ClinVar

Description

The FANCC p.Pro211Arg variant was identified in 3 of 2744 proband chromosomes (frequency: 0.001) from individuals or families with leukaemia or Alzheimer’s Disease and was present in 2 of 1362 control chromosomes (Balmana 2016, Barber 2003, Kim 2016). The variant was also identified in dbSNP (ID: rs140781259) as "With other allele ", ClinVar (classified as benign by Invitae; as likely benign by GeneDx; as uncertain significance by two submitters), MutDB, and in LOVD 3.0. The variant was not identified in Cosmic database. The variant was identified in control databases in 382 of 275066 chromosomes (1 homozygous) at a frequency of 0.001 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 7 of 23782 chromosomes (freq: 0.0003), Other in 8 of 6438 chromosomes (freq: 0.001), Latino in 8 of 34190 chromosomes (freq: 0.0002), European in 150 of 125766 chromosomes (freq: 0.001), Finnish in 208 of 25744 chromosomes (freq: 0.008), and South Asian in 1 of 30286 chromosomes (freq: 0.00003); it was not observed in the Ashkenazi Jewish, and in East Asian populations. The p.Pro211 residue is not conserved in mammals 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 variant occurs outside of the splicing consensus sequence and 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.