ClinVar Miner

Submissions for variant NM_005245.4(FAT1):c.8535G>A (p.Met2845Ile)

gnomAD frequency: 0.00261  dbSNP: rs138948513
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000963145 SCV001110281 likely benign not provided 2024-01-22 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000963145 SCV004151906 benign not provided 2024-02-01 criteria provided, single submitter clinical testing FAT1: BP4, BS1, BS2
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355896 SCV001550913 benign not specified no assertion criteria provided clinical testing The FAT1 p.Met2845Ile variant was not identified in the literature nor was it identified in ClinVar or Cosmic. The variant was identified in dbSNP (ID: rs138948513) and LOVD 3.0 (classified as likely benign). The variant was identified in control databases in 853 of 280628 chromosomes (7 homozygous) at a frequency of 0.00304 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: Ashkenazi Jewish in 330 of 10350 chromosomes (freq: 0.03188), Other in 39 of 7136 chromosomes (freq: 0.005465), European (non-Finnish) in 366 of 128420 chromosomes (freq: 0.00285), Latino in 69 of 35364 chromosomes (freq: 0.001951), South Asian in 33 of 30600 chromosomes (freq: 0.001078), African in 8 of 24198 chromosomes (freq: 0.000331) and European (Finnish) in 8 of 25024 chromosomes (freq: 0.00032), but was not observed in the East Asian population. The p.Met2845 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out 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 this variant meets our laboratory's criteria to be classified as benign.

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