NM_001909.5(CTSD):c.294G>A (p.Thr98=) AND not provided

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001355385.1

Allele description [Variation Report for NM_001909.5(CTSD):c.294G>A (p.Thr98=)]

NM_001909.5(CTSD):c.294G>A (p.Thr98=)

Gene:
CTSD:cathepsin D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.5
Genomic location:
Preferred name:
NM_001909.5(CTSD):c.294G>A (p.Thr98=)
Other names:
p.T98T:ACG>ACA
HGVS:
  • NC_000011.10:g.1759574C>T
  • NG_008655.1:g.9419G>A
  • NM_001909.5:c.294G>AMANE SELECT
  • NP_001900.1:p.Thr98=
  • NC_000011.9:g.1780804C>T
  • NM_001909.4:c.294G>A
Links:
dbSNP: rs369373285
NCBI 1000 Genomes Browser:
rs369373285
Molecular consequence:
  • NM_001909.5:c.294G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001550259Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001550259.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CTSD p.Thr98Thr variant was not identified in the literature but was identified in dbSNP (ID: rs369373285) and ClinVar (classified as benign by GeneDx and uncertain significance by Invitae). The variant was identified in control databases in 22 of 281814 chromosomes at a frequency of 0.00007807 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 21 of 128398 chromosomes (freq: 0.000164) and African in 1 of 24862 chromosomes (freq: 0.00004), but was not observed in the Latino, Ashkenazi Jewish, East Asian, European (Finnish), Other, or South Asian populations. The p.Thr98Thr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 3' splice site. However, this has not been confirmed by RNA analysis and is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2021

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