VCV001328443.4 - ClinVar

GRCh37/hg19 20p12.2-11.23(chr20:11702911-19179706)x3

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.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 20p12.2-11.23(chr20:11702911-19179706)x3

Variation ID: 1328443 Accession: VCV001328443.4

Type and length

copy number gain, 7,476,796 bp

Location

Cytogenetic: 20p12.2-11.23 20: 11702911-19179706 (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	Dec 18, 2021	Dec 18, 2021	Dec 14, 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.

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.
BANF2	-	-	-	GRCh38 GRCh37	2	25
BFSP1		-	-	GRCh38 GRCh37	185	206
BTBD3		-	-	GRCh38 GRCh37	10	46
DSTN		-	-	GRCh38 GRCh37	6	27
DTD1		-	-	GRCh38 GRCh37	13	39
DZANK1		-	-	GRCh38 GRCh37	46	75
ESF1		-	-	GRCh38 GRCh37	48	85
FLRT3		-	-	GRCh38 GRCh37	-	97
ISM1		-	-	GRCh38 GRCh37	2	84
KAT14		-	-	GRCh38 GRCh37	7	42

There are 20 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37).

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.
not provided	Uncertain significance (1)	criteria provided, single submitter	Dec 14, 2020	RCV001795841.4

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.
Uncertain significance (Dec 14, 2020)	criteria provided, single submitter (ICSL CNVClassificationCriteria Aug2020) Method: clinical testing	not provided Affected status: unknown Allele origin: unknown	Illumina Laboratory Services, Illumina Accession: SCV002037165.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021	Publications: PubMed (2) PubMed: 21841781‚ 24174537 Comment: This CNV is an inherited heterozygous ~7.5 Mb duplication on chromosome 20 of 20p12.2- p11.23, (seq[GRCh37]dup(20)(p12.2p11.23); chr20:g.11702911_19179706dup). This event encompasses over 45 genes, including 30 … (more) This CNV is an inherited heterozygous ~7.5 Mb duplication on chromosome 20 of 20p12.2- p11.23, (seq[GRCh37]dup(20)(p12.2p11.23); chr20:g.11702911_19179706dup). This event encompasses over 45 genes, including 30 protein-coding genes. However, no genes in this this interval are currently known to be dosage-sensitive. Individuals with similar gains have not been reported in the peer-reviewed literature nor are they reported in control populations from the Database of Genomic Variants or the Developmental Delay controls (Cooper et al. 2011; MacDonald et al. 2014). A similar event is reported in an unpublished, symptomatic individual referred for chromosomal microarray testing in a ClinVar submission, however phenotypic and inheritance data are unavailable for this case (Variation ID: 625735, Accession: VCV000625735.1, Last evaluated: Nov 1, 2018). Based on the limited evidence, this CNV is classified as a variant of uncertain significance. (less)

Comment:

This CNV is an inherited heterozygous ~7.5 Mb duplication on chromosome 20 of 20p12.2- p11.23, (seq[GRCh37]dup(20)(p12.2p11.23); chr20:g.11702911_19179706dup). This event encompasses over 45 genes, including 30 protein-coding genes. However, no genes in this this interval are currently known to be dosage-sensitive. Individuals with similar gains have not been reported in the peer-reviewed literature nor are they reported in control populations from the Database of Genomic Variants or the Developmental Delay controls (Cooper et al. 2011; MacDonald et al. 2014). A similar event is reported in an unpublished, symptomatic individual referred for chromosomal microarray testing in a ClinVar submission, however phenotypic and inheritance data are unavailable for this case (Variation ID: 625735, Accession: VCV000625735.1, Last evaluated: Nov 1, 2018). Based on the limited evidence, this CNV is classified as a variant of uncertain significance.

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

Title	Author	Journal	Year	Link
The Database of Genomic Variants: a curated collection of structural variation in the human genome.	MacDonald JR	Nucleic acids research	2014	PMID: 24174537
A copy number variation morbidity map of developmental delay.	Cooper GM	Nature genetics	2011	PMID: 21841781

Text-mined citations for this variant ...

Record last updated Sep 01, 2024

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 20p12.2-11.23(chr20:11702911-19179706)x3

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...