ClinVar Miner

Submissions for variant NM_178335.3(CCDC50):c.1276A>G (p.Lys426Glu)

gnomAD frequency: 0.00170  dbSNP: rs114146378
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000223270 SCV000270022 benign not specified 2017-03-31 criteria provided, single submitter clinical testing p.Lys426Glu in Exon 10 of CCDC50: This variant is not expected to have clinical significance because it has been identified in 0.5% (131/24026) of African chrom osomes including 1 homozygote by the Genome Aggregation Database (http://gnomad. broadinstitute.org/; dbSNP rs114146378).
Invitae RCV000896233 SCV001040315 likely benign not provided 2024-01-02 criteria provided, single submitter clinical testing
GeneDx RCV000896233 SCV001813329 likely benign not provided 2020-11-17 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003917891 SCV004730992 benign CCDC50-related condition 2019-05-23 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000223270 SCV001550415 benign not specified no assertion criteria provided clinical testing The CCDC50 p.K426E variant was not identified in the literature but was identified in dbSNP (ID: rs114146378) and ClinVar (classified as likely benign by Invitae and as benign by Laboratory for Molecular Medicine). The variant was identified in control databases in 143 of 282448 chromosomes (1 homozygous) at a frequency of 0.0005063, and was observed at the highest frequency in the African population in 135 of 24962 chromosomes (1 homozygous) (freq: 0.005408) (Genome Aggregation Database March 6, 2019, v2.1.1). The p.K426 residue is not conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) do not suggest a high likelihood of impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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