VCV002498203.1 - ClinVar

NC_000010.11:g.45704708_(49974954_50015268)del

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.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000010.11:g.45704708_(49974954_50015268)del

Variation ID: 2498203 Accession: VCV002498203.1

Type and length

Deletion, 4,310,561 bp

Location

Cytogenetic: 10q11.22-11.23 10: 45704708-50015268 (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	Apr 15, 2023	Apr 15, 2023	Apr 30, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000010.11:g.45704708_(49974954_50015268)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.
GDF2		No evidence available	No evidence available	GRCh38 GRCh37	264	381
AGAP4	-	-	-	GRCh38 GRCh37	82	120
AGAP6	-	-	-	GRCh38 GRCh37	-	126
AGAP9	-	-	-	GRCh38 GRCh37	-	111
ANTXRL	-	-	-	GRCh38	-	55
ANXA8		-	-	GRCh38 GRCh38 GRCh37	-	123
ANXA8L1	-	-	-	GRCh38 GRCh37	10	120
ARHGAP22		-	-	GRCh38 GRCh37	74	162
ARHGAP22-IT1	-	-	-	GRCh38	-	22
C10orf53	-	-	-	GRCh38 GRCh37	2	88

There are 114 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.
10q11.22q11.23 deletion syndrome	Likely pathogenic (1)	criteria provided, single submitter	Apr 30, 2021	RCV003221322.2

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.
Likely pathogenic (Apr 30, 2021)	criteria provided, single submitter (NYGC Assertion Criteria 2020) Method: clinical testing	10q11.22q11.23 deletion syndrome Affected status: yes Allele origin: germline	New York Genome Center Study: CSER-NYCKidSeq Accession: SCV003915656.1 First in ClinVar: Apr 15, 2023 Last updated: Apr 15, 2023	Comment: The 10q11.22q11.23 region contains many low copy repeat regions associated with segmental duplications, and several recurrent duplication and deletions have been reported. Recurrent 10q11.22q11.23 deletions … (more) The 10q11.22q11.23 region contains many low copy repeat regions associated with segmental duplications, and several recurrent duplication and deletions have been reported. Recurrent 10q11.22q11.23 deletions very similar to the one identified here and containing genes CHAT and SLC18A3 have been described in individuals with phenotypes including variable degrees of intellectual disability and developmental delay, seizures, speech delay, behavioral abnormalities including Autism Spectrum Disorder, repetitive behaviors and ADHD, variable dysmorphic features, variable musculoskeletal findings, and other neurological disorders [PMID:21948486, 32938993,20466309, 25217958]. These copy number variants have been identified de novo in affected individuals, but also often found to be inherited from asymptomatic or mildly affected parents [PMID:21948486] suggesting variable expressivity or reduced penetrance. The 10q11.22q11.23 deletion identified here is reported as Likely Pathogenic. (less) Number of individuals with the variant: 1 Clinical Features: Seizure (present) , Intellectual disability (present) , Headache (present) Secondary finding: no

Comment:

The 10q11.22q11.23 region contains many low copy repeat regions associated with segmental duplications, and several recurrent duplication and deletions have been reported. Recurrent 10q11.22q11.23 deletions very similar to the one identified here and containing genes CHAT and SLC18A3 have been described in individuals with phenotypes including variable degrees of intellectual disability and developmental delay, seizures, speech delay, behavioral abnormalities including Autism Spectrum Disorder, repetitive behaviors and ADHD, variable dysmorphic features, variable musculoskeletal findings, and other neurological disorders [PMID:21948486, 32938993,20466309, 25217958]. These copy number variants have been identified de novo in affected individuals, but also often found to be inherited from asymptomatic or mildly affected parents [PMID:21948486] suggesting variable expressivity or reduced penetrance. The 10q11.22q11.23 deletion identified here is reported as Likely Pathogenic.

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 Oct 15, 2023

ClinVar Genomic variation as it relates to human health

NC_000010.11:g.45704708_(49974954_50015268)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...