Uncertain significance(17), Likely benign (1)
ClinVar Genomic variation as it relates to human health
GRCh38/hg38 15q11.2(chr15:22572809-23066575)x1
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(2)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Conflicting classifications of pathogenicity
Benign(1); conflicting data from submitters(1)
Benign(1); conflicting data from submitters(1)
2
no assertion criteria provided
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
GRCh38/hg38 15q11.2(chr15:22572809-23066575)x1
Variation ID: 144192 Accession: VCV000144192.3
- Type and length
-
copy number loss, 534,632 bp
- Location
-
Cytogenetic: 15q11.2 15: 22572809-23066575 (GRCh38) [ NCBI UCSC ] 15: 22765628-23300287 (GRCh37) [ NCBI UCSC ] 15: 20316992-20851728 (NCBI36) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Aug 31, 2015 Oct 26, 2017 Jul 18, 2014 - HGVS
-
Nucleotide Protein Molecular
consequenceNC_000015.10:g.(?_22572809)_(23066575_?)del NC_000015.9:g.(?_22765628)_(23300287_?)del NC_000015.8:g.(?_20316992)_(20851728_?)del - Protein change
- -
- Other names
- -
- Canonical SPDI
- -
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
-
dbVar: nssv13653540 dbVar: nssv1415497 dbVar: nssv1415504 dbVar: nssv1415524 dbVar: nssv1415525 dbVar: nssv1495458 dbVar: nssv1495470 dbVar: nssv1495474 dbVar: nssv1495475 dbVar: nssv1602220 dbVar: nssv1602716 dbVar: nssv1602739 dbVar: nssv1604117 dbVar: nssv1604662 dbVar: nssv1604678 dbVar: nssv1605198 dbVar: nssv1605203 dbVar: nssv1610150 dbVar: nssv3395824 dbVar: nssv575544 dbVar: nsv491728 VarSome
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| NIPA1 | No evidence available | No evidence available |
GRCh38 GRCh38 GRCh37 |
272 | 682 | |
| NIPA2 | No evidence available | No evidence available |
GRCh38 GRCh38 GRCh37 |
56 | 390 | |
| CYFIP1 | - | - |
GRCh38 GRCh38 GRCh38 GRCh37 |
112 | 453 | |
| LOC112272575 | - | - | - |
GRCh38 GRCh38 |
- | 129 |
| LOC112272576 | - | - | - | GRCh38 | - | 96 |
| LOC126862074 | - | - | - |
GRCh38 GRCh38 |
- | 120 |
| LOC130056707 | - | - | - |
GRCh38 GRCh38 |
- | 80 |
| LOC130056708 | - | - | - |
GRCh38 GRCh38 |
- | 93 |
| LOC130056709 | - | - | - |
GRCh38 GRCh38 |
- | 179 |
| LOC130056710 | - | - | - |
GRCh38 GRCh38 |
- | 112 |
There are 10 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38 , GRCh37 , NCBI36) and ClinGen Dosage Sensitivity Map.
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
|
See cases
|
Conflicting interpretations of pathogenicity (2) |
no assertion criteria provided
|
Jul 18, 2014 | RCV000133674.10 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
|---|---|---|---|---|---|
|
Benign
(May 27, 2010)
|
no assertion criteria provided
Method: clinical testing
|
See cases
Affected status: yes
Allele origin:
unknown
|
ISCA site 4
Additional submitter:
International Standards For Cytogenomic Arrays Consortium (ISCA)
Accession: SCV000173084.5
First in ClinVar: Aug 30, 2014 Last updated: Aug 31, 2015
Comments (2):
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For … (more)
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For data from the original published study, [Kaminsky, et al. 2011|/pubmed/21844811], please see [nstd101|/dbvar/studies/nstd101/]. (less)
|
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
|
|
|
conflicting data from submitters
(Jul 18, 2014)
|
no assertion criteria provided
Method: clinical testing
|
See cases
Affected status: yes
Allele origin:
paternal,
unknown,
de novo,
maternal
|
ISCA site 1
Additional submitter:
International Standards For Cytogenomic Arrays Consortium (ISCA)
Accession: SCV000173085.5
First in ClinVar: Aug 30, 2014 Last updated: Oct 26, 2017
Comments (2):
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For … (more)
Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter. For data from the original published study, [Kaminsky, et al. 2011|/pubmed/21844811], please see [nstd101|/dbvar/studies/nstd101/]. (less)
|
Comment:
Uncertain significance(17), Likely benign (1)
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Age: 0-9 years
Sex: female
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 3:
Number of individuals with the variant: 1
Clinical Features:
Hydrocephalus (present)
Method: Microarray
Result:
Pass
Observation 4:
Number of individuals with the variant: 1
Clinical Features:
Autism (present)
Method: Microarray
Result:
Pass
Observation 5:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 6:
Number of individuals with the variant: 1
Clinical Features:
Cerebral palsy (present)
Method: Microarray
Result:
Pass
Observation 7:
Number of individuals with the variant: 1
Clinical Features:
Autism (present)
Method: Microarray
Result:
Pass
Observation 8:
Number of individuals with the variant: 1
Clinical Features:
Microcephaly (present)
Method: Microarray
Result:
Pass
Observation 9:
Number of individuals with the variant: 1
Clinical Features:
Encephalopathy (present)
Method: Microarray
Result:
Pass
Observation 10:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present) , Bilateral ptosis (present)
Method: Microarray
Result:
Pass
Observation 11:
Number of individuals with the variant: 1
Clinical Features:
Autism (present)
Method: Microarray
Result:
Pass
Observation 12:
Number of individuals with the variant: 1
Clinical Features:
Tetralogy of Fallot (present) , Aplasia/Hypoplasia of the nails (present) , Clinodactyly (present)
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 13:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
Observation 14:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Result:
Pass
Observation 15:
Number of individuals with the variant: 1
Clinical Features:
Hyperactivity (present) , Delayed gross motor development (present)
Method: Microarray
Result:
Pass
Observation 16:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Age: 0-9 years
Sex: male
Ethnicity/Population group: human
Method: Microarray
Result:
Pass
Observation 17:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present)
Method: Microarray
Result:
Pass
Observation 18:
Number of individuals with the variant: 1
Clinical Features:
Developmental delay AND/OR other significant developmental or morphological phenotypes (present)
Method: Microarray
Result:
Pass
|
Comment:
Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Comment:
Uncertain significance(17), Likely benign (1)
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated May 08, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.