VCV003235943.1 - ClinVar

GRCh38/hg38 15q11.2(chr15:22600363-23120182)

Germline

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.

(1)

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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh38/hg38 15q11.2(chr15:22600363-23120182)

Variation ID: 3235943 Accession: VCV003235943.1

Type and length

copy number loss, -

Location

Cytogenetic: 15q11.2 15: 22288167-23409060 (GRCh38) [ 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	May 19, 2024	May 19, 2024	Feb 1, 2022

HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

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

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	274	685
NIPA2		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	56	391
CYFIP1		-	-	GRCh38 GRCh38 GRCh38 GRCh37	112	454
GOLGA6L1	-	-	-	GRCh38 GRCh38 GRCh38 GRCh38 GRCh37	10	110
GOLGA6L22	-	-	-	GRCh38 GRCh38	7	44
GOLGA6L26	-	-	-	GRCh38 GRCh38	-	101
GOLGA8S	-	-	-	GRCh38 GRCh38	4	106
LOC112272575	-	-	-	GRCh38 GRCh38	-	129
LOC112272576	-	-	-	GRCh38	-	96
LOC126862074	-	-	-	GRCh38 GRCh38	-	120

There are 16 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38).

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.
Chromosome 15q11.2 deletion syndrome	Pathogenic (1)	criteria provided, single submitter	Feb 1, 2022	RCV004555204.1

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.
Pathogenic (Feb 01, 2022)	criteria provided, single submitter (NYGC Assertion Criteria 2020) Method: clinical testing	Chromosome 15q11.2 deletion syndrome Affected status: unknown Allele origin: de novo	New York Genome Center Study: PrenatalSEQ Accession: SCV005044166.1 First in ClinVar: May 19, 2024 Last updated: May 19, 2024	Comment: The de novo interstitial 15q11.2 BP1-BP2 deletion identified in this fetus contains 4 OMIM associated genes (NIPA1, NIPA2, CYFIP1, and TUBGCP5). This proximal 15q11.2 region … (more) The de novo interstitial 15q11.2 BP1-BP2 deletion identified in this fetus contains 4 OMIM associated genes (NIPA1, NIPA2, CYFIP1, and TUBGCP5). This proximal 15q11.2 region harbors a cluster of low copy repeats that lead to recurrent copy number changes in this region. Deletions in this region are associated with 15q11.2 BP1-BP2 recurrent deletion syndrome. The 15q11.2 BP1-BP2 microdeletion is associated with both phenotypic variability as well as reduced penetrance, and while it is enriched in patient populations (PMID:25689425, 28387067), it is also often inherited from asymptomatic parents (PMID:21841781, 23258348, 25689425). (less) Number of individuals with the variant: 1 Clinical Features: Congenital diaphragmatic hernia (present) , Pulmonary hypoplasia (present) , Bilateral fetal pyelectasis (present) , Pulmonary arterial hypertension (present) Age: 30-39 weeks gestation Secondary finding: no

Comment:

The de novo interstitial 15q11.2 BP1-BP2 deletion identified in this fetus contains 4 OMIM associated genes (NIPA1, NIPA2, CYFIP1, and TUBGCP5). This proximal 15q11.2 region harbors a cluster of low copy repeats that lead to recurrent copy number changes in this region. Deletions in this region are associated with 15q11.2 BP1-BP2 recurrent deletion syndrome. The 15q11.2 BP1-BP2 microdeletion is associated with both phenotypic variability as well as reduced penetrance, and while it is enriched in patient populations (PMID:25689425, 28387067), it is also often inherited from asymptomatic parents (PMID:21841781, 23258348, 25689425).

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:

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 Aug 25, 2024

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 15q11.2(chr15:22600363-23120182)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...