VCV000816497.1 - ClinVar

GRCh37/hg19 4p16.3-15.2(chr4:49450-24280482)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 4p16.3-15.2(chr4:49450-24280482)x1

Variation ID: 816497 Accession: VCV000816497.1

Type and length

copy number loss, 24,231,033 bp

Location

Cytogenetic: 4p16.3-15.2 4: 49450-24280482 (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	Mar 7, 2020	Mar 7, 2020	Jun 29, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NC_000004.11:g.(?_49450)_(24280482_?)del

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.
MSX1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	90	231
CLNK		No evidence available	No evidence available	GRCh38 GRCh37	41	117
DRD5		No evidence available	No evidence available	GRCh38 GRCh37	2	138
FGFR3		No evidence available	No evidence available	GRCh38 GRCh37	976	1126
FGFRL1		No evidence available	No evidence available	GRCh38 GRCh37	284	440
LETM1		No evidence available	No evidence available	GRCh38 GRCh37	251	398
NELFA		No evidence available	No evidence available	GRCh38 GRCh37	70	220
NSD2		No evidence available	No evidence available	GRCh38 GRCh37	500	651
WFS1		No evidence available	No evidence available	GRCh38 GRCh37	1753	1854
ABLIM2		-	-	GRCh38 GRCh37	67	142

There are 138 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.
See cases	Pathogenic (1)	criteria provided, single submitter	Jun 29, 2018	RCV001007422.1

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 (Jun 29, 2018)	criteria provided, single submitter (Clinical Cytogenomics Laboratory Policy on CNV Interpretation) Method: clinical testing	See Cases Affected status: yes Allele origin: unknown	Clinical Genomics Laboratory, Laboratory for Precision Diagnostics, University of Washington Accession: SCV001167037.1 First in ClinVar: Mar 07, 2020 Last updated: Mar 07, 2020	Publications: PubMed (3) PubMed: 17726485‚ 18932124‚ 17480006 Bookshelf: NBK1183 Bookshelf: NBK1183 Number of individuals with the variant: 1 Clinical Features: Intrauterine growth restriction (present) , Micrognathia (present) , Absent nasal bone (present) , Splayed cerebellum (present) , Single umbilical artery (present) , Pelvic kidney (present) … (more) Intrauterine growth restriction (present) , Micrognathia (present) , Absent nasal bone (present) , Splayed cerebellum (present) , Single umbilical artery (present) , Pelvic kidney (present) , Unilateral hydronephrosis (present) , Ventricular septal defect (present) , Dilated fourth ventricle (present) , Hypotonia (present) (less) Age: 10-19 weeks gestation Sex: female Tissue: Amniotic fluid

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Wolf-Hirschhorn Syndrome – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY.	Adam MP	-	2015	PMID: 20301362
On the nosology and pathogenesis of Wolf-Hirschhorn syndrome: genotype-phenotype correlation analysis of 80 patients and literature review.	Zollino M	American journal of medical genetics. Part C, Seminars in medical genetics	2008	PMID: 18932124
Comprehensive analysis of Wolf-Hirschhorn syndrome using array CGH indicates a high prevalence of translocations.	South ST	European journal of human genetics : EJHG	2008	PMID: 17726485
Mother to son amplification of a small subtelomeric deletion: a new mechanism of familial recurrence in microdeletion syndromes.	Faravelli F	American journal of medical genetics. Part A	2007	PMID: 17480006

Text-mined citations for this variant ...

Record last updated Mar 26, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 4p16.3-15.2(chr4:49450-24280482)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...