ClinVar

Description

The p.Pro3243Leu variant was not identified in the literature, nor was it identified in NHLBI Exome Sequencing Project (Exome Variant Server), HGMD, LOVD, COSMIC, GeneInsight VariantWire, BIC or UMD. The variant was identified in the dbSNP database (ID#:rs80359241), but no frequency information was provided, thus the prevalence of this variant in the general population could not be determined; the Exome Aggregation Consortium (ExAC) (released Oct 20th, 2014) in 2 of 121336 chromosomes (frequency: 0.0000) from a population of East Asian (2/8642 individuals), and not in European (Non-Finnish or Finnish), Other, African, Latino, South Asian individuals; and, it was identified in ClinVar (classified as a likely benign variant by the Sharing Clinical Reports Project, derived from Myriad reports; classified as uncertain significance by BIC; and classification not provided by Invitae). The Breast Cancer IARC database notes a weak/null probability the variant creates a de novo splice donor at nt 9728 and a low probability of creating a de novo splice acceptor at nt 9736. The p.Pro3243 residue is not conserved in mammals and lower organisms and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The c.9728C>T variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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 unknown significance.