VCV003235952.1 - ClinVar

GRCh38/hg38 4q31.3-32.1(chr4:153986026-156952467)

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

GRCh38/hg38 4q31.3-32.1(chr4:153986026-156952467)

Variation ID: 3235952 Accession: VCV003235952.1

Type and length

copy number loss, 2,966,442 bp

Location

Cytogenetic: 4q31.3-32.1 4: 153986026-156952467 (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	May 19, 2024	May 19, 2024	Feb 16, 2023

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.
ASIC5		-	-	GRCh38 GRCh38 GRCh37	39	77
CTSO		-	-	GRCh38 GRCh38 GRCh37	28	65
DCHS2		-	-	GRCh38 GRCh38 GRCh37	191	224
FGA		-	-	GRCh38 GRCh37	222	254
FGB		-	-	GRCh38 GRCh37	202	234
FGG		-	-	GRCh38 GRCh37	144	178
GUCY1A1		-	-	GRCh38 GRCh37	96	135
GUCY1B1		-	-	GRCh38 GRCh37	20	60
LOC105377500	-	-	-	GRCh38	-	12
LOC105377502	-	-	-	GRCh38	-	12

There are 37 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.
not provided	Uncertain significance (1)	criteria provided, single submitter	Feb 16, 2023	RCV004555213.1

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.
Uncertain significance (Feb 16, 2023)	criteria provided, single submitter (NYGC Assertion Criteria 2020) Method: clinical testing	Not provided Affected status: unknown Allele origin: de novo	New York Genome Center Study: PrenatalSEQ Accession: SCV005044186.1 First in ClinVar: May 19, 2024 Last updated: May 19, 2024	Comment: The exact ~2.97Mb deletion identified here is not reported in the literature to the best of our knowledge. However, a larger 6.9Mb de novo interstitial … (more) The exact ~2.97Mb deletion identified here is not reported in the literature to the best of our knowledge. However, a larger 6.9Mb de novo interstitial deletion on 4q31.3-q32.1 (encompassing the 2.97Mb deletion observed in this fetus) has been reported in a female with club foot, severe speech delay, mild facial dysmorphisms but without micrognathia or cleft lip [PMID: 22407795]. Calcia et al, 2013 reported a male child with features of bilateral cleft of the primary palate, duplicated triphalangeal thumbs, patent foramen ovale and developmental delay who had two de novo deletions on chromosome 4q, one of which overlaps with the deleted region observed in this fetus and includes the PDGFC gene [PMID: 24038848]. Several interstitial deletions on 4q31-q32 involving the PDGFC gene have been reported in DECIPHER database without features of micrognathia or cleft lip/palate. Due to the lack of compelling evidence for its pathogenicity, the de novo ~2.97Mb deletion observed here is reported as a Variant of Uncertain Significance. (less) Number of individuals with the variant: 1 Clinical Features: Cleft palate (present) , Micrognathia (present) , Femoral bowing (present) Age: 10-19 weeks gestation Secondary finding: no

Comment:

The exact ~2.97Mb deletion identified here is not reported in the literature to the best of our knowledge. However, a larger 6.9Mb de novo interstitial deletion on 4q31.3-q32.1 (encompassing the 2.97Mb deletion observed in this fetus) has been reported in a female with club foot, severe speech delay, mild facial dysmorphisms but without micrognathia or cleft lip [PMID: 22407795]. Calcia et al, 2013 reported a male child with features of bilateral cleft of the primary palate, duplicated triphalangeal thumbs, patent foramen ovale and developmental delay who had two de novo deletions on chromosome 4q, one of which overlaps with the deleted region observed in this fetus and includes the PDGFC gene [PMID: 24038848]. Several interstitial deletions on 4q31-q32 involving the PDGFC gene have been reported in DECIPHER database without features of micrognathia or cleft lip/palate. Due to the lack of compelling evidence for its pathogenicity, the de novo ~2.97Mb deletion observed here is reported 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

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 May 27, 2024

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 4q31.3-32.1(chr4:153986026-156952467)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...