ClinVar Miner

Submissions for variant NM_001371623.1(TCOF1):c.3628C>T (p.Pro1210Ser)

gnomAD frequency: 0.00005  dbSNP: rs558530968
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001356339 SCV001947451 benign not provided 2019-08-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002058521 SCV002405304 benign Treacher Collins syndrome 1 2023-08-10 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356339 SCV001551477 uncertain significance not provided no assertion criteria provided clinical testing The TCOF1 p.Pro1132Ser variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs558530968) and ClinVar (classified as a VUS by Illumina). The variant was also identified in control databases in 132 of 282798 chromosomes at a frequency of 0.000467 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: South Asian in 104 of 30616 chromosomes (freq: 0.003397), Ashkenazi Jewish in 22 of 10370 chromosomes (freq: 0.002122) and European (non-Finnish) in 6 of 129128 chromosomes (freq: 0.000046), while the variant was not observed in the African, Latino, East Asian, European (Finnish), and Other populations. The p.Pro1132 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. This variant is classified as a variant of uncertain significance.

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