VCV000988888.2 - ClinVar

NC_000003.12:g.176518923_176519268dup

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 benign

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000003.12:g.176518923_176519268dup

Variation ID: 988888 Accession: VCV000988888.2

Type and length

Duplication, 346 bp

Location

Cytogenetic: 3q26.32 3: 176236710-176236711 (GRCh37) [ NCBI UCSC ] 3: 176518922-176518923 (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 10, 2021	Oct 7, 2023	Dec 1, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NC_000003.12:g.176518923_176519268dup
NC_000003.11:g.176236711_176237056dup

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

dbSNP: rs2108347906 VarSome

Genes

No affected genes found.

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.
Developmental cataract	Likely benign (1)	criteria provided, single submitter	Dec 1, 2020	RCV001376650.2

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 benign (Dec 01, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: research	Developmental cataract Affected status: yes Allele origin: germline	Dept. Genetics and Cancer, Menzies Institute for Medical Research, University of Tasmania Accession: SCV001450780.2 First in ClinVar: May 10, 2021 Last updated: Oct 07, 2023 Comment: The allele frequency of this variant in a control population is greater than expected for the condition. Lack of evidence of variant having a putative … (more) The allele frequency of this variant in a control population is greater than expected for the condition. Lack of evidence of variant having a putative damaging impact on a gene or gene product. gnomAD structual variant DUP_3_10278 and dbVar nsv4651094. (less)	Publications: PubMed (1) PubMed: 33867527 Sex: male

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract.	Jones JL	European journal of human genetics : EJHG	2021	PMID: 33867527

Text-mined citations for rs2108347906 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 08, 2024

ClinVar Genomic variation as it relates to human health

NC_000003.12:g.176518923_176519268dup

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2108347906 ...