VCV000565044.3 - ClinVar

GRCh37/hg19 22q11.21(chr22:18644790-21915509)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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 22q11.21(chr22:18644790-21915509)x1

Variation ID: 565044 Accession: VCV000565044.3

Type and length

copy number loss, 3,270,720 bp

Location

Cytogenetic: 22q11.21 22: 18644790-21915509 (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	Feb 13, 2022	Feb 13, 2022	May 1, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000022.10:g.(?_18644790)_(21915509_?)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.
TBX1		Some evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	968	1360
CRKL		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	27	430
HIRA		No evidence available	No evidence available	GRCh38 GRCh37	108	492
AIFM3		-	-	GRCh38 GRCh37	42	446
ARVCF		-	-	GRCh38 GRCh37	176	653
C22orf39	-	-	-	GRCh38 GRCh37	-	383
CDC45		-	-	GRCh38 GRCh37	287	672
CLDN5		-	-	GRCh38 GRCh37	20	403
CLTCL1		-	-	GRCh38 GRCh37	173	572
COMT		-	-	GRCh38 GRCh37	88	612

There are 44 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)	no assertion criteria provided	May 1, 2021	RCV000684519.3

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 (May 01, 2021)	no assertion criteria provided Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Quest Diagnostics Nichols Institute San Juan Capistrano Accession: SCV000812042.3 First in ClinVar: Sep 30, 2018 Last updated: Feb 13, 2022	Comment: The 22q11.21 interstitial deletion corresponds to the critical region of chromosome 22q11.2 deletion syndrome (a.k.a., Velocardiofacial syndrome (VCFS) or DiGeorge syndrome (DGS) (OMIM #192430; OMIM … (more) The 22q11.21 interstitial deletion corresponds to the critical region of chromosome 22q11.2 deletion syndrome (a.k.a., Velocardiofacial syndrome (VCFS) or DiGeorge syndrome (DGS) (OMIM #192430; OMIM #188400). Haploinsufficiency of the TBX1 gene in particular is responsible for most of the clinical features of DiGeorge syndrome. Individuals with chromosome 22q11.21 deletion syndrome have a range of phenotypic findings, including congenital heart defects, particularly conotruncal malformations (tetralogy of Fallot, interrupted aortic arch, ventricular septal defect, and truncus arteriosus), palatal abnormalities, characteristic facial features, learning difficulties, and immune deficiency (GeneReviews [Internet]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1523/). Familial cases with microdeletion of this region are relatively common. (less)

Comment:

The 22q11.21 interstitial deletion corresponds to the critical region of chromosome 22q11.2 deletion syndrome (a.k.a., Velocardiofacial syndrome (VCFS) or DiGeorge syndrome (DGS) (OMIM #192430; OMIM #188400). Haploinsufficiency of the TBX1 gene in particular is responsible for most of the clinical features of DiGeorge syndrome. Individuals with chromosome 22q11.21 deletion syndrome have a range of phenotypic findings, including congenital heart defects, particularly conotruncal malformations (tetralogy of Fallot, interrupted aortic arch, ventricular septal defect, and truncus arteriosus), palatal abnormalities, characteristic facial features, learning difficulties, and immune deficiency (GeneReviews [Internet]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1523/). Familial cases with microdeletion of this region are relatively common.

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 Mar 26, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 22q11.21(chr22:18644790-21915509)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...