ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.1071G>T (rs556651007)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001082664 SCV000554124 likely benign Peutz-Jeghers syndrome 2020-08-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV000571538 SCV000664355 uncertain significance Hereditary cancer-predisposing syndrome 2018-10-29 criteria provided, single submitter clinical testing The p.E357D variant (also known as c.1071G>T), located in coding exon 8 of the STK11 gene, results from a G to T substitution at nucleotide position 1071. The glutamic acid at codon 357 is replaced by aspartic acid, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Health, Inc RCV000571538 SCV000910897 likely benign Hereditary cancer-predisposing syndrome 2015-11-24 criteria provided, single submitter clinical testing
GeneDx RCV000833846 SCV000975610 likely benign not provided 2018-03-30 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Institute of Medical Sciences, Banaras Hindu University RCV001255638 SCV001432199 pathogenic Lip and oral cavity carcinoma 2019-04-30 no assertion criteria provided research
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356730 SCV001551976 likely benign Familial ovarian cancer no assertion criteria provided clinical testing The STK11 p.Glu357Asp variant was not identified in the literature nor was it identified in the Cosmic, MutDB, LOVD 3.0, Zhejiang University Database, or Insight Hereditary Tumors, databases. The variant was identified in dbSNP (ID: rs556651007) as "With Uncertain significance allele", and in ClinVar (classified as likely benign by Invitae and uncertain significance by Ambry Genetics). The variant was identified in control databases in 30 of 242974 chromosomes (1 homozygous) at a frequency of 0.0001 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the South Asian population in 30 of 30492 chromosomes (freq: 0.00098), while the variant was not observed in the African, Other, Latino, European, Ashkenazi Jewish, East Asian, and Finnish, populations. The p.Glu357 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 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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