Submissions for variant NM_001080517.3(SETD5):c.4243_4244del (p.Pro1415fs)

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Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV001871439	SCV002155862	uncertain significance	not provided	2024-05-14	criteria provided, single submitter	clinical testing	This sequence change results in a frameshift in the SETD5 gene (p.Pro1415Thrfs*38). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 28 amino acid(s) of the SETD5 protein and extend the protein by 9 additional amino acid residues. This variant is present in population databases (rs775402365, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SETD5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1385729). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx	RCV001871439	SCV002588244	likely benign	not provided	2021-03-02	criteria provided, single submitter	clinical testing	See Variant Classification Assertion Criteria.
Fulgent Genetics, Fulgent Genetics	RCV002478246	SCV002785799	uncertain significance	Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency	2021-09-14	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002552932	SCV003675997	likely benign	Inborn genetic diseases	2022-01-31	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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