VCV000242852.1 - ClinVar

GRCh37/hg19 5p15.33-14.3(chr5:25328-19661628)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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 5p15.33-14.3(chr5:25328-19661628)x3

Variation ID: 242852 Accession: VCV000242852.1

Type and length

copy number gain, -

Location

Cytogenetic: 5p15.33-14.3 5: 25328-19661628 (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	Jul 10, 2016	Jul 10, 2016	Mar 29, 2016

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.
TRIO		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1382	1569
CTNND2		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	284	396
TERT		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2990	3433
SLC6A18		Dosage sensitivity unlikely	No evidence available	GRCh38 GRCh37	86	243
ANKH		No evidence available	No evidence available	GRCh38 GRCh37	211	564
ADAMTS16		-	-	GRCh38 GRCh37	89	211
ADCY2		-	-	GRCh38 GRCh37	45	154
AHRR		-	-	GRCh38 GRCh37	1	241
ANKRD33B	-	-	-	GRCh38 GRCh37	50	156
ATPSCKMT		-	-	GRCh38 GRCh37	19	121

There are 54 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.
not provided	Pathogenic (1)	criteria provided, single submitter	Mar 29, 2016	RCV000234904.1

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 (Mar 29, 2016)	criteria provided, single submitter (Clinical Cytogenomics Laboratory Policy on CNV Interpretation) Method: clinical testing	not provided Affected status: yes Allele origin: unknown	Clinical Genomics Laboratory, Laboratory for Precision Diagnostics, University of Washington Accession: SCV000292070.2 First in ClinVar: Jul 10, 2016 Last updated: Jul 10, 2016	Publications: PubMed (8) PubMed: 3829442‚ 8291556‚ 14564214‚ 10636453‚ 12030892‚ 18777129‚ 10482877‚ 18266247 Comment: Patient also had 4q35.2(188,498,590-190,915,650)x1 pat Number of individuals with the variant: 1 Indication for testing: Father with t(4, 5) Age: 20-29 weeks gestation Sex: female Tissue: Amniocytes

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
Partial 5p monosomy or trisomy in 11 patients from a family with a t(5;15)(p13.3;p12) translocation.	de Carvalho AF	Human genetics	2008	PMID: 18777129
Inverted duplication with terminal deletion of 5p and no cat-like cry.	Wang JC	American journal of medical genetics. Part A	2008	PMID: 18266247
Partial distal 5p trisomy resulting from paternal translocation (5;15)(p15.1;p13) in a boy with no mental retardation.	Baialardo EM	Clinical dysmorphology	2003	PMID: 14564214
Identification of a dup(5)(p15.3) by multicolor banding.	Riordan D	Clinical genetics	2002	PMID: 12030892
A half cryptic derivative der(18)t(5;18)pat identified by M-FISH and subtelomere probes: clinical findings and review of subtelomeric rearrangements.	Reddy KS	Clinical genetics	1999	PMID: 10636453
Characterization of a complex chromosomal rearrangement in a patient with a typical catlike cry and no other clinical findings of cri-du-chat syndrome.	Sreekantaiah C	American journal of medical genetics	1999	PMID: 10482877
Inverted duplication of chromosome 5p14p15.3 confirmed with in situ hybridization.	Zenger-Hain JL	American journal of medical genetics	1993	PMID: 8291556
A case report of a de novo tandem duplication (5p) (p14----pter).	Chia NL	Clinical genetics	1987	PMID: 3829442

Text-mined citations for this variant ...

Record last updated Mar 26, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 5p15.33-14.3(chr5:25328-19661628)x3

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...