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Five of the ALS samples (ND09546, ND10023, ND09582, ND10379, ND10379) carried the synonymous variation p.A66A (c.198 T>C) in exon 2 of TARDBP, but this sequence variant was likely to be a benign polymorphism as it was found in eight of the Caucasian controls and in a single Bedouin sample of the HGDP.
This suggests that the variant is not a high-risk mutation but, as suggested previously [ 13], is more likely to be a benign polymorphism.
The de novo character of this variation in patient CMT-127.04 could not be proven due to lack of the parent's DNA samples; it may therefore still be a benign polymorphism.
The MLH1 Lys618Ala mutation (AAG>GCG; rs35502531), initially supposed to be a benign polymorphism, has been found to be significantly over-represented in sporadic cancers associated with Lynch syndrome; MLH1 appearsappears to have a reduced ability to bind PMS2, one of the MLH1 protein's mismatch repair partners (Medeiros et al. 2012).
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This variation was also present in pooled DNA from 10 healthy individuals, demonstrating that it is a benign polymorphism.
This raised the interesting question whether the identified mutation is a benign polymorphism or should be considered a genuine genetic risk factor for disease.
P23L (rs41298432) is a benign polymorphism present in population controls at a frequency of 1 2% (Jarman et al., 1997; Hauf et al., 2000).
Instead, our results support the proposal that the G13964C site is a benign polymorphism, as originally suggested by Buller et al [ 13].
Together with the clinical data [ 21] a likely explanation for the lack of effects is that the hcTnCL29Q mutation is a benign polymorphism accidentally found in an HCM patient.
For the purpose of molecular diagnosis and for adequate surgical management of patients and their relatives, it is crucial to know whether a RET gene variant identified via genetic testing is a benign polymorphism, a variant of unknown clinical significance or a pathological disease-causing mutation (Toledo et al. 2006).
However, although 7501T>C was not found in the mtDNA databases with more than 5,000 sequences [28], [29], it is possible that 7501T>C is only a benign polymorphism not found in the specific mtDNA haplogroups comprising the databases.
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