ClinVar

Description

The TFR2 p.A205D variant was not identified in the literature nor was it identified in Cosmic and LOVD 3.0. The variant was identified in dbSNP (ID: rs41303495) and in ClinVar (classified as likely benign by Invitae for associated condition of Hereditary Hemochromatosis). The variant was identified in control databases in 683 of 252548 chromosomes (3 homozygous) at a frequency of 0.002704 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 487 of 115588 chromosomes (freq: 0.004213), Other in 21 of 6406 chromosomes (freq: 0.003278), Latino in 76 of 30012 chromosomes (freq: 0.002532), South Asian in 46 of 27714 chromosomes (freq: 0.00166), European (Finnish) in 35 of 23298 chromosomes (freq: 0.001502), African in 17 of 22612 chromosomes (freq: 0.000752) and Ashkenazi Jewish in 1 of 8620 chromosomes (freq: 0.000116), but was not observed in the East Asian population. The p.Ala205 residue is 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.