VCV001339872.2 - ClinVar

GRCh37/hg19 3p25.3-25.2(chr3:10970972-12295919)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.

not provided

no classification provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 3p25.3-25.2(chr3:10970972-12295919)x1

Variation ID: 1339872 Accession: VCV001339872.2

Type and length

copy number loss, 1,324,948 bp

Location

Cytogenetic: 3p25.3-25.2 3: 10970972-12295919 (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 12, 2022	Jun 17, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NC_000003.11:g.(?_10970972)_(12295919_?)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.
SLC6A1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	678	971
ATG7		-	-	GRCh38 GRCh37	73	131
HRH1		-	-	GRCh38 GRCh37	13	49
SLC6A11		-	-	GRCh38 GRCh37	44	88
SYN2		-	-	GRCh38 GRCh37	34	89
TAMM41		-	-	GRCh38 GRCh38 GRCh37	31	60
TIMP4		-	-	GRCh38 GRCh37	-	52
VGLL4		-	-	GRCh38 GRCh37	5	58

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.
Schizophrenia	not provided (1)	no classification provided	-	RCV001825255.2

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.
not provided (-)	no classification provided Method: phenotyping only	Schizophrenia Myoclonic-atonic epilepsy Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: de novo	GenomeConnect, ClinGen Accession: SCV002075046.2 First in ClinVar: Feb 12, 2022 Last updated: Jun 17, 2024	Comment: Variant interpreted as Pathogenic and reported on 10-12-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided … (more) Variant interpreted as Pathogenic and reported on 10-12-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less) Clinical Features: Abnormality of eye movement (present) , Hypermetropia (present) , Abnormal optic nerve morphology (present) , Cognitive impairment (present) , Hypertonia (present) , Seizure (present) , … (more) Abnormality of eye movement (present) , Hypermetropia (present) , Abnormal optic nerve morphology (present) , Cognitive impairment (present) , Hypertonia (present) , Seizure (present) , Autistic behavior (present) , Motor stereotypies (present) , Feeding difficulties (present) , Abnormal esophagus morphology (present) , Abnormal stomach morphology (present) (less) Indication for testing: Diagnostic Age: 0-9 years Sex: female Testing laboratory: GeneDx Date variant was reported to submitter: 2017-10-12 Testing laboratory interpretation: Pathogenic

Comment:

Variant interpreted as Pathogenic and reported on 10-12-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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 Jun 17, 2024

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 3p25.3-25.2(chr3:10970972-12295919)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...