ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.972G>A (p.Pro324=) (rs553474397)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164564 SCV000215222 likely benign Hereditary cancer-predisposing syndrome 2014-06-05 criteria provided, single submitter clinical testing
Invitae RCV000538505 SCV000629163 likely benign Peutz-Jeghers syndrome 2018-01-10 criteria provided, single submitter clinical testing
Color RCV000164564 SCV000686711 likely benign Hereditary cancer-predisposing syndrome 2017-04-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000781889 SCV000920274 benign not specified 2017-11-09 criteria provided, single submitter clinical testing Variant summary: The STK11 c.972G>A (p.Pro324Pro) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may alter ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 8/216018 (2 homozygotes) control chromosomes (gnomAD), predominantly observed in the South Asian subpopulation at a frequency of 0.00029 (8/27558, 2 homozygotes)). This frequency is about 46 times the estimated maximal expected allele frequency of a pathogenic STK11 variant (0.0000063), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. In addition, a clinical diagnostic laboratory classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as benign.

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