VCV003062004.1 - ClinVar

GRCh38/hg38 15q11.2-13.1(chr15:22612582-29993699)

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 15q11.2-13.1(chr15:22612582-29993699)

Variation ID: 3062004 Accession: VCV003062004.1

Type and length

copy number gain, -

Location

Cytogenetic: 15q11.2-13.1 15: 22612582-29993699 (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	Mar 23, 2024	Mar 23, 2024	Jan 15, 2024

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.
UBE3A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	40	1234
MAGEL2		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh38 GRCh37	1055	1359
SNURF	-	Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	-	370
ATP10A		No evidence available	No evidence available	GRCh38 GRCh37	197	504
GABRB3		No evidence available	No evidence available	GRCh38 GRCh37	649	963
MKRN3		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	72	376
NDN		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	41	344
NIPA1		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	275	686
NIPA2		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	56	391
SNORD107	-	No evidence available	No evidence available	GRCh38	-	153

There are 181 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.
15q11q13 microduplication syndrome	Pathogenic (1)	criteria provided, single submitter	Jan 15, 2024	RCV003985067.2

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 15, 2024)	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019) Method: clinical testing	15q11q13 microduplication syndrome Affected status: yes Allele origin: germline	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan Accession: SCV004801375.1 First in ClinVar: Mar 23, 2024 Last updated: Mar 23, 2024	Comment: Maternal isodicentric chromosome 15 (idic(15)) The variant was initially identified through a Next Generation Sequencing (NGS) gene panel with bioinformatic prediction of copy number variants … (more) Maternal isodicentric chromosome 15 (idic(15)) The variant was initially identified through a Next Generation Sequencing (NGS) gene panel with bioinformatic prediction of copy number variants (CNVs), sequenced on a MiSeq sequencer. Subsequently, it was confirmed using multiplex ligation-dependent probe amplification (MLPA, SALSA MLPA Probemix ME028 Prader-Willi/Angelman version C1), which includes both copy number variations and methylation status of the 15q11 region. The observed copy number gains were as follows: asymmetrical breakpoints cen-BP3 (4 copies), BP3-BP4 (3 copies). Additionally, this copy number gain was also studied through karyotype (Giemsa-Trypsin banding from peripheral blood lymphocytes using standard G-banding-procedures) and fluorescence in situ hybridization (FISH, on metaphase chromosomes and interphase nucleus, using the Prader-Willi/Angelman Critical Region probe SNRPN; Vysis, Abbott Laboratories, USA). Finally, the genomic content of this chromosomal rearrangement was characterized by array comparative genomic hybridization (a-CGH, SurePrint G3 Unrestricted CGH ISCA v2, 8x60K oligo-array; Analysis software: Agilent CytoGenomics 5.2.1.4; Equipment: SureScan Microarray Scanner, Agilent Technologies, USA). 47,XY,+mar.ish idic(15)(q12)(SNRPN++).arr[GRCh38] 15q11.2q13.1(22612582_28435882x4,28785312_29993699x3) (less) Clinical Features: Epileptic spasm (present) Geographic origin: Argentina

Comment:

Maternal isodicentric chromosome 15 (idic(15)) The variant was initially identified through a Next Generation Sequencing (NGS) gene panel with bioinformatic prediction of copy number variants (CNVs), sequenced on a MiSeq sequencer. Subsequently, it was confirmed using multiplex ligation-dependent probe amplification (MLPA, SALSA MLPA Probemix ME028 Prader-Willi/Angelman version C1), which includes both copy number variations and methylation status of the 15q11 region. The observed copy number gains were as follows: asymmetrical breakpoints cen-BP3 (4 copies), BP3-BP4 (3 copies). Additionally, this copy number gain was also studied through karyotype (Giemsa-Trypsin banding from peripheral blood lymphocytes using standard G-banding-procedures) and fluorescence in situ hybridization (FISH, on metaphase chromosomes and interphase nucleus, using the Prader-Willi/Angelman Critical Region probe SNRPN; Vysis, Abbott Laboratories, USA). Finally, the genomic content of this chromosomal rearrangement was characterized by array comparative genomic hybridization (a-CGH, SurePrint G3 Unrestricted CGH ISCA v2, 8x60K oligo-array; Analysis software: Agilent CytoGenomics 5.2.1.4; Equipment: SureScan Microarray Scanner, Agilent Technologies, USA). 47,XY,+mar.ish idic(15)(q12)(SNRPN++).arr[GRCh38] 15q11.2q13.1(22612582_28435882x4,28785312_29993699x3)

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 Jun 23, 2024

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 15q11.2-13.1(chr15:22612582-29993699)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...