VCV000146154.3 - ClinVar

GRCh38/hg38 15q11.2(chr15:22572809-23066575)x3

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

Conflicting classifications of pathogenicity
Uncertain significance (1); Benign (2)

3 out of 3 submissions contributed to this classification

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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh38/hg38 15q11.2(chr15:22572809-23066575)x3

Variation ID: 146154 Accession: VCV000146154.3

Type and length

copy number gain, 601,738 bp

Location

Cytogenetic: 15q11.2 15: 22572809-23066575 (GRCh38) [ NCBI UCSC ] 15: 22698522-23300287 (GRCh37) [ NCBI UCSC ] 15: 20249886-20851728 (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	Jul 13, 2015	Mar 14, 2017	Oct 19, 2010

HGVS

Nucleotide	Protein	Molecular consequence
NC_000015.10:g.(?_22572809)_(23066575_?)dup
NC_000015.9:g.(?_22698522)_(23300287_?)dup
NC_000015.8:g.(?_20249886)_(20851728_?)dup

Protein change

Other names

Canonical SPDI

Global minor allele frequency (GMAF) Help The 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: nssv576845 dbVar: nssv582016 dbVar: nssv707166 dbVar: nsv529157 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
Gene	OMIM	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	295	734
NIPA2		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	98	450
CYFIP1		-	-	GRCh38 GRCh38 GRCh38 GRCh37	222	593
LOC112272575	-	-	-	GRCh38 GRCh38	-	153
LOC112272576	-	-	-	GRCh38	-	108
LOC126862074	-	-	-	GRCh38 GRCh38	-	136
LOC130056707	-	-	-	GRCh38 GRCh38	-	90
LOC130056708	-	-	-	GRCh38 GRCh38	-	105
LOC130056709	-	-	-	GRCh38 GRCh38	-	203
LOC130056710	-	-	-	GRCh38 GRCh38	-	125

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 classifications of pathogenicity (3)	no assertion criteria provided	Oct 19, 2010	RCV000135477.12

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.	Expand all rows Collapse all rows 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 (Jul 30, 2009) C Contributing to aggregate classification	no assertion criteria provided	See cases	ISCA site 17 Additional submitter: International Standards For Cytogenomic Arrays Consortium (ISCA) Accession: SCV000196262.2 First in ClinVar: Jan 02, 2015 Last updated: Jul 13, 2015 Comment: Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.	Publications: PubMed (1) PubMed: 20466091 Observation: 1 Collection method: clinical testing Allele origin: unknown Affected status: yes more Observation 1 Collection method: clinical testing Allele origin: unknown Affected status: yes Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Platform type: Oligo aCGH Platform name: Agilent 023097 Method: Microarray

Uncertain significance (Oct 19, 2010) C Contributing to aggregate classification	no assertion criteria provided	See cases	ISCA site 8 Additional submitter: International Standards For Cytogenomic Arrays Consortium (ISCA) Accession: SCV000175214.3 First in ClinVar: Aug 30, 2014 Last updated: Jul 13, 2015 Comment: Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.	Publications: PubMed (1) PubMed: 20466091 Observation: 1 Collection method: clinical testing Allele origin: unknown Affected status: yes more Observation 1 Collection method: clinical testing Allele origin: unknown Affected status: yes Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Platform type: Oligo aCGH Platform name: Cyto Custom HD-CGH Microarray (4x44K) design ID 16267 Method: Microarray

Benign (Jan 30, 2010) C Contributing to aggregate classification	no assertion criteria provided	See cases	ISCA site 4 Additional submitter: International Standards For Cytogenomic Arrays Consortium (ISCA) Accession: SCV000196263.3 First in ClinVar: Jan 02, 2015 Last updated: Mar 14, 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)	Publications: PubMed (1) PubMed: 20466091 Observation: 1 Collection method: clinical testing Allele origin: unknown Affected status: yes more Observation 1 Collection method: clinical testing Allele origin: unknown Affected status: yes Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Platform type: Oligo aCGH Platform name: ISCA 44K 024614, v2 Method: Microarray

Citations for germline classification of this variant

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 ...

Record last updated Jan 19, 2025