"saphetor_class": "Benign",
"approx_score": 0.0,
"saphetor_score": -1.0,
"acmg_class": "Uncertain Significance",
"name": "Gene",
"saphetor_user_explain": {
"Benign": [
"This structural variant affects 0 coding genes."
]
}
},
{
"saphetor_class": "Uncertain Significance",
"approx_score": -0.6,
"saphetor_score": 0.0,
"acmg_class": "Uncertain Significance",
"name": "Content",
"user_explain": {
"Uncertain Significance": [
"This structural variant doesn't affect any known domain or coding genes."
]
}
},
{
"saphetor_class": "Uncertain Significance",
"approx_score": 0.0,
"saphetor_score": 0.0,
"acmg_class": "Uncertain Significance",
"name": "Inheritance"
},
{
"saphetor_class": "Uncertain Significance",
"approx_score": 0.0,
"saphetor_score": 0.0,
"acmg_class": "Uncertain Significance",
"name": "Literature"
},
{
"saphetor_class": "Uncertain Significance",
"approx_score": -1.0,
"saphetor_score": 0.0,
"acmg_class": "Benign",
"name": "Overlap",
"user_explain": {
"Benign": [
"Found 1 reported benign cnv reported by DGV."
]
}
}
],
"sample_findings": {
"mode_of_inheritance": "Assumed AD/AR."
},
"version_name": "12.1.1"
},
"deleted_data_reason": null,
"publications": {
"regions": [
{
"referenced_by": [
"DGV"
],
"pub_med_id": 15286789
}
],
"genes": []
},
"cytobands": "1p36.33"
}