VCV000684477.1 - ClinVar

Single allele

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

Single allele

Variation ID: 684477 Accession: VCV000684477.1

Type and length

Deletion, 2,167,084 bp

Location

Cytogenetic: 19p13.2 19: 10642984-12810067 (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	Aug 31, 2019	Aug 31, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NC_000019.9:g.(?_10642984)_(12810067_?)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.
LDLR		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	4075	4351
SMARCA4		Some evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	5676	5702
ACP5		-	-	GRCh38 GRCh37	300	318
ANGPTL8		-	-	GRCh38 GRCh37	-	20
AP1M2		-	-	GRCh38 GRCh37	28	49
ATG4D		-	-	GRCh38 GRCh37	45	70
C19orf38	-	-	-	GRCh38 GRCh37	1	25
CARM1		-	-	GRCh38 GRCh37	17	44
CCDC159	-	-	-	GRCh38 GRCh37	27	43
CDKN2D		-	-	GRCh38 GRCh37	7	30

There are 55 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	not provided (1)	no classification provided	-	RCV000844961.1

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.
not provided (-)	no classification provided Method: phenotyping only	Not Provided Affected status: yes Allele origin: unknown	GenomeConnect, ClinGen Accession: SCV000986786.1 First in ClinVar: Aug 31, 2019 Last updated: Aug 31, 2019	Comment: Variant interpretted as pathogenic and reported on 05/09/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from … (more) Variant interpretted as pathogenic and reported on 05/09/2018 by 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: Abnormal delivery (present) , Failure to thrive (present) , Hyperthyroidism (present) , Abnormality of the skull (present) , Oral-pharyngeal dysphagia (present) , Hyperacusis (present) , … (more) Abnormal delivery (present) , Failure to thrive (present) , Hyperthyroidism (present) , Abnormality of the skull (present) , Oral-pharyngeal dysphagia (present) , Hyperacusis (present) , Abnormality of the nervous system (present) , Cognitive impairment (present) , EEG abnormality (present) , Encephalopathy (present) , Hypertonia (present) , Generalized hypotonia (present) , Abnormality of movement (present) , Seizures (present) , Anxiety (present) , Depressivity (present) , Obsessive-compulsive behavior (present) , Short attention span (present) , Multiple cafe-au-lait spots (present) , Abnormality of limb bone morphology (present) , Abnormality of digit (present) , Abnormality of muscle physiology (present) , Feeding difficulties (present) , Abnormality of esophagus morphology (present) (less) Age: 30-39 years Sex: male Testing laboratory: GeneDx Date variant was reported to submitter: 2018-05-09 Testing laboratory interpretation: Pathogenic

Comment:

Variant interpretted as pathogenic and reported on 05/09/2018 by 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 Nov 05, 2022

ClinVar Genomic variation as it relates to human health

Single allele

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...