VCV000805881.1 - ClinVar

GRCh37/hg19 15q26.2-26.3(chr15:96878099-102397836)x1

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

GRCh37/hg19 15q26.2-26.3(chr15:96878099-102397836)x1

Variation ID: 805881 Accession: VCV000805881.1

Type and length

copy number loss, -

Location

Cytogenetic: 15q26.2-26.3 15: 96878099-102397836 (GRCh37) [ 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	Jan 23, 2020	Jan 23, 2020	Jan 6, 2020

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.

loss_of_function_variant; Sequence Ontology [ SO:0002054]

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.
IGF1R		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1013	1156
NR2F2		No evidence available	No evidence available	GRCh38 GRCh37	120	179
ADAMTS17		-	-	GRCh38 GRCh37	1210	1324
ALDH1A3		-	-	GRCh38 GRCh37	36	227
ARRDC4		-	-	GRCh38 GRCh37	30	99
ASB7		-	-	GRCh38 GRCh37	14	111
CERS3		-	-	GRCh38 GRCh37	85	203
CHSY1		-	-	GRCh38 GRCh37	190	332
LINS1		-	-	GRCh38 GRCh37	188	287
LRRC28	-	-	-	GRCh38 GRCh37	20	118

There are 14 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) 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.
Chromosome 15q26-qter deletion syndrome	Pathogenic (1)	criteria provided, single submitter	Jan 6, 2020	RCV000993689.2

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 (Jan 06, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Chromosome 15q26-qter deletion syndrome (Sporadic) Affected status: yes Allele origin: de novo	Cytogenomics Laboratory, University of Sao Paulo Accession: SCV001135146.1 First in ClinVar: Jan 23, 2020 Last updated: Jan 23, 2020	Comment: Chromosome 15q26-qter deletion syndrome is a genetic condition that generally affects development and growth. It was first described in 1977 by Drayer et al., who … (more) Chromosome 15q26-qter deletion syndrome is a genetic condition that generally affects development and growth. It was first described in 1977 by Drayer et al., who described two siblings with intellectual disability and multiple congenital abnormalities, including facial dysmorphic features and skeletal abnormalities (Jezela-Stanek et al., 2012; Poot et al., 2013; Rump et al., 2008). There have been few reports to date on chromosome 15q26-qter deletion syndrome, which is considered rare. Indeed, there have been only 24 cases of deletions described in the literature, with variations in the associated clinical characteristics and phenotypes (Bhakta et al., 2005; Bruce et al., 2010; Jezela-Stanek et al., 2012; Okubo et al., 2003; Poot et al., 2007; Poot et al., 2013; Roback et al., 1991; Siebler et al., 1995). (less) Clinical Features: Association with the PWS phenotype (present) Indication for testing: Array Age: 20-29 years Sex: female Geographic origin: Brazil Method: For SNP microarray testing, the iScanSQ system (Illumina BeadArray Technology) and HumanCytoSNP-12 BeadChipÂ® (Illumina Inc., San Diego, CA, USA) were used in accordance with the manufacturerâ€™s instructions. The slide was then scanned in the iScan ReaderÂ® and data analysis was conducted using the Illumina GenomeStudio software package, version 2010.1Â® and the KaryoStudio software, version 1.4.3.0 Build 37Â® (CNV Plugin V3.0.7.0). The results were compared to the database of genomic variants (DGV), Database of genomic variation and phenotype in humans using ensembl resources (DECIPHER) and UCSC Genome Bioinformatics (hg 19).

Comment:

Chromosome 15q26-qter deletion syndrome is a genetic condition that generally affects development and growth. It was first described in 1977 by Drayer et al., who described two siblings with intellectual disability and multiple congenital abnormalities, including facial dysmorphic features and skeletal abnormalities (Jezela-Stanek et al., 2012; Poot et al., 2013; Rump et al., 2008). There have been few reports to date on chromosome 15q26-qter deletion syndrome, which is considered rare. Indeed, there have been only 24 cases of deletions described in the literature, with variations in the associated clinical characteristics and phenotypes (Bhakta et al., 2005; Bruce et al., 2010; Jezela-Stanek et al., 2012; Okubo et al., 2003; Poot et al., 2007; Poot et al., 2013; Roback et al., 1991; Siebler et al., 1995).

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
loss_of_function_variant (SO:0002054)			Cytogenomics Laboratory, University of Sao Paulo Accession: SCV001135146.1

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 Jun 23, 2024

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 15q26.2-26.3(chr15:96878099-102397836)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...