ClinVar Miner

Submissions for variant NM_001151.4(SLC25A4):c.490A>G (p.Ile164Val) (rs143511445)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000876376 SCV000252279 likely benign not provided 2020-11-27 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000196396 SCV000615312 benign not specified 2017-01-16 criteria provided, single submitter clinical testing
Invitae RCV000876376 SCV001018941 likely benign not provided 2018-07-31 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000876376 SCV001552496 uncertain significance not provided no assertion criteria provided clinical testing The SLC25A4 p.Ile164Val variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs143511445) and ClinVar (classified as likely benign by GeneDx and benign by Athena Diagnostics Inc). The variant was identified in control databases in 146 of 281816 chromosomes at a frequency of 0.000518 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 135 of 24898 chromosomes (freq: 0.005422), Other in 3 of 7190 chromosomes (freq: 0.000417) and Latino in 8 of 35326 chromosomes (freq: 0.000227), while the variant was not observed in the Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), and South Asian populations. The p.Ile164 residue is conserved in mammals but not in more distantly related organisms and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan) predict a greater than 10% difference in splicing, however 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. This variant is classified as a variant of uncertain significance.

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