ClinVar Miner

Submissions for variant NM_001447.3(FAT2):c.8206A>G (p.Lys2736Glu)

gnomAD frequency: 0.00047  dbSNP: rs570674049
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001354693 SCV004526195 likely benign not provided 2023-06-03 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001354693 SCV004700762 benign not provided 2024-01-01 criteria provided, single submitter clinical testing FAT2: BP4, BS1, BS2
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354693 SCV001549370 likely benign not provided no assertion criteria provided clinical testing The FAT2 p.Lys2736Glu variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs570674049) and in control databases in 117 of 251274 chromosomes (2 homozygous) at a frequency of 0.0004656 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: South Asian in 116 of 30616 chromosomes (freq: 0.003789) and European (non-Finnish) in 1 of 113570 chromosomes (freq: 0.000009), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish) or Other populations. The p.Lys2736 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 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.

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